Changes between Initial Version and Version 1 of Ticket #8866


Ignore:
Timestamp:
Apr 18, 2023, 9:52:02 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Reported by Leonardo Lima

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #8866

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Dead PositionRestraintMgr (and other problems)

  • Ticket #8866 – Description

    initial v1  
    49234923Flipping the peptide bond for 1 residues 
    49244924
    4925 > select clear
    4926 
    4927 [Repeated 1 time(s)]
    4928 
    4929 > ui tool show "Ramachandran Plot"
    4930 
    4931 > isolde pepflip sel
    4932 
    4933 Flipping the peptide bond for 1 residues 
    4934 
    4935 > isolde pepflip sel
    4936 
    4937 Flipping the peptide bond for 1 residues 
    4938 
    4939 > select clear
    4940 
    4941 > isolde pepflip sel
    4942 
    4943 Flipping the peptide bond for 1 residues 
    4944 
    4945 > select clear
    4946 
    4947 > isolde pepflip sel
    4948 
    4949 Flipping the peptide bond for 1 residues 
    4950 
    4951 > isolde pepflip sel
    4952 
    4953 Flipping the peptide bond for 1 residues 
    4954 
    4955 > select clear
    4956 
    4957 > isolde pepflip sel
    4958 
    4959 Flipping the peptide bond for 1 residues 
    4960 
    4961 > select clear
    4962 
    4963 > ui tool show "Ramachandran Plot"
    4964 
    4965 > isolde pepflip sel
    4966 
    4967 Flipping the peptide bond for 1 residues 
    4968 
    4969 > select clear
    4970 
    4971 > isolde pepflip sel
    4972 
    4973 Flipping the peptide bond for 1 residues 
    4974 
    4975 > isolde pepflip sel
    4976 
    4977 Flipping the peptide bond for 1 residues 
    4978 
    4979 > select clear
    4980 
    4981 [Repeated 4 time(s)]
    4982 
    4983 > ui tool show "Ramachandran Plot"
    4984 
    4985 > isolde pepflip sel
    4986 
    4987 Flipping the peptide bond for 1 residues 
    4988 
    4989 > select clear
    4990 
    4991 > isolde pepflip sel
    4992 
    4993 Flipping the peptide bond for 1 residues 
    4994 
    4995 > ui tool show "Ramachandran Plot"
    4996 
    4997 > isolde pepflip sel
    4998 
    4999 Flipping the peptide bond for 1 residues 
    5000 
    5001 > isolde pepflip sel
    5002 
    5003 Flipping the peptide bond for 1 residues 
    5004 
    5005 > isolde pepflip sel
    5006 
    5007 Flipping the peptide bond for 1 residues 
    5008 
    5009 > ui tool show "Ramachandran Plot"
    5010 
    5011 > isolde pepflip sel
    5012 
    5013 Flipping the peptide bond for 1 residues 
    5014 
    5015 > isolde pepflip sel
    5016 
    5017 Flipping the peptide bond for 1 residues 
    5018 
    5019 > select clear
    5020 
    5021 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    5022 
    5023 > ui tool show "Ramachandran Plot"
    5024 
    5025 Traceback (most recent call last): 
    5026 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5027 packages/matplotlib/cbook/__init__.py", line 287, in process 
    5028 func(*args, **kwargs) 
    5029 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    5030 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    5031 on_resize 
    5032 c.draw() 
    5033 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5034 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    5035 self.figure.draw(self.renderer) 
    5036 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5037 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    5038 result = draw(artist, renderer, *args, **kwargs) 
    5039 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5040 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    5041 return draw(artist, renderer) 
    5042 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5043 packages/matplotlib/figure.py", line 2796, in draw 
    5044 artists = self._get_draw_artists(renderer) 
    5045 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5046 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    5047 ax.apply_aspect() 
    5048 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5049 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    5050 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    5051 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5052 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    5053 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    5054 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    5055 
    5056 > isolde pepflip sel
    5057 
    5058 Flipping the peptide bond for 1 residues 
    5059 
    5060 > isolde pepflip sel
    5061 
    5062 Flipping the peptide bond for 1 residues 
    5063 
    5064 > isolde pepflip sel
    5065 
    5066 Flipping the peptide bond for 1 residues 
    5067 
    5068 > select clear
    5069 
    5070 > ui tool show "Ramachandran Plot"
    5071 
    5072 > isolde pepflip sel
    5073 
    5074 Flipping the peptide bond for 1 residues 
    5075 
    5076 > select clear
    5077 
    5078 [Repeated 1 time(s)]
    5079 
    5080 > ui tool show "Ramachandran Plot"
    5081 
    5082 > view #1/u:37
    5083 
    5084 > ui tool show "Ramachandran Plot"
    5085 
    5086 > isolde pepflip sel
    5087 
    5088 Flipping the peptide bond for 1 residues 
    5089 
    5090 > select clear
    5091 
    5092 > ui tool show "Ramachandran Plot"
    5093 
    5094 > isolde pepflip sel
    5095 
    5096 Flipping the peptide bond for 1 residues 
    5097 
    5098 > isolde pepflip sel
    5099 
    5100 Flipping the peptide bond for 1 residues 
    5101 
    5102 > ui tool show "Ramachandran Plot"
    5103 
    5104 > select clear
    5105 
    5106 > ui tool show "Ramachandran Plot"
    5107 
    5108 [Repeated 1 time(s)]
    5109 
    5110 > isolde pepflip sel
    5111 
    5112 Flipping the peptide bond for 1 residues 
    5113 
    5114 > select clear
    5115 
    5116 > ui tool show "Ramachandran Plot"
    5117 
    5118 > ui tool show ISOLDE
    5119 
    5120 > ui tool show "Ramachandran Plot"
    5121 
    5122 > isolde pepflip sel
    5123 
    5124 Flipping the peptide bond for 1 residues 
    5125 
    5126 > isolde pepflip sel
    5127 
    5128 Flipping the peptide bond for 1 residues 
    5129 
    5130 > select clear
    5131 
    5132 > ui tool show "Ramachandran Plot"
    5133 
    5134 [Repeated 2 time(s)]
    5135 
    5136 > isolde pepflip sel
    5137 
    5138 Flipping the peptide bond for 1 residues 
    5139 
    5140 > ui tool show "Ramachandran Plot"
    5141 
    5142 > select clear
    5143 
    5144 > ui tool show "Ramachandran Plot"
    5145 
    5146 > isolde pepflip sel
    5147 
    5148 Flipping the peptide bond for 1 residues 
    5149 
    5150 > select clear
    5151 
    5152 > isolde pepflip sel
    5153 
    5154 Flipping the peptide bond for 1 residues 
    5155 
    5156 > isolde pepflip sel
    5157 
    5158 Flipping the peptide bond for 1 residues 
    5159 
    5160 > ui tool show "Ramachandran Plot"
    5161 
    5162 > isolde pepflip sel
    5163 
    5164 Flipping the peptide bond for 1 residues 
    5165 
    5166 > isolde pepflip sel
    5167 
    5168 Flipping the peptide bond for 1 residues 
    5169 
    5170 > select clear
    5171 
    5172 [Repeated 1 time(s)]
    5173 
    5174 > isolde pepflip sel
    5175 
    5176 Flipping the peptide bond for 1 residues 
    5177 
    5178 > isolde pepflip sel
    5179 
    5180 Flipping the peptide bond for 1 residues 
    5181 
    5182 > select clear
    5183 
    5184 > isolde pepflip sel
    5185 
    5186 Flipping the peptide bond for 1 residues 
    5187 
    5188 > isolde pepflip sel
    5189 
    5190 Flipping the peptide bond for 1 residues 
    5191 
    5192 > ui tool show "Ramachandran Plot"
    5193 
    5194 > isolde pepflip sel
    5195 
    5196 Flipping the peptide bond for 1 residues 
    5197 
    5198 > select clear
    5199 
    5200 [Repeated 1 time(s)]
    5201 
    5202 > ui tool show "Ramachandran Plot"
    5203 
    5204 [Repeated 1 time(s)]
    5205 
    5206 > select clear
    5207 
    5208 [Repeated 3 time(s)]
    5209 
    5210 > ui tool show "Ramachandran Plot"
    5211 
    5212 [Repeated 2 time(s)]
    5213 
    5214 > isolde pepflip sel
    5215 
    5216 Flipping the peptide bond for 1 residues 
    5217 
    5218 > isolde pepflip sel
    5219 
    5220 Flipping the peptide bond for 1 residues 
    5221 
    5222 > isolde pepflip sel
    5223 
    5224 Flipping the peptide bond for 1 residues 
    5225 
    5226 > isolde pepflip sel
    5227 
    5228 Flipping the peptide bond for 1 residues 
    5229 
    5230 > select clear
    5231 
    5232 Unable to flip peptide bond after 50 rounds. Giving up. 
    5233 
    5234 > ui tool show "Ramachandran Plot"
    5235 
    5236 > select clear
    5237 
    5238 > ui tool show "Ramachandran Plot"
    5239 
    5240 > isolde pepflip sel
    5241 
    5242 Flipping the peptide bond for 1 residues 
    5243 
    5244 > isolde pepflip sel
    5245 
    5246 Flipping the peptide bond for 1 residues 
    5247 
    5248 > select clear
    5249 
    5250 [Repeated 1 time(s)]
    5251 
    5252 > ui tool show "Ramachandran Plot"
    5253 
    5254 > hide #!1.2 models
    5255 
    5256 > show #!1.2 models
    5257 
    5258 > ui tool show "Ramachandran Plot"
    5259 
    5260 > select clear
    5261 
    5262 [Repeated 3 time(s)]
    5263 
    5264 > ui tool show "Ramachandran Plot"
    5265 
    5266 > isolde pepflip sel
    5267 
    5268 Flipping the peptide bond for 1 residues 
    5269 
    5270 > isolde pepflip sel
    5271 
    5272 Flipping the peptide bond for 1 residues 
    5273 
    5274 > isolde pepflip sel
    5275 
    5276 Flipping the peptide bond for 1 residues 
    5277 
    5278 > isolde pepflip sel
    5279 
    5280 Flipping the peptide bond for 1 residues 
    5281 
    5282 > isolde pepflip sel
    5283 
    5284 Flipping the peptide bond for 1 residues 
    5285 
    5286 > isolde pepflip sel
    5287 
    5288 Flipping the peptide bond for 1 residues 
    5289 
    5290 > isolde pepflip sel
    5291 
    5292 Flipping the peptide bond for 1 residues 
    5293 
    5294 > isolde pepflip sel
    5295 
    5296 Flipping the peptide bond for 1 residues 
    5297 
    5298 > select clear
    5299 
    5300 > isolde pepflip sel
    5301 
    5302 Flipping the peptide bond for 1 residues 
    5303 
    5304 > isolde pepflip sel
    5305 
    5306 Flipping the peptide bond for 1 residues 
    5307 
    5308 > isolde pepflip sel
    5309 
    5310 Flipping the peptide bond for 1 residues 
    5311 
    5312 > ui tool show "Ramachandran Plot"
    5313 
    5314 > select clear
    5315 
    5316 > isolde pepflip sel
    5317 
    5318 Flipping the peptide bond for 1 residues 
    5319 
    5320 > isolde pepflip sel
    5321 
    5322 Flipping the peptide bond for 1 residues 
    5323 
    5324 > select clear
    5325 
    5326 [Repeated 1 time(s)]
    5327 
    5328 > isolde pepflip sel
    5329 
    5330 Flipping the peptide bond for 1 residues 
    5331 
    5332 > isolde pepflip sel
    5333 
    5334 Flipping the peptide bond for 1 residues 
    5335 
    5336 > select clear
    5337 
    5338 > isolde pepflip sel
    5339 
    5340 Flipping the peptide bond for 1 residues 
    5341 
    5342 > isolde pepflip sel
    5343 
    5344 Flipping the peptide bond for 1 residues 
    5345 
    5346 > isolde pepflip sel
    5347 
    5348 Flipping the peptide bond for 1 residues 
    5349 
    5350 > isolde pepflip sel
    5351 
    5352 Flipping the peptide bond for 1 residues 
    5353 
    5354 > select clear
    5355 
    5356 > isolde pepflip sel
    5357 
    5358 Flipping the peptide bond for 1 residues 
    5359 
    5360 > select clear
    5361 
    5362 > ui tool show "Ramachandran Plot"
    5363 
    5364 > isolde pepflip sel
    5365 
    5366 Flipping the peptide bond for 1 residues 
    5367 
    5368 > select clear
    5369 
    5370 [Repeated 1 time(s)]
    5371 
    5372 > isolde pepflip sel
    5373 
    5374 Flipping the peptide bond for 1 residues 
    5375 
    5376 > isolde pepflip sel
    5377 
    5378 Flipping the peptide bond for 1 residues 
    5379 
    5380 > isolde pepflip sel
    5381 
    5382 Flipping the peptide bond for 1 residues 
    5383 
    5384 > isolde pepflip sel
    5385 
    5386 Flipping the peptide bond for 1 residues 
    5387 
    5388 > isolde pepflip sel
    5389 
    5390 Flipping the peptide bond for 1 residues 
    5391 
    5392 > select clear
    5393 
    5394 > ui tool show "Ramachandran Plot"
    5395 
    5396 > isolde pepflip sel
    5397 
    5398 Flipping the peptide bond for 1 residues 
    5399 
    5400 > select clear
    5401 
    5402 > ui tool show "Ramachandran Plot"
    5403 
    5404 > isolde pepflip sel
    5405 
    5406 Flipping the peptide bond for 1 residues 
    5407 Unable to flip peptide bond after 50 rounds. Giving up. 
    5408 
    5409 > select clear
    5410 
    5411 > isolde pepflip sel
    5412 
    5413 Flipping the peptide bond for 1 residues 
    5414 
    5415 > isolde pepflip sel
    5416 
    5417 Flipping the peptide bond for 1 residues 
    5418 
    5419 > ui tool show "Ramachandran Plot"
    5420 
    5421 > isolde sim pause
    5422 
    5423 > ui tool show "Ramachandran Plot"
    5424 
    5425 > isolde sim resume
    5426 
    5427 > ui tool show "Ramachandran Plot"
    5428 
    5429 > isolde sim pause
    5430 
    5431 > isolde sim stop
    5432 
    5433 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5434 chains... 
    5435 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    5436 standards. 
    5437 ISOLDE: stopped sim 
    5438 
    5439 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5440 > mut8-no-C-ter/12-KSRP-no-C-ter-Step1-twelventhSubsteps-
    5441 > simulatedAnnealingIn-u37-o55-region.csx.cxs
    5442 
    5443 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5444 
    5445 ——— End of log from Fri Mar 17 17:24:40 2023 ———
    5446 
    5447 opened ChimeraX session 
    5448 
    5449 > isolde start
    5450 
    5451 > set selectionWidth 4
    5452 
    5453 > select clear
    5454 
    5455 > view #1/o:55
    5456 
    5457 > select #1/o:55
    5458 
    5459 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5460 
    5461 > isolde sim start sel
    5462 
    5463 Launching using CUDA failed with the below message. Falling back to using
    5464 OpenCL. 
    5465  
    5466 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    5467 (-arch) 
    5468  
    5469 
    5470 ISOLDE: started sim 
    5471 
    5472 > isolde sim stop discardTo start
    5473 
    5474 reverting to start 
    5475 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5476 chains... 
    5477 ISOLDE: stopped sim 
    5478 
    5479 > select #1/o:55
    5480 
    5481 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5482 
    5483 > isolde sim start sel
    5484 
    5485 ISOLDE: started sim 
    5486 
    5487 > ui tool show "Ramachandran Plot"
    5488 
    5489 > select clear
    5490 
    5491 > isolde sim stop
    5492 
    5493 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5494 chains... 
    5495 ISOLDE: stopped sim 
    5496 
    5497 > view #1/u:49
    5498 
    5499 > select #1/u:49
    5500 
    5501 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5502 
    5503 > isolde sim start sel
    5504 
    5505 ISOLDE: started sim 
    5506 
    5507 > isolde sim stop discardTo start
    5508 
    5509 reverting to start 
    5510 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5511 chains... 
    5512 ISOLDE: stopped sim 
    5513 
    5514 > select #1/u:49
    5515 
    5516 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5517 
    5518 > isolde sim start sel
    5519 
    5520 ISOLDE: started sim 
    5521 
    5522 > ui tool show "Ramachandran Plot"
    5523 
    5524 > select clear
    5525 
    5526 > isolde pepflip sel
    5527 
    5528 Flipping the peptide bond for 1 residues 
    5529 
    5530 > select clear
    5531 
    5532 > ui tool show "Ramachandran Plot"
    5533 
    5534 > isolde sim pause
    5535 
    5536 > isolde sim resume
    5537 
    5538 > isolde sim pause
    5539 
    5540 3 models selected 
    5541 [Repeated 1 time(s)]
    5542 
    5543 > view #1
    5544 
    5545 > view #1/u:49
    5546 
    5547 > view #1/P
    5548 
    5549 > ui tool show "Ramachandran Plot"
    5550 
    5551 > view #1/u:49
    5552 
    5553 > isolde sim resume
    5554 
    5555 > ui tool show "Ramachandran Plot"
    5556 
    5557 [Repeated 2 time(s)]
    5558 
    5559 > isolde sim stop
    5560 
    5561 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5562 chains... 
    5563 ISOLDE: stopped sim 
    5564 
    5565 > view #1/u:63
    5566 
    5567 > select #1/u:63
    5568 
    5569 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5570 
    5571 > isolde sim start sel
    5572 
    5573 ISOLDE: started sim 
    5574 
    5575 > ui tool show "Ramachandran Plot"
    5576 
    5577 > isolde pepflip sel
    5578 
    5579 Flipping the peptide bond for 1 residues 
    5580 
    5581 > isolde pepflip sel
    5582 
    5583 Flipping the peptide bond for 1 residues 
    5584 
    5585 > isolde pepflip sel
    5586 
    5587 Flipping the peptide bond for 1 residues 
    5588 
    5589 > ui tool show "Ramachandran Plot"
    5590 
    5591 [Repeated 1 time(s)]
    5592 
    5593 > select clear
    5594 
    5595 [Repeated 1 time(s)]
    5596 
    5597 > isolde pepflip sel
    5598 
    5599 Flipping the peptide bond for 1 residues 
    5600 
    5601 > isolde pepflip sel
    5602 
    5603 Flipping the peptide bond for 1 residues 
    5604 
    5605 > isolde pepflip sel
    5606 
    5607 Flipping the peptide bond for 1 residues 
    5608 
    5609 > ui tool show "Ramachandran Plot"
    5610 
    5611 > select clear
    5612 
    5613 > ui tool show "Ramachandran Plot"
    5614 
    5615 > select clear
    5616 
    5617 > isolde sim stop
    5618 
    5619 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5620 chains... 
    5621 ISOLDE: stopped sim 
    5622 
    5623 > view #1/u:49
    5624 
    5625 > select #1/u:49
    5626 
    5627 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5628 
    5629 > isolde sim start sel
    5630 
    5631 ISOLDE: started sim 
    5632 
    5633 > ui tool show "Ramachandran Plot"
    5634 
    5635 > isolde sim stop
    5636 
    5637 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5638 chains... 
    5639 ISOLDE: stopped sim 
    5640 
    5641 > view #1/u:43
    5642 
    5643 > select #1/u:43
    5644 
    5645 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5646 
    5647 > isolde sim start sel
    5648 
    5649 ISOLDE: started sim 
    5650 
    5651 > ui tool show "Ramachandran Plot"
    5652 
    5653 > select clear
    5654 
    5655 > isolde pepflip sel
    5656 
    5657 Flipping the peptide bond for 1 residues 
    5658 
    5659 > select clear
    5660 
    5661 > ui tool show "Ramachandran Plot"
    5662 
    5663 > view #1/u:43
    5664 
    5665 > ui tool show "Ramachandran Plot"
    5666 
    5667 > select clear
    5668 
    5669 > ui tool show "Ramachandran Plot"
    5670 
    5671 > select clear
    5672 
    5673 [Repeated 1 time(s)]
    5674 
    5675 > isolde pepflip sel
    5676 
    5677 Flipping the peptide bond for 1 residues 
    5678 
    5679 > select clear
    5680 
    5681 > isolde pepflip sel
    5682 
    5683 Flipping the peptide bond for 1 residues 
    5684 
    5685 > select clear
    5686 
    5687 [Repeated 1 time(s)]
    5688 
    5689 > isolde pepflip sel
    5690 
    5691 Flipping the peptide bond for 1 residues 
    5692 
    5693 > select clear
    5694 
    5695 [Repeated 1 time(s)]
    5696 
    5697 > hide #!1.1 models
    5698 
    5699 > show #!1.1 models
    5700 
    5701 > hide #!1.2 models
    5702 
    5703 > show #!1.2 models
    5704 
    5705 > hide #!1.2 models
    5706 
    5707 > show #!1.2 models
    5708 
    5709 > hide #!1.2 models
    5710 
    5711 > show #!1.2 models
    5712 
    5713 > hide #!1.2 models
    5714 
    5715 > show #!1.2 models
    5716 
    5717 > ui tool show "Ramachandran Plot"
    5718 
    5719 > select clear
    5720 
    5721 > view #1/u:43
    5722 
    5723 > isolde sim stop
    5724 
    5725 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5726 chains... 
    5727 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5728 standards. 
    5729 ISOLDE: stopped sim 
    5730 
    5731 > isolde sim start sel
    5732 
    5733 ISOLDE: started sim 
    5734 
    5735 > select clear
    5736 
    5737 [Repeated 1 time(s)]
    5738 
    5739 > isolde sim stop
    5740 
    5741 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5742 chains... 
    5743 ISOLDE: stopped sim 
    5744 
    5745 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5746 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.pdb
    5747 
    5748 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5749 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.cxs
    5750 
    5751 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5752 
    5753 > view #1/u:42|u:55
    5754 
    5755 Expected an objects specifier or a view name or a keyword 
    5756 
    5757 > view #1/u:42|/u:55
    5758 
    5759 > select #1/u:42|/u:55
    5760 
    5761 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5762 
    5763 > isolde sim start sel
    5764 
    5765 ISOLDE: started sim 
    5766 
    5767 > isolde sim stop discardTo start
    5768 
    5769 reverting to start 
    5770 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5771 chains... 
    5772 ISOLDE: stopped sim 
    5773 
    5774 > select #1/u:42|/u:55
    5775 
    5776 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5777 
    5778 > isolde sim start sel
    5779 
    5780 ISOLDE: started sim 
    5781 
    5782 > ui tool show "Ramachandran Plot"
    5783 
    5784 > select clear
    5785 
    5786 [Repeated 2 time(s)]
    5787 
    5788 > isolde pepflip sel
    5789 
    5790 Flipping the peptide bond for 1 residues 
    5791 
    5792 > isolde pepflip sel
    5793 
    5794 Flipping the peptide bond for 1 residues 
    5795 
    5796 > select clear
    5797 
    5798 > ui tool show "Ramachandran Plot"
    5799 
    5800 Unable to flip peptide bond after 50 rounds. Giving up. 
    5801 
    5802 > ui tool show "Ramachandran Plot"
    5803 
    5804 > isolde sim stop
    5805 
    5806 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5807 chains... 
    5808 ISOLDE: stopped sim 
    5809 
    5810 > view #1/u:43
    5811 
    5812 > select #1/u:43
    5813 
    5814 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5815 
    5816 > isolde sim start sel
    5817 
    5818 ISOLDE: started sim 
    5819 
    5820 > ui tool show "Ramachandran Plot"
    5821 
    5822 > select clear
    5823 
    5824 > isolde sim stop
    5825 
    5826 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5827 chains... 
    5828 ISOLDE: stopped sim 
    5829 
    5830 > view #1/u:63
    5831 
    5832 > select #1/u:63
    5833 
    5834 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5835 
    5836 > select #1/u:63
    5837 
    5838 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5839 
    5840 > isolde sim start sel
    5841 
    5842 ISOLDE: started sim 
    5843 
    5844 > ui tool show "Ramachandran Plot"
    5845 
    5846 > isolde sim stop
    5847 
    5848 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5849 chains... 
    5850 ISOLDE: stopped sim 
    5851 
    5852 > ui tool show "Ramachandran Plot"
    5853 
    5854 > select #1/u:49
    5855 
    5856 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5857 
    5858 > view #1/u:49
    5859 
    5860 > select #1/u:49
    5861 
    5862 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5863 
    5864 > isolde sim start sel
    5865 
    5866 ISOLDE: started sim 
    5867 
    5868 > ui tool show "Ramachandran Plot"
    5869 
    5870 [Repeated 1 time(s)]
    5871 
    5872 > isolde sim stop
    5873 
    5874 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5875 chains... 
    5876 ISOLDE: stopped sim 
    5877 
    5878 > view #1/o:55
    5879 
    5880 > select #1/o:55
    5881 
    5882 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5883 
    5884 > isolde sim start sel
    5885 
    5886 ISOLDE: started sim 
    5887 
    5888 > ui tool show "Ramachandran Plot"
    5889 
    5890 > isolde sim stop
    5891 
    5892 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5893 chains... 
    5894 ISOLDE: stopped sim 
    5895 
    5896 > view #1/u:12
    5897 
    5898 > select #1/u:12
    5899 
    5900 17 atoms, 17 bonds, 1 residue, 1 model selected 
    5901 
    5902 > isolde sim start sel
    5903 
    5904 ISOLDE: started sim 
    5905 
    5906 > ui tool show "Ramachandran Plot"
    5907 
    5908 > select clear
    5909 
    5910 > isolde sim stop
    5911 
    5912 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5913 chains... 
    5914 ISOLDE: stopped sim 
    5915 
    5916 > view #1/u:28-42|/o:53-56|/u:43-47
    5917 
    5918 > select #1/u:28-42|/o:53-56|/u:43-47
    5919 
    5920 400 atoms, 402 bonds, 24 residues, 1 model selected 
    5921 
    5922 > isolde sim start sel
    5923 
    5924 ISOLDE: started sim 
    5925 
    5926 > ui tool show "Ramachandran Plot"
    5927 
    5928 > isolde sim pause
    5929 
    5930 > ui tool show "Ramachandran Plot"
    5931 
    5932 [Repeated 2 time(s)]
    5933 
    5934 > isolde sim resume
    5935 
    5936 > isolde sim stop
    5937 
    5938 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5939 chains... 
    5940 ISOLDE: stopped sim 
    5941 
    5942 > select #1/u:35
    5943 
    5944 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5945 
    5946 > view #1/u:35
    5947 
    5948 > select #1/u:35
    5949 
    5950 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5951 
    5952 > select #1/u:35
    5953 
    5954 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5955 
    5956 > isolde sim start sel
    5957 
    5958 ISOLDE: started sim 
    5959 
    5960 > ui tool show "Ramachandran Plot"
    5961 
    5962 > isolde sim stop
    5963 
    5964 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5965 chains... 
    5966 ISOLDE: stopped sim 
    5967 
    5968 > view #1/u:25
    5969 
    5970 > select #1/u:25
    5971 
    5972 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5973 
    5974 > isolde sim start sel
    5975 
    5976 ISOLDE: started sim 
    5977 
    5978 > ui tool show "Ramachandran Plot"
    5979 
    5980 > select clear
    5981 
    5982 > isolde sim stop
    5983 
    5984 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5985 chains... 
    5986 ISOLDE: stopped sim 
    5987 
    5988 > view #1/u:60-65|/u:8-12
    5989 
    5990 > select #1/u:60-65|/u:8-12
    5991 
    5992 180 atoms, 180 bonds, 11 residues, 1 model selected 
    5993 
    5994 > isolde sim start sel
    5995 
    5996 ISOLDE: started sim 
    5997 
    5998 > ui tool show "Ramachandran Plot"
    5999 
    6000 > isolde sim stop
    6001 
    6002 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6003 chains... 
    6004 ISOLDE: stopped sim 
    6005 
    6006 > view #1/u:12
    6007 
    6008 > select sim start sel
    6009 
    6010 Expected an objects specifier or a keyword 
    6011 
    6012 > view #1/u:12
    6013 
    6014 > select #1/u:12
    6015 
    6016 17 atoms, 17 bonds, 1 residue, 1 model selected 
    6017 
    6018 > isolde sim start sel
    6019 
    6020 ISOLDE: started sim 
    6021 
    6022 > ui tool show "Ramachandran Plot"
    6023 
    6024 > isolde sim stop
    6025 
    6026 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6027 chains... 
    6028 ISOLDE: stopped sim 
    6029 
    6030 > isolde sim start sel
    6031 
    6032 ISOLDE: started sim 
    6033 
    6034 > ui tool show "Ramachandran Plot"
    6035 
    6036 [Repeated 1 time(s)]
    6037 
    6038 > select clear
    6039 
    6040 > isolde sim stop
    6041 
    6042 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6043 chains... 
    6044 ISOLDE: stopped sim 
    6045 
    6046 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6047 > mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.cxs
    6048 
    6049 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6050 
    6051 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6052 > mut8-no-C-ter/14-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.pdb
    6053 
    6054 > isolde cisflip #1.2/Q:137
    6055 
    6056 Performing cis<\-->trans flip for 1 residues 
    6057 ISOLDE: started sim 
    6058 
    6059 > isolde sim stop discardTo start
    6060 
    6061 reverting to start 
    6062 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6063 chains... 
    6064 ISOLDE: stopped sim 
    6065 
    6066 > isolde sim start sel
    6067 
    6068 ISOLDE: started sim 
    6069 
    6070 > isolde sim stop discardTo start
    6071 
    6072 reverting to start 
    6073 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6074 chains... 
    6075 ISOLDE: stopped sim 
    6076 
    6077 > isolde sim start sel
    6078 
    6079 ISOLDE: started sim 
    6080 
    6081 > isolde cisflip sel
    6082 
    6083 Performing cis<\-->trans flip for 1 residues 
    6084 
    6085 > isolde cisflip #1.2/Q:137
    6086 
    6087 Performing cis<\-->trans flip for 1 residues 
    6088 
    6089 > isolde pepflip sel
    6090 
    6091 Flipping the peptide bond for 1 residues 
    6092 
    6093 > select clear
    6094 
    6095 [Repeated 2 time(s)]
    6096 
    6097 > ui tool show "Ramachandran Plot"
    6098 
    6099 > select clear
    6100 
    6101 > ui tool show "Ramachandran Plot"
    6102 
    6103 > view #1/Q:137
    6104 
    6105 > isolde sim pause
    6106 
    6107 > isolde sim stop
    6108 
    6109 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6110 chains... 
    6111 ISOLDE: stopped sim 
    6112 
    6113 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6114 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.pdb
    6115 
    6116 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6117 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.cxs
    6118 
    6119 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6120 
    6121 > view #1/Q:137
    6122 
    6123 > select #1/Q:137
    6124 
    6125 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6126 
    6127 > isolde sim start sel
    6128 
    6129 ISOLDE: started sim 
    6130 
    6131 > ui tool show "Ramachandran Plot"
    6132 
    6133 > isolde pepflip sel
    6134 
    6135 Flipping the peptide bond for 1 residues 
    6136 
    6137 > ui tool show "Ramachandran Plot"
    6138 
    6139 > isolde pepflip sel
    6140 
    6141 Flipping the peptide bond for 1 residues 
    6142 
    6143 > select clear
    6144 
    6145 > isolde pepflip sel
    6146 
    6147 Flipping the peptide bond for 1 residues 
    6148 
    6149 > select clear
    6150 
    6151 [Repeated 1 time(s)]
    6152 
    6153 > ui tool show "Ramachandran Plot"
    6154 
    6155 [Repeated 1 time(s)]
    6156 
    6157 > isolde sim stop
    6158 
    6159 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6160 chains... 
    6161 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6162 standards. 
    6163 ISOLDE: stopped sim 
    6164 
    6165 > isolde sim start sel
    6166 
    6167 ISOLDE: started sim 
    6168 
    6169 > isolde sim stop discardTo start
    6170 
    6171 reverting to start 
    6172 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6173 chains... 
    6174 ISOLDE: stopped sim 
    6175 
    6176 > select #1/Q:181
    6177 
    6178 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6179 
    6180 > isolde sim start sel
    6181 
    6182 ISOLDE: started sim 
    6183 
    6184 > ui tool show "Ramachandran Plot"
    6185 
    6186 > isolde sim stop
    6187 
    6188 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6189 chains... 
    6190 ISOLDE: stopped sim 
    6191 
    6192 > view #1/Q:137
    6193 
    6194 > select #1/Q:137
    6195 
    6196 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6197 
    6198 > isolde sim start sel
    6199 
    6200 ISOLDE: started sim 
    6201 
    6202 > ui tool show "Ramachandran Plot"
    6203 
    6204 > select clear
    6205 
    6206 > isolde sim stop
    6207 
    6208 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6209 chains... 
    6210 ISOLDE: stopped sim 
    6211 
    6212 > isolde sim start sel
    6213 
    6214 ISOLDE: started sim 
    6215 
    6216 > isolde cisflip #1.2/O:156
    6217 
    6218 Performing cis<\-->trans flip for 1 residues 
    6219 
    6220 > isolde pepflip sel
    6221 
    6222 Flipping the peptide bond for 1 residues 
    6223 
    6224 > isolde pepflip sel
    6225 
    6226 Flipping the peptide bond for 1 residues 
    6227 
    6228 > select clear
    6229 
    6230 > isolde pepflip sel
    6231 
    6232 Flipping the peptide bond for 1 residues 
    6233 
    6234 > isolde pepflip sel
    6235 
    6236 Flipping the peptide bond for 1 residues 
    6237 
    6238 > isolde sim stop discardTo start
    6239 
    6240 reverting to start 
    6241 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6242 chains... 
    6243 ISOLDE: stopped sim 
    6244 
    6245 > view #1/Q:137
    6246 
    6247 [Repeated 1 time(s)]
    6248 
    6249 > view #1/Q:156
    6250 
    6251 > select #1/Q:156
    6252 
    6253 22 atoms, 21 bonds, 1 residue, 1 model selected 
    6254 
    6255 > select #1/O:156
    6256 
    6257 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6258 
    6259 > view #1/O:156
    6260 
    6261 > select clear
    6262 
    6263 > isolde sim start sel
    6264 
    6265 ISOLDE: started sim 
    6266 
    6267 > isolde cisflip #1.2/Q:44
    6268 
    6269 Performing cis<\-->trans flip for 1 residues 
    6270 
    6271 > isolde pepflip sel
    6272 
    6273 Flipping the peptide bond for 1 residues 
    6274 
    6275 > isolde pepflip sel
    6276 
    6277 Flipping the peptide bond for 1 residues 
    6278 
    6279 > isolde pepflip sel
    6280 
    6281 Flipping the peptide bond for 1 residues 
    6282 
    6283 > isolde pepflip sel
    6284 
    6285 Flipping the peptide bond for 1 residues 
    6286 
    6287 > select clear
    6288 
    6289 > isolde pepflip sel
    6290 
    6291 Flipping the peptide bond for 1 residues 
    6292 
    6293 > isolde pepflip sel
    6294 
    6295 Flipping the peptide bond for 1 residues 
    6296 
    6297 > ui tool show "Ramachandran Plot"
    6298 
    6299 > isolde sim stop discardTo start
    6300 
    6301 reverting to start 
    6302 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6303 chains... 
    6304 ISOLDE: stopped sim 
    6305 
    6306 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6307 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.cxs
    6308 
    6309 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6310 
    6311 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6312 > mut8-no-C-ter/16-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.pdb
    6313 
    6314 > ui tool show "Ramachandran Plot"
    6315 
    6316 [Repeated 1 time(s)]
    6317 
    6318 > isolde sim start sel
    6319 
    6320 ISOLDE: started sim 
    6321 
    6322 > ui tool show "Ramachandran Plot"
    6323 
    6324 > select clear
    6325 
    6326 > isolde pepflip sel
    6327 
    6328 Flipping the peptide bond for 1 residues 
    6329 
    6330 > isolde pepflip sel
    6331 
    6332 Flipping the peptide bond for 1 residues 
    6333 
    6334 > select clear
    6335 
    6336 [Repeated 1 time(s)]
    6337 
    6338 > isolde sim pause
    6339 
    6340 > isolde sim resume
    6341 
    6342 > isolde pepflip sel
    6343 
    6344 Flipping the peptide bond for 1 residues 
    6345 
    6346 > isolde pepflip sel
    6347 
    6348 Flipping the peptide bond for 1 residues 
    6349 
    6350 > select clear
    6351 
    6352 3 models selected 
    6353 
    6354 > select clear
    6355 
    6356 > ui tool show "Ramachandran Plot"
    6357 
    6358 > isolde sim pause
    6359 
    6360 > ui tool show "Ramachandran Plot"
    6361 
    6362 > view #1/h:163
    6363 
    6364 > ui tool show "Ramachandran Plot"
    6365 
    6366 > isolde sim stop
    6367 
    6368 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6369 chains... 
    6370 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6371 standards. 
    6372 ISOLDE: stopped sim 
    6373 
    6374 > ui tool show "Ramachandran Plot"
    6375 
    6376 > view #1/h:163
    6377 
    6378 > isolde sim start sel
    6379 
    6380 ISOLDE: started sim 
    6381 
    6382 > ui tool show "Ramachandran Plot"
    6383 
    6384 Traceback (most recent call last): 
    6385 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6386 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6387 func(*args, **kwargs) 
    6388 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6389 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6390 on_resize 
    6391 c.draw() 
    6392 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6393 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6394 self.figure.draw(self.renderer) 
    6395 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6396 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6397 result = draw(artist, renderer, *args, **kwargs) 
    6398 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6399 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6400 return draw(artist, renderer) 
    6401 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6402 packages/matplotlib/figure.py", line 2796, in draw 
    6403 artists = self._get_draw_artists(renderer) 
    6404 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6405 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6406 ax.apply_aspect() 
    6407 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6408 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6409 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6410 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6411 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6412 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6413 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6414 
    6415 > select clear
    6416 
    6417 [Repeated 3 time(s)]
    6418 
    6419 > isolde pepflip sel
    6420 
    6421 Flipping the peptide bond for 1 residues 
    6422 
    6423 > isolde pepflip sel
    6424 
    6425 Flipping the peptide bond for 1 residues 
    6426 
    6427 > isolde pepflip sel
    6428 
    6429 Flipping the peptide bond for 1 residues 
    6430 
    6431 > select clear
    6432 
    6433 > isolde pepflip sel
    6434 
    6435 Flipping the peptide bond for 1 residues 
    6436 
    6437 > isolde pepflip sel
    6438 
    6439 Flipping the peptide bond for 1 residues 
    6440 
    6441 > select clear
    6442 
    6443 > ui tool show "Ramachandran Plot"
    6444 
    6445 Unable to flip peptide bond after 50 rounds. Giving up. 
    6446 
    6447 > isolde pepflip sel
    6448 
    6449 Flipping the peptide bond for 1 residues 
    6450 
    6451 > isolde pepflip sel
    6452 
    6453 Flipping the peptide bond for 1 residues 
    6454 
    6455 > select clear
    6456 
    6457 Unable to flip peptide bond after 50 rounds. Giving up. 
    6458 
    6459 > isolde sim pause
    6460 
    6461 > select #1/h:180|/h:184
    6462 
    6463 28 atoms, 26 bonds, 2 residues, 1 model selected 
    6464 
    6465 > isolde sim start sel
    6466 
    6467 Simulation already running! 
    6468 
    6469 > isolde sim stop
    6470 
    6471 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6472 chains... 
    6473 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6474 standards. 
    6475 ISOLDE: stopped sim 
    6476 
    6477 > isolde sim start sel
    6478 
    6479 ISOLDE: started sim 
    6480 
    6481 > select clear
    6482 
    6483 > isolde pepflip sel
    6484 
    6485 Flipping the peptide bond for 1 residues 
    6486 
    6487 > isolde pepflip sel
    6488 
    6489 Flipping the peptide bond for 1 residues 
    6490 
    6491 > isolde pepflip sel
    6492 
    6493 Flipping the peptide bond for 1 residues 
    6494 
    6495 > select clear
    6496 
    6497 [Repeated 1 time(s)]
    6498 
    6499 > isolde pepflip sel
    6500 
    6501 Flipping the peptide bond for 1 residues 
    6502 
    6503 > select clear
    6504 
    6505 > isolde pepflip sel
    6506 
    6507 Flipping the peptide bond for 1 residues 
    6508 
    6509 > select clear
    6510 
    6511 > isolde sim pause
    6512 
    6513 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6514 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.pdb
    6515 
    6516 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6517 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.cxs
    6518 
    6519 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6520 
    6521 > isolde sim start sel
    6522 
    6523 Simulation already running! 
    6524 
    6525 > isolde sim resume
    6526 
    6527 > select clear
    6528 
    6529 [Repeated 4 time(s)]
    6530 
    6531 > isolde pepflip sel
    6532 
    6533 Flipping the peptide bond for 1 residues 
    6534 
    6535 > isolde pepflip sel
    6536 
    6537 Flipping the peptide bond for 1 residues 
    6538 
    6539 > select clear
    6540 
    6541 > isolde pepflip sel
    6542 
    6543 Flipping the peptide bond for 1 residues 
    6544 
    6545 > select #1/h
    6546 
    6547 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6548 
    6549 > select clear
    6550 
    6551 > ui tool show "Ramachandran Plot"
    6552 
    6553 > view #1/h:N183
    6554 
    6555 No objects specified. 
    6556 
    6557 > view #1/h:183
    6558 
    6559 > isolde sim pause
    6560 
    6561 > isolde sim resume
    6562 
    6563 > select clear
    6564 
    6565 [Repeated 2 time(s)]
    6566 
    6567 > isolde pepflip sel
    6568 
    6569 Flipping the peptide bond for 1 residues 
    6570 
    6571 > isolde pepflip sel
    6572 
    6573 Flipping the peptide bond for 1 residues 
    6574 
    6575 > isolde pepflip sel
    6576 
    6577 Flipping the peptide bond for 1 residues 
    6578 Unable to flip peptide bond after 50 rounds. Giving up. 
    6579 [Repeated 1 time(s)]
    6580 
    6581 > select clear
    6582 
    6583 > isolde sim stop
    6584 
    6585 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6586 chains... 
    6587 ISOLDE: stopped sim 
    6588 
    6589 > view #1/h
    6590 
    6591 > select #1/h
    6592 
    6593 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6594 
    6595 > isolde sim start sel
    6596 
    6597 ISOLDE: started sim 
    6598 
    6599 > ui tool show "Ramachandran Plot"
    6600 
    6601 > isolde pepflip sel
    6602 
    6603 Flipping the peptide bond for 1 residues 
    6604 
    6605 > select clear
    6606 
    6607 > isolde sim pause
    6608 
    6609 > isolde sim resume
    6610 
    6611 > select clear
    6612 
    6613 > isolde pepflip sel
    6614 
    6615 Flipping the peptide bond for 1 residues 
    6616 
    6617 > select clear
    6618 
    6619 > isolde sim stop
    6620 
    6621 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6622 chains... 
    6623 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6624 standards. 
    6625 ISOLDE: stopped sim 
    6626 
    6627 > select #1/h
    6628 
    6629 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6630 
    6631 > isolde sim start sel
    6632 
    6633 ISOLDE: started sim 
    6634 
    6635 > select clear
    6636 
    6637 > isolde pepflip sel
    6638 
    6639 Flipping the peptide bond for 1 residues 
    6640 
    6641 > isolde pepflip sel
    6642 
    6643 Flipping the peptide bond for 1 residues 
    6644 
    6645 > isolde sim pause
    6646 
    6647 > ui tool show "Ramachandran Plot"
    6648 
    6649 > isolde sim resume
    6650 
    6651 > isolde pepflip sel
    6652 
    6653 Flipping the peptide bond for 1 residues 
    6654 
    6655 > isolde pepflip sel
    6656 
    6657 Flipping the peptide bond for 1 residues 
    6658 
    6659 > select #1/h:115-119
    6660 
    6661 85 atoms, 84 bonds, 5 residues, 1 model selected 
    6662 
    6663 > select clear
    6664 
    6665 > select #1/h:215-219
    6666 
    6667 70 atoms, 69 bonds, 5 residues, 1 model selected 
    6668 
    6669 > select #1/h:152-155
    6670 
    6671 61 atoms, 62 bonds, 4 residues, 1 model selected 
    6672 
    6673 > select #1/h:152-156
    6674 
    6675 80 atoms, 81 bonds, 5 residues, 1 model selected 
    6676 
    6677 > select #1/h
    6678 
    6679 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6680 
    6681 > select clear
    6682 
    6683 [Repeated 1 time(s)]
    6684 
    6685 > isolde pepflip sel
    6686 
    6687 Flipping the peptide bond for 1 residues 
    6688 
    6689 > select clear
    6690 
    6691 > isolde pepflip sel
    6692 
    6693 Flipping the peptide bond for 1 residues 
    6694 
    6695 > isolde pepflip sel
    6696 
    6697 Flipping the peptide bond for 1 residues 
    6698 Unable to flip peptide bond after 50 rounds. Giving up. 
    6699 
    6700 > select clear
    6701 
    6702 [Repeated 1 time(s)]
    6703 
    6704 > isolde pepflip sel
    6705 
    6706 Flipping the peptide bond for 1 residues 
    6707 
    6708 > select clear
    6709 
    6710 > isolde sim pause
    6711 
    6712 > isolde sim resume
    6713 
    6714 > ui tool show "Ramachandran Plot"
    6715 
    6716 > isolde sim pause
    6717 
    6718 > isolde sim resume
    6719 
    6720 > view #1/P:244
    6721 
    6722 > view #1/h
    6723 
    6724 > ui tool show "Ramachandran Plot"
    6725 
    6726 3 models selected 
    6727 [Repeated 2 time(s)]
    6728 
    6729 > isolde sim pause
    6730 
    6731 > isolde sim resume
    6732 
    6733 > isolde sim pause
    6734 
    6735 > isolde sim resume
    6736 
    6737 > select clear
    6738 
    6739 3 models selected 
    6740 
    6741 > select clear
    6742 
    6743 > ui tool show "Ramachandran Plot"
    6744 
    6745 [Repeated 1 time(s)]
    6746 
    6747 > isolde sim pause
    6748 
    6749 > isolde sim resume
    6750 
    6751 > isolde sim pause
    6752 
    6753 > ui tool show "Ramachandran Plot"
    6754 
    6755 > isolde sim resume
    6756 
    6757 > select clear
    6758 
    6759 > isolde pepflip sel
    6760 
    6761 Flipping the peptide bond for 1 residues 
    6762 
    6763 > select clear
    6764 
    6765 > isolde pepflip sel
    6766 
    6767 Flipping the peptide bond for 1 residues 
    6768 
    6769 > select clear
    6770 
    6771 Unable to flip peptide bond after 50 rounds. Giving up. 
    6772 
    6773 > ui tool show "Ramachandran Plot"
    6774 
    6775 > isolde sim pause
    6776 
    6777 > isolde sim resume
    6778 
    6779 > select clear
    6780 
    6781 [Repeated 2 time(s)]
    6782 
    6783 > isolde pepflip sel
    6784 
    6785 Flipping the peptide bond for 1 residues 
    6786 
    6787 > select clear
    6788 
    6789 > isolde pepflip sel
    6790 
    6791 Flipping the peptide bond for 1 residues 
    6792 Unable to flip peptide bond after 50 rounds. Giving up. 
    6793 
    6794 > select clear
    6795 
    6796 > ui tool show "Ramachandran Plot"
    6797 
    6798 > isolde pepflip sel
    6799 
    6800 Flipping the peptide bond for 1 residues 
    6801 
    6802 > select clear
    6803 
    6804 > isolde pepflip sel
    6805 
    6806 Flipping the peptide bond for 1 residues 
    6807 
    6808 > select clear
    6809 
    6810 > ui tool show "Ramachandran Plot"
    6811 
    6812 > select clear
    6813 
    6814 [Repeated 3 time(s)]
    6815 
    6816 > ui tool show "Ramachandran Plot"
    6817 
    6818 > isolde sim pause
    6819 
    6820 > isolde sim resume
    6821 
    6822 > ui tool show "Ramachandran Plot"
    6823 
    6824 > select clear
    6825 
    6826 [Repeated 1 time(s)]
    6827 
    6828 > ui tool show "Ramachandran Plot"
    6829 
    6830 [Repeated 5 time(s)]
    6831 
    6832 > isolde pepflip sel
    6833 
    6834 Flipping the peptide bond for 1 residues 
    6835 
    6836 > select clear
    6837 
    6838 > isolde pepflip sel
    6839 
    6840 Flipping the peptide bond for 1 residues 
    6841 
    6842 > select clear
    6843 
    6844 > isolde pepflip sel
    6845 
    6846 Flipping the peptide bond for 1 residues 
    6847 
    6848 > select clear
    6849 
    6850 > isolde pepflip sel
    6851 
    6852 Flipping the peptide bond for 1 residues 
    6853 
    6854 > isolde pepflip sel
    6855 
    6856 Flipping the peptide bond for 1 residues 
    6857 
    6858 > ui tool show "Ramachandran Plot"
    6859 
    6860 > select clear
    6861 
    6862 > isolde pepflip sel
    6863 
    6864 Flipping the peptide bond for 1 residues 
    6865 
    6866 > isolde pepflip sel
    6867 
    6868 Flipping the peptide bond for 1 residues 
    6869 
    6870 > ui tool show "Ramachandran Plot"
    6871 
    6872 [Repeated 1 time(s)]Traceback (most recent call last): 
    6873 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6874 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6875 func(*args, **kwargs) 
    6876 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6877 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6878 on_resize 
    6879 c.draw() 
    6880 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6881 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6882 self.figure.draw(self.renderer) 
    6883 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6884 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6885 result = draw(artist, renderer, *args, **kwargs) 
    6886 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6887 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6888 return draw(artist, renderer) 
    6889 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6890 packages/matplotlib/figure.py", line 2796, in draw 
    6891 artists = self._get_draw_artists(renderer) 
    6892 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6893 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6894 ax.apply_aspect() 
    6895 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6896 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6897 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6898 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6899 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6900 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6901 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6902 
    6903 > select clear
    6904 
    6905 > ui tool show "Ramachandran Plot"
    6906 
    6907 > isolde pepflip sel
    6908 
    6909 Flipping the peptide bond for 1 residues 
    6910 
    6911 > select clear
    6912 
    6913 > isolde pepflip sel
    6914 
    6915 Flipping the peptide bond for 1 residues 
    6916 
    6917 > isolde pepflip sel
    6918 
    6919 Flipping the peptide bond for 1 residues 
    6920 Unable to flip peptide bond after 50 rounds. Giving up. 
    6921 Traceback (most recent call last): 
    6922 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6923 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6924 func(*args, **kwargs) 
    6925 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6926 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6927 on_resize 
    6928 c.draw() 
    6929 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6930 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6931 self.figure.draw(self.renderer) 
    6932 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6933 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6934 result = draw(artist, renderer, *args, **kwargs) 
    6935 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6936 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6937 return draw(artist, renderer) 
    6938 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6939 packages/matplotlib/figure.py", line 2796, in draw 
    6940 artists = self._get_draw_artists(renderer) 
    6941 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6942 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6943 ax.apply_aspect() 
    6944 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6945 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6946 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6947 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6948 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6949 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6950 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6951 
    6952 > isolde pepflip sel
    6953 
    6954 Flipping the peptide bond for 1 residues 
    6955 
    6956 > select #1/h
    6957 
    6958 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6959 
    6960 > select clear
    6961 
    6962 [Repeated 1 time(s)]
    6963 
    6964 > ui tool show "Ramachandran Plot"
    6965 
    6966 Traceback (most recent call last): 
    6967 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6968 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6969 func(*args, **kwargs) 
    6970 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6971 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6972 on_resize 
    6973 c.draw() 
    6974 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6975 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6976 self.figure.draw(self.renderer) 
    6977 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6978 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6979 result = draw(artist, renderer, *args, **kwargs) 
    6980 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6981 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6982 return draw(artist, renderer) 
    6983 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6984 packages/matplotlib/figure.py", line 2796, in draw 
    6985 artists = self._get_draw_artists(renderer) 
    6986 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6987 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6988 ax.apply_aspect() 
    6989 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6990 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6991 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6992 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6993 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6994 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6995 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6996 Traceback (most recent call last): 
    6997 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6998 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6999 func(*args, **kwargs) 
    7000 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7001 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7002 on_resize 
    7003 c.draw() 
    7004 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7005 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7006 self.figure.draw(self.renderer) 
    7007 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7008 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7009 result = draw(artist, renderer, *args, **kwargs) 
    7010 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7011 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7012 return draw(artist, renderer) 
    7013 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7014 packages/matplotlib/figure.py", line 2796, in draw 
    7015 artists = self._get_draw_artists(renderer) 
    7016 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7017 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7018 ax.apply_aspect() 
    7019 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7020 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7021 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7022 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7023 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7024 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7025 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7026 
    7027 > isolde pepflip sel
    7028 
    7029 Flipping the peptide bond for 1 residues 
    7030 
    7031 > select clear
    7032 
    7033 > isolde pepflip sel
    7034 
    7035 Flipping the peptide bond for 1 residues 
    7036 
    7037 > select clear
    7038 
    7039 [Repeated 2 time(s)]
    7040 
    7041 > isolde pepflip sel
    7042 
    7043 Flipping the peptide bond for 1 residues 
    7044 
    7045 > ui tool show "Ramachandran Plot"
    7046 
    7047 [Repeated 1 time(s)]
    7048 
    7049 > select clear
    7050 
    7051 > isolde pepflip sel
    7052 
    7053 Flipping the peptide bond for 1 residues 
    7054 
    7055 > isolde pepflip sel
    7056 
    7057 Flipping the peptide bond for 1 residues 
    7058 
    7059 > ui tool show "Ramachandran Plot"
    7060 
    7061 > select clear
    7062 
    7063 [Repeated 1 time(s)]
    7064 
    7065 > isolde pepflip sel
    7066 
    7067 Flipping the peptide bond for 1 residues 
    7068 
    7069 > select clear
    7070 
    7071 > isolde pepflip sel
    7072 
    7073 Flipping the peptide bond for 1 residues 
    7074 
    7075 > isolde pepflip sel
    7076 
    7077 Flipping the peptide bond for 1 residues 
    7078 
    7079 > select clear
    7080 
    7081 > isolde pepflip sel
    7082 
    7083 Flipping the peptide bond for 1 residues 
    7084 
    7085 > select clear
    7086 
    7087 [Repeated 1 time(s)]
    7088 
    7089 > select #1/h
    7090 
    7091 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7092 
    7093 > select #1/h
    7094 
    7095 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7096 
    7097 > ui tool show "Ramachandran Plot"
    7098 
    7099 > select clear
    7100 
    7101 Traceback (most recent call last): 
    7102 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7103 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7104 func(*args, **kwargs) 
    7105 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7106 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7107 on_resize 
    7108 c.draw() 
    7109 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7110 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7111 self.figure.draw(self.renderer) 
    7112 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7113 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7114 result = draw(artist, renderer, *args, **kwargs) 
    7115 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7116 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7117 return draw(artist, renderer) 
    7118 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7119 packages/matplotlib/figure.py", line 2796, in draw 
    7120 artists = self._get_draw_artists(renderer) 
    7121 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7122 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7123 ax.apply_aspect() 
    7124 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7125 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7126 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7127 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7128 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7129 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7130 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7131 Traceback (most recent call last): 
    7132 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7133 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7134 func(*args, **kwargs) 
    7135 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7136 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7137 on_resize 
    7138 c.draw() 
    7139 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7140 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7141 self.figure.draw(self.renderer) 
    7142 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7143 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7144 result = draw(artist, renderer, *args, **kwargs) 
    7145 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7146 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7147 return draw(artist, renderer) 
    7148 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7149 packages/matplotlib/figure.py", line 2796, in draw 
    7150 artists = self._get_draw_artists(renderer) 
    7151 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7152 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7153 ax.apply_aspect() 
    7154 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7155 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7156 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7157 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7158 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7159 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7160 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7161 
    7162 > isolde pepflip sel
    7163 
    7164 Flipping the peptide bond for 1 residues 
    7165 
    7166 > isolde pepflip sel
    7167 
    7168 Flipping the peptide bond for 1 residues 
    7169 Traceback (most recent call last): 
    7170 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7171 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7172 func(*args, **kwargs) 
    7173 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7174 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7175 on_resize 
    7176 c.draw() 
    7177 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7178 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7179 self.figure.draw(self.renderer) 
    7180 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7181 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7182 result = draw(artist, renderer, *args, **kwargs) 
    7183 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7184 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7185 return draw(artist, renderer) 
    7186 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7187 packages/matplotlib/figure.py", line 2796, in draw 
    7188 artists = self._get_draw_artists(renderer) 
    7189 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7190 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7191 ax.apply_aspect() 
    7192 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7193 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7194 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7195 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7196 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7197 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7198 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7199 
    7200 > ui tool show "Ramachandran Plot"
    7201 
    7202 > select #1/h
    7203 
    7204 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7205 
    7206 > select clear
    7207 
    7208 > ui tool show "Ramachandran Plot"
    7209 
    7210 [Repeated 1 time(s)]
    7211 
    7212 > select clear
    7213 
    7214 > ui tool show "Ramachandran Plot"
    7215 
    7216 Traceback (most recent call last): 
    7217 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7218 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7219 func(*args, **kwargs) 
    7220 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7221 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7222 on_resize 
    7223 c.draw() 
    7224 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7225 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7226 self.figure.draw(self.renderer) 
    7227 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7228 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7229 result = draw(artist, renderer, *args, **kwargs) 
    7230 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7231 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7232 return draw(artist, renderer) 
    7233 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7234 packages/matplotlib/figure.py", line 2796, in draw 
    7235 artists = self._get_draw_artists(renderer) 
    7236 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7237 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7238 ax.apply_aspect() 
    7239 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7240 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7241 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7242 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7243 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7244 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7245 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7246 
    7247 > ui tool show "Ramachandran Plot"
    7248 
    7249 [Repeated 1 time(s)]
    7250 
    7251 > select clear
    7252 
    7253 > ui tool show "Ramachandran Plot"
    7254 
    7255 > isolde pepflip sel
    7256 
    7257 Flipping the peptide bond for 1 residues 
    7258 
    7259 > select clear
    7260 
    7261 [Repeated 1 time(s)]
    7262 
    7263 > ui tool show "Ramachandran Plot"
    7264 
    7265 > select #1/h
    7266 
    7267 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7268 
    7269 > select #1/h
    7270 
    7271 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7272 
    7273 > select clear
    7274 
    7275 [Repeated 1 time(s)]
    7276 
    7277 > ui tool show "Ramachandran Plot"
    7278 
    7279 > select clear
    7280 
    7281 > isolde pepflip sel
    7282 
    7283 Flipping the peptide bond for 1 residues 
    7284 
    7285 > isolde pepflip sel
    7286 
    7287 Flipping the peptide bond for 1 residues 
    7288 
    7289 > select clear
    7290 
    7291 > isolde pepflip sel
    7292 
    7293 Flipping the peptide bond for 1 residues 
    7294 
    7295 > select clear
    7296 
    7297 > isolde pepflip sel
    7298 
    7299 Flipping the peptide bond for 1 residues 
    7300 
    7301 > select clear
    7302 
    7303 Traceback (most recent call last): 
    7304 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7305 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7306 func(*args, **kwargs) 
    7307 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7308 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7309 on_resize 
    7310 c.draw() 
    7311 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7312 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7313 self.figure.draw(self.renderer) 
    7314 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7315 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7316 result = draw(artist, renderer, *args, **kwargs) 
    7317 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7318 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7319 return draw(artist, renderer) 
    7320 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7321 packages/matplotlib/figure.py", line 2796, in draw 
    7322 artists = self._get_draw_artists(renderer) 
    7323 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7324 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7325 ax.apply_aspect() 
    7326 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7327 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7328 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7329 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7330 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7331 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7332 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7333 
    7334 > isolde pepflip sel
    7335 
    7336 Flipping the peptide bond for 1 residues 
    7337 
    7338 > ui tool show "Ramachandran Plot"
    7339 
    7340 > select clear
    7341 
    7342 [Repeated 1 time(s)]
    7343 
    7344 > ui tool show "Ramachandran Plot"
    7345 
    7346 > isolde pepflip sel
    7347 
    7348 Flipping the peptide bond for 1 residues 
    7349 
    7350 > ui tool show "Ramachandran Plot"
    7351 
    7352 > isolde pepflip sel
    7353 
    7354 Flipping the peptide bond for 1 residues 
    7355 
    7356 > isolde pepflip sel
    7357 
    7358 Flipping the peptide bond for 1 residues 
    7359 
    7360 > select clear
    7361 
    7362 [Repeated 3 time(s)]
    7363 
    7364 > ui tool show "Ramachandran Plot"
    7365 
    7366 > isolde pepflip sel
    7367 
    7368 Flipping the peptide bond for 1 residues 
    7369 
    7370 > select clear
    7371 
    7372 > ui tool show "Ramachandran Plot"
    7373 
    7374 > select #1/h
    7375 
    7376 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7377 
    7378 > select clear
    7379 
    7380 Traceback (most recent call last): 
    7381 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7382 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7383 func(*args, **kwargs) 
    7384 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7385 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7386 on_resize 
    7387 c.draw() 
    7388 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7389 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7390 self.figure.draw(self.renderer) 
    7391 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7392 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7393 result = draw(artist, renderer, *args, **kwargs) 
    7394 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7395 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7396 return draw(artist, renderer) 
    7397 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7398 packages/matplotlib/figure.py", line 2796, in draw 
    7399 artists = self._get_draw_artists(renderer) 
    7400 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7401 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7402 ax.apply_aspect() 
    7403 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7404 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7405 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7406 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7407 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7408 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7409 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7410 
    7411 > select #1/h
    7412 
    7413 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7414 
    7415 > select #1/h
    7416 
    7417 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7418 
    7419 > ui tool show "Ramachandran Plot"
    7420 
    7421 > select clear
    7422 
    7423 [Repeated 1 time(s)]
    7424 
    7425 > ui tool show "Ramachandran Plot"
    7426 
    7427 Traceback (most recent call last): 
    7428 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7429 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7430 func(*args, **kwargs) 
    7431 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7432 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7433 on_resize 
    7434 c.draw() 
    7435 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7436 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7437 self.figure.draw(self.renderer) 
    7438 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7439 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7440 result = draw(artist, renderer, *args, **kwargs) 
    7441 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7442 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7443 return draw(artist, renderer) 
    7444 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7445 packages/matplotlib/figure.py", line 2796, in draw 
    7446 artists = self._get_draw_artists(renderer) 
    7447 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7448 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7449 ax.apply_aspect() 
    7450 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7451 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7452 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7453 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7454 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7455 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7456 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7457 
    7458 > isolde pepflip sel
    7459 
    7460 Flipping the peptide bond for 1 residues 
    7461 
    7462 > select clear
    7463 
    7464 > ui tool show "Ramachandran Plot"
    7465 
    7466 [Repeated 1 time(s)]
    7467 
    7468 > isolde pepflip sel
    7469 
    7470 Flipping the peptide bond for 1 residues 
    7471 
    7472 > ui tool show "Ramachandran Plot"
    7473 
    7474 > select clear
    7475 
    7476 > ui tool show "Ramachandran Plot"
    7477 
    7478 > select clear
    7479 
    7480 [Repeated 1 time(s)]
    7481 
    7482 > ui tool show "Ramachandran Plot"
    7483 
    7484 [Repeated 2 time(s)]Traceback (most recent call last): 
    7485 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7486 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7487 func(*args, **kwargs) 
    7488 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7489 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7490 on_resize 
    7491 c.draw() 
    7492 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7493 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7494 self.figure.draw(self.renderer) 
    7495 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7496 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7497 result = draw(artist, renderer, *args, **kwargs) 
    7498 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7499 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7500 return draw(artist, renderer) 
    7501 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7502 packages/matplotlib/figure.py", line 2796, in draw 
    7503 artists = self._get_draw_artists(renderer) 
    7504 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7505 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7506 ax.apply_aspect() 
    7507 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7508 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7509 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7510 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7511 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7512 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7513 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7514 
    7515 > isolde pepflip sel
    7516 
    7517 Flipping the peptide bond for 1 residues 
    7518 Traceback (most recent call last): 
    7519 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7520 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7521 func(*args, **kwargs) 
    7522 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7523 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7524 on_resize 
    7525 c.draw() 
    7526 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7527 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7528 self.figure.draw(self.renderer) 
    7529 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7530 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7531 result = draw(artist, renderer, *args, **kwargs) 
    7532 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7533 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7534 return draw(artist, renderer) 
    7535 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7536 packages/matplotlib/figure.py", line 2796, in draw 
    7537 artists = self._get_draw_artists(renderer) 
    7538 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7539 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7540 ax.apply_aspect() 
    7541 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7542 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7543 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7544 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7545 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7546 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7547 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7548 
    7549 > isolde pepflip sel
    7550 
    7551 Flipping the peptide bond for 1 residues 
    7552 
    7553 > isolde sim stop
    7554 
    7555 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7556 chains... 
    7557 ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
    7558 standards. 
    7559 ISOLDE: stopped sim 
    7560 
    7561 > select #1/h
    7562 
    7563 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7564 
    7565 > isolde sim start sel
    7566 
    7567 ISOLDE: started sim 
    7568 
    7569 > ui tool show "Ramachandran Plot"
    7570 
    7571 [Repeated 1 time(s)]
    7572 
    7573 > isolde sim pause
    7574 
    7575 > isolde sim resume
    7576 
    7577 > ui tool show "Ramachandran Plot"
    7578 
    7579 > select clear
    7580 
    7581 > isolde pepflip sel
    7582 
    7583 Flipping the peptide bond for 1 residues 
    7584 
    7585 > isolde pepflip sel
    7586 
    7587 Flipping the peptide bond for 1 residues 
    7588 
    7589 > isolde pepflip sel
    7590 
    7591 Flipping the peptide bond for 1 residues 
    7592 
    7593 > isolde pepflip sel
    7594 
    7595 Flipping the peptide bond for 1 residues 
    7596 
    7597 > isolde pepflip sel
    7598 
    7599 Flipping the peptide bond for 1 residues 
    7600 
    7601 > isolde pepflip sel
    7602 
    7603 Flipping the peptide bond for 1 residues 
    7604 Unable to flip peptide bond after 50 rounds. Giving up. 
    7605 
    7606 > select clear
    7607 
    7608 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    7609 
    7610 > isolde pepflip sel
    7611 
    7612 Flipping the peptide bond for 1 residues 
    7613 
    7614 > select #1/h
    7615 
    7616 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7617 
    7618 > select clear
    7619 
    7620 > isolde sim pause
    7621 
    7622 > isolde sim resume
    7623 
    7624 > ui tool show "Ramachandran Plot"
    7625 
    7626 > isolde pepflip sel
    7627 
    7628 Flipping the peptide bond for 1 residues 
    7629 
    7630 > isolde pepflip sel
    7631 
    7632 Flipping the peptide bond for 1 residues 
    7633 
    7634 > isolde pepflip sel
    7635 
    7636 Flipping the peptide bond for 1 residues 
    7637 
    7638 > select clear
    7639 
    7640 Unable to flip peptide bond after 50 rounds. Giving up. 
    7641 
    7642 > isolde pepflip sel
    7643 
    7644 Flipping the peptide bond for 1 residues 
    7645 
    7646 > isolde pepflip sel
    7647 
    7648 Flipping the peptide bond for 1 residues 
    7649 
    7650 > isolde pepflip sel
    7651 
    7652 Flipping the peptide bond for 1 residues 
    7653 
    7654 > select clear
    7655 
    7656 > select #1/h
    7657 
    7658 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7659 
    7660 > ui tool show "Ramachandran Plot"
    7661 
    7662 > select clear
    7663 
    7664 > ui tool show "Ramachandran Plot"
    7665 
    7666 > select clear
    7667 
    7668 > ui tool show "Ramachandran Plot"
    7669 
    7670 > select clear
    7671 
    7672 > ui tool show "Ramachandran Plot"
    7673 
    7674 > isolde pepflip sel
    7675 
    7676 Flipping the peptide bond for 1 residues 
    7677 
    7678 > isolde pepflip sel
    7679 
    7680 Flipping the peptide bond for 1 residues 
    7681 
    7682 > isolde pepflip sel
    7683 
    7684 Flipping the peptide bond for 1 residues 
    7685 Unable to flip peptide bond after 50 rounds. Giving up. 
    7686 
    7687 > select clear
    7688 
    7689 > ui tool show "Ramachandran Plot"
    7690 
    7691 > isolde pepflip sel
    7692 
    7693 Flipping the peptide bond for 1 residues 
    7694 
    7695 > isolde pepflip sel
    7696 
    7697 Flipping the peptide bond for 1 residues 
    7698 
    7699 > select clear
    7700 
    7701 > ui tool show "Ramachandran Plot"
    7702 
    7703 > isolde pepflip sel
    7704 
    7705 Flipping the peptide bond for 1 residues 
    7706 
    7707 > isolde pepflip sel
    7708 
    7709 Flipping the peptide bond for 1 residues 
    7710 
    7711 > isolde pepflip sel
    7712 
    7713 Flipping the peptide bond for 1 residues 
    7714 
    7715 > isolde pepflip sel
    7716 
    7717 Flipping the peptide bond for 1 residues 
    7718 Unable to flip peptide bond after 50 rounds. Giving up. 
    7719 
    7720 > isolde pepflip sel
    7721 
    7722 Flipping the peptide bond for 1 residues 
    7723 Traceback (most recent call last): 
    7724 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7725 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7726 func(*args, **kwargs) 
    7727 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7728 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7729 on_resize 
    7730 c.draw() 
    7731 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7732 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7733 self.figure.draw(self.renderer) 
    7734 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7735 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7736 result = draw(artist, renderer, *args, **kwargs) 
    7737 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7738 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7739 return draw(artist, renderer) 
    7740 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7741 packages/matplotlib/figure.py", line 2796, in draw 
    7742 artists = self._get_draw_artists(renderer) 
    7743 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7744 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7745 ax.apply_aspect() 
    7746 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7747 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7748 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7749 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7750 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7751 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7752 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7753 Unable to flip peptide bond after 50 rounds. Giving up. 
    7754 
    7755 > isolde sim pause
    7756 
    7757 > isolde sim resume
    7758 
    7759 > ui tool show "Ramachandran Plot"
    7760 
    7761 Traceback (most recent call last): 
    7762 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7763 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7764 func(*args, **kwargs) 
    7765 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7766 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7767 on_resize 
    7768 c.draw() 
    7769 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7770 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7771 self.figure.draw(self.renderer) 
    7772 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7773 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7774 result = draw(artist, renderer, *args, **kwargs) 
    7775 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7776 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7777 return draw(artist, renderer) 
    7778 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7779 packages/matplotlib/figure.py", line 2796, in draw 
    7780 artists = self._get_draw_artists(renderer) 
    7781 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7782 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7783 ax.apply_aspect() 
    7784 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7785 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7786 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7787 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7788 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7789 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7790 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7791 
    7792 > select clear
    7793 
    7794 > ui tool show "Ramachandran Plot"
    7795 
    7796 > select clear
    7797 
    7798 > style #1/h:84|/h:125 sphere
    7799 
    7800 Changed 39 atom styles 
    7801 
    7802 > style #1/h:84|/h:125 stick
    7803 
    7804 Changed 39 atom styles 
    7805 
    7806 > ui tool show "Ramachandran Plot"
    7807 
    7808 [Repeated 1 time(s)]
    7809 
    7810 > isolde sim stop
    7811 
    7812 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7813 chains... 
    7814 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7815 standards. 
    7816 ISOLDE: stopped sim 
    7817 
    7818 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7819 > mut8-no-C-ter/18-KSRP-no-C-ter-Step1-SevententhSubsteps-POST-FIRST-SIM-ANN-
    7820 > KSRP.cxs
    7821 
    7822 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    7823 
    7824 ——— End of log from Fri Mar 24 14:43:56 2023 ———
    7825 
    7826 opened ChimeraX session 
    7827 
    7828 > isolde start
    7829 
    7830 > set selectionWidth 4
    7831 
    7832 > isolde restrain ligands #1
    7833 
    7834 > select clear
    7835 
    7836 > select #1/h
    7837 
    7838 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7839 
    7840 > isolde sim start sel
    7841 
    7842 Launching using CUDA failed with the below message. Falling back to using
    7843 OpenCL. 
    7844  
    7845 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    7846 (-arch) 
    7847  
    7848 
    7849 ISOLDE: started sim 
    7850 
    7851 > isolde sim stop discardTo start
    7852 
    7853 reverting to start 
    7854 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7855 chains... 
    7856 ISOLDE: stopped sim 
    7857 
    7858 > select #1/h
    7859 
    7860 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7861 
    7862 > isolde sim start sel
    7863 
    7864 ISOLDE: started sim 
    7865 
    7866 > isolde sim stop discardTo start
    7867 
    7868 reverting to start 
    7869 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7870 chains... 
    7871 ISOLDE: stopped sim 
    7872 
    7873 > select #1/h
    7874 
    7875 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7876 
    7877 > isolde sim start sel
    7878 
    7879 ISOLDE: started sim 
    7880 
    7881 > ui tool show "Ramachandran Plot"
    7882 
    7883 > select clear
    7884 
    7885 > ui tool show "Ramachandran Plot"
    7886 
    7887 [Repeated 2 time(s)]
    7888 
    7889 > isolde sim pause
    7890 
    7891 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7892 > mut8-no-C-ter/19a-Test-KSRP-Env-System-on-the-middle-of-
    7893 > overFittingTo-6Times-densityField.pdb
    7894 
    7895 > isolde sim resume
    7896 
    7897 > ui tool show "Ramachandran Plot"
    7898 
    7899 [Repeated 1 time(s)]
    7900 
    7901 > isolde sim pause
    7902 
    7903 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7904 > mut8-no-C-ter/19b-Test-KSRP-Env-System-on-the-overFittingTo-6Times-
    7905 > densityFieldSmoth-NoSmoth.pdb
    7906 
    7907 > isolde sim resume
    7908 
    7909 > ui tool show "Ramachandran Plot"
    7910 
    7911 [Repeated 4 time(s)]
    7912 
    7913 > isolde sim pause
    7914 
    7915 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7916 > mut8-no-C-ter/19c-Test-KSRP-Env-System-After-the-overFittingTo-6Times-And-
    7917 > ComeBack-to-Default.pdb
    7918 
    7919 > isolde sim resume
    7920 
    7921 > ui tool show "Ramachandran Plot"
    7922 
    7923 [Repeated 3 time(s)]
    7924 
    7925 > select clear
    7926 
    7927 [Repeated 3 time(s)]
    7928 
    7929 > ui tool show "Ramachandran Plot"
    7930 
    7931 > isolde pepflip sel
    7932 
    7933 Flipping the peptide bond for 1 residues 
    7934 
    7935 > ui tool show "Ramachandran Plot"
    7936 
    7937 > select clear
    7938 
    7939 > isolde pepflip sel
    7940 
    7941 Flipping the peptide bond for 1 residues 
    7942 
    7943 > ui tool show "Ramachandran Plot"
    7944 
    7945 > select clear
    7946 
    7947 > isolde pepflip sel
    7948 
    7949 Flipping the peptide bond for 1 residues 
    7950 
    7951 > ui tool show "Ramachandran Plot"
    7952 
    7953 > select clear
    7954 
    7955 > isolde pepflip sel
    7956 
    7957 Flipping the peptide bond for 1 residues 
    7958 
    7959 > isolde pepflip sel
    7960 
    7961 Flipping the peptide bond for 1 residues 
    7962 
    7963 > select clear
    7964 
    7965 > ui tool show "Ramachandran Plot"
    7966 
    7967 [Repeated 3 time(s)]
    7968 
    7969 > isolde pepflip sel
    7970 
    7971 Flipping the peptide bond for 1 residues 
    7972 
    7973 > ui tool show "Ramachandran Plot"
    7974 
    7975 > select clear
    7976 
    7977 > ui tool show "Ramachandran Plot"
    7978 
    7979 > select clear
    7980 
    7981 > isolde pepflip sel
    7982 
    7983 Flipping the peptide bond for 1 residues 
    7984 
    7985 > select clear
    7986 
    7987 > isolde pepflip sel
    7988 
    7989 Flipping the peptide bond for 1 residues 
    7990 
    7991 > ui tool show "Ramachandran Plot"
    7992 
    7993 > select clear
    7994 
    7995 [Repeated 1 time(s)]
    7996 
    7997 > ui tool show "Ramachandran Plot"
    7998 
    7999 > isolde pepflip sel
    8000 
    8001 Flipping the peptide bond for 1 residues 
    8002 
    8003 > isolde pepflip sel
    8004 
    8005 Flipping the peptide bond for 1 residues 
    8006 
    8007 > select clear
    8008 
    8009 > ui tool show "Ramachandran Plot"
    8010 
    8011 [Repeated 1 time(s)]
    8012 
    8013 > select clear
    8014 
    8015 > ui tool show "Ramachandran Plot"
    8016 
    8017 > select clear
    8018 
    8019 > isolde pepflip sel
    8020 
    8021 Flipping the peptide bond for 1 residues 
    8022 
    8023 > select clear
    8024 
    8025 > ui tool show "Ramachandran Plot"
    8026 
    8027 [Repeated 1 time(s)]
    8028 
    8029 > isolde pepflip sel
    8030 
    8031 Flipping the peptide bond for 1 residues 
    8032 
    8033 > select clear
    8034 
    8035 > ui tool show "Ramachandran Plot"
    8036 
    8037 > select clear
    8038 
    8039 [Repeated 3 time(s)]
    8040 
    8041 > isolde pepflip sel
    8042 
    8043 Flipping the peptide bond for 1 residues 
    8044 
    8045 > isolde pepflip sel
    8046 
    8047 Flipping the peptide bond for 1 residues 
    8048 
    8049 > ui tool show "Ramachandran Plot"
    8050 
    8051 [Repeated 1 time(s)]
    8052 
    8053 > isolde pepflip sel
    8054 
    8055 Flipping the peptide bond for 1 residues 
    8056 
    8057 > select clear
    8058 
    8059 > ui tool show "Ramachandran Plot"
    8060 
    8061 [Repeated 2 time(s)]
    8062 
    8063 > select clear
    8064 
    8065 > ui tool show "Ramachandran Plot"
    8066 
    8067 [Repeated 1 time(s)]
    8068 
    8069 > isolde pepflip sel
    8070 
    8071 Flipping the peptide bond for 1 residues 
    8072 
    8073 > select clear
    8074 
    8075 [Repeated 1 time(s)]
    8076 
    8077 > isolde pepflip sel
    8078 
    8079 Flipping the peptide bond for 1 residues 
    8080 
    8081 > select clear
    8082 
    8083 > isolde pepflip sel
    8084 
    8085 Flipping the peptide bond for 1 residues 
    8086 
    8087 > ui tool show "Ramachandran Plot"
    8088 
    8089 [Repeated 1 time(s)]Traceback (most recent call last): 
    8090 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8091 packages/matplotlib/cbook/__init__.py", line 287, in process 
    8092 func(*args, **kwargs) 
    8093 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    8094 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    8095 on_resize 
    8096 c.draw() 
    8097 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8098 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    8099 self.figure.draw(self.renderer) 
    8100 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8101 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    8102 result = draw(artist, renderer, *args, **kwargs) 
    8103 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8104 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    8105 return draw(artist, renderer) 
    8106 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8107 packages/matplotlib/figure.py", line 2796, in draw 
    8108 artists = self._get_draw_artists(renderer) 
    8109 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8110 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    8111 ax.apply_aspect() 
    8112 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8113 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    8114 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    8115 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8116 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    8117 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    8118 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    8119 
    8120 > select clear
    8121 
    8122 [Repeated 2 time(s)]
    8123 
    8124 > ui tool show "Ramachandran Plot"
    8125 
    8126 [Repeated 2 time(s)]
    8127 
    8128 > select clear
    8129 
    8130 > ui tool show "Ramachandran Plot"
    8131 
    8132 > select clear
    8133 
    8134 [Repeated 1 time(s)]
    8135 
    8136 > ui tool show "Ramachandran Plot"
    8137 
    8138 > select clear
    8139 
    8140 > ui tool show "Ramachandran Plot"
    8141 
    8142 > isolde sim stop
    8143 
    8144 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8145 chains... 
    8146 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    8147 standards. 
    8148 ISOLDE: stopped sim 
    8149 
    8150 > ui tool show "Ramachandran Plot"
    8151 
    8152 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8153 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8154 > KSRP.pdb
    8155 
    8156 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8157 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8158 > KSRP.cxs
    8159 
    8160 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8161 
    8162 ——— End of log from Mon Mar 27 09:38:45 2023 ———
    8163 
    8164 opened ChimeraX session 
    8165 
    8166 > isolde start
    8167 
    8168 > ui tool show "Ramachandran Plot"
    8169 
    8170 > view #1/P:240-249
    8171 
    8172 > select #1/P:240-249
    8173 
    8174 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8175 
    8176 > isolde sim start sel
    8177 
    8178 ISOLDE: started sim 
    8179 
    8180 > isolde sim stop discardTo start
    8181 
    8182 reverting to start 
    8183 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8184 chains... 
    8185 ISOLDE: stopped sim 
    8186 
    8187 > select #1/P:240-249
    8188 
    8189 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8190 
    8191 > isolde sim start sel
    8192 
    8193 ISOLDE: started sim 
    8194 
    8195 > isolde sim stop discardTo start
    8196 
    8197 reverting to start 
    8198 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8199 chains... 
    8200 ISOLDE: stopped sim 
    8201 
    8202 > select #1/P:240-249
    8203 
    8204 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8205 
    8206 > isolde sim start sel
    8207 
    8208 ISOLDE: started sim 
    8209 
    8210 > isolde sim stop discardTo start
    8211 
    8212 reverting to start 
    8213 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8214 chains... 
    8215 ISOLDE: stopped sim 
    8216 
    8217 > ui tool show "Ramachandran Plot"
    8218 
    8219 > select clear
    8220 
    8221 > isolde sim start sel
    8222 
    8223 ISOLDE: started sim 
    8224 
    8225 > isolde sim stop discardTo start
    8226 
    8227 reverting to start 
    8228 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8229 chains... 
    8230 ISOLDE: stopped sim 
    8231 
    8232 > select #1/V:92
    8233 
    8234 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8235 
    8236 > isolde sim start sel
    8237 
    8238 ISOLDE: started sim 
    8239 
    8240 > isolde pepflip sel
    8241 
    8242 Flipping the peptide bond for 1 residues 
    8243 
    8244 > select clear
    8245 
    8246 > isolde pepflip sel
    8247 
    8248 Flipping the peptide bond for 1 residues 
    8249 
    8250 > select clear
    8251 
    8252 > ui tool show "Ramachandran Plot"
    8253 
    8254 [Repeated 1 time(s)]
    8255 
    8256 > isolde sim stop
    8257 
    8258 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8259 chains... 
    8260 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8261 standards. 
    8262 ISOLDE: stopped sim 
    8263 
    8264 > isolde sim start sel
    8265 
    8266 ISOLDE: started sim 
    8267 
    8268 > ui tool show "Ramachandran Plot"
    8269 
    8270 > isolde pepflip sel
    8271 
    8272 Flipping the peptide bond for 1 residues 
    8273 
    8274 > select clear
    8275 
    8276 > ui tool show "Ramachandran Plot"
    8277 
    8278 > isolde sim stop
    8279 
    8280 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8281 chains... 
    8282 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8283 standards. 
    8284 ISOLDE: stopped sim 
    8285 
    8286 > isolde sim start sel
    8287 
    8288 ISOLDE: started sim 
    8289 
    8290 > select clear
    8291 
    8292 > isolde pepflip sel
    8293 
    8294 Flipping the peptide bond for 1 residues 
    8295 
    8296 > ui tool show "Ramachandran Plot"
    8297 
    8298 [Repeated 1 time(s)]
    8299 
    8300 > isolde sim stop
    8301 
    8302 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8303 chains... 
    8304 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8305 standards. 
    8306 ISOLDE: stopped sim 
    8307 
    8308 > view #1/V:92
    8309 
    8310 > select #1/V:92
    8311 
    8312 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8313 
    8314 > isolde sim start sel
    8315 
    8316 ISOLDE: started sim 
    8317 
    8318 > ui tool show "Ramachandran Plot"
    8319 
    8320 > isolde pepflip sel
    8321 
    8322 Flipping the peptide bond for 1 residues 
    8323 
    8324 > isolde pepflip sel
    8325 
    8326 Flipping the peptide bond for 1 residues 
    8327 
    8328 > select clear
    8329 
    8330 > isolde pepflip sel
    8331 
    8332 Flipping the peptide bond for 1 residues 
    8333 
    8334 > select clear
    8335 
    8336 > ui tool show "Ramachandran Plot"
    8337 
    8338 > isolde sim stop
    8339 
    8340 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8341 chains... 
    8342 ISOLDE: stopped sim 
    8343 
    8344 > ui tool show "Ramachandran Plot"
    8345 
    8346 > isolde sim start sel
    8347 
    8348 ISOLDE: started sim 
    8349 
    8350 > ui tool show "Ramachandran Plot"
    8351 
    8352 > select clear
    8353 
    8354 > ui tool show "Ramachandran Plot"
    8355 
    8356 > isolde pepflip sel
    8357 
    8358 Flipping the peptide bond for 1 residues 
    8359 
    8360 > select clear
    8361 
    8362 > isolde pepflip sel
    8363 
    8364 Flipping the peptide bond for 1 residues 
    8365 
    8366 > isolde pepflip sel
    8367 
    8368 Flipping the peptide bond for 1 residues 
    8369 
    8370 > ui tool show "Ramachandran Plot"
    8371 
    8372 > select clear
    8373 
    8374 [Repeated 1 time(s)]
    8375 
    8376 > isolde pepflip sel
    8377 
    8378 Flipping the peptide bond for 1 residues 
    8379 
    8380 > isolde pepflip sel
    8381 
    8382 Flipping the peptide bond for 1 residues 
    8383 
    8384 > select clear
    8385 
    8386 > ui tool show "Ramachandran Plot"
    8387 
    8388 > isolde pepflip sel
    8389 
    8390 Flipping the peptide bond for 1 residues 
    8391 
    8392 > select clear
    8393 
    8394 [Repeated 1 time(s)]
    8395 
    8396 > ui tool show "Ramachandran Plot"
    8397 
    8398 > style #1/i:72|/i:75 sphere
    8399 
    8400 Changed 37 atom styles 
    8401 
    8402 > style #1/i:72|/i:75 stick
    8403 
    8404 Changed 37 atom styles 
    8405 
    8406 > select clear
    8407 
    8408 [Repeated 1 time(s)]
    8409 
    8410 > ui tool show "Ramachandran Plot"
    8411 
    8412 > isolde sim stop
    8413 
    8414 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8415 chains... 
    8416 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8417 standards. 
    8418 ISOLDE: stopped sim 
    8419 
    8420 > ui tool show "Ramachandran Plot"
    8421 
    8422 > isolde sim start sel
    8423 
    8424 ISOLDE: started sim 
    8425 
    8426 > isolde pepflip sel
    8427 
    8428 Flipping the peptide bond for 1 residues 
    8429 
    8430 > select clear
    8431 
    8432 [Repeated 3 time(s)]
    8433 
    8434 > isolde pepflip sel
    8435 
    8436 Flipping the peptide bond for 1 residues 
    8437 
    8438 > isolde pepflip sel
    8439 
    8440 Flipping the peptide bond for 1 residues 
    8441 
    8442 > isolde pepflip sel
    8443 
    8444 Flipping the peptide bond for 1 residues 
    8445 
    8446 > select clear
    8447 
    8448 [Repeated 1 time(s)]
    8449 
    8450 > isolde pepflip sel
    8451 
    8452 Flipping the peptide bond for 1 residues 
    8453 
    8454 > isolde pepflip sel
    8455 
    8456 Flipping the peptide bond for 1 residues 
    8457 
    8458 > isolde pepflip sel
    8459 
    8460 Flipping the peptide bond for 1 residues 
    8461 
    8462 > isolde pepflip sel
    8463 
    8464 Flipping the peptide bond for 1 residues 
    8465 
    8466 > isolde pepflip sel
    8467 
    8468 Flipping the peptide bond for 1 residues 
    8469 
    8470 > isolde pepflip sel
    8471 
    8472 Flipping the peptide bond for 1 residues 
    8473 
    8474 > select clear
    8475 
    8476 [Repeated 1 time(s)]
    8477 
    8478 > ui tool show "Ramachandran Plot"
    8479 
    8480 > select clear
    8481 
    8482 [Repeated 1 time(s)]
    8483 
    8484 > ui tool show "Ramachandran Plot"
    8485 
    8486 [Repeated 1 time(s)]
    8487 
    8488 > isolde sim stop
    8489 
    8490 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8491 chains... 
    8492 ISOLDE: stopped sim 
    8493 
    8494 > ui tool show "Ramachandran Plot"
    8495 
    8496 > isolde sim start sel
    8497 
    8498 ISOLDE: started sim 
    8499 
    8500 > isolde pepflip sel
    8501 
    8502 Flipping the peptide bond for 1 residues 
    8503 
    8504 > isolde pepflip sel
    8505 
    8506 Flipping the peptide bond for 1 residues 
    8507 
    8508 > isolde pepflip sel
    8509 
    8510 Flipping the peptide bond for 1 residues 
    8511 
    8512 > select clear
    8513 
    8514 > ui tool show "Ramachandran Plot"
    8515 
    8516 > isolde pepflip sel
    8517 
    8518 Flipping the peptide bond for 1 residues 
    8519 
    8520 > select clear
    8521 
    8522 > ui tool show "Ramachandran Plot"
    8523 
    8524 [Repeated 1 time(s)]
    8525 
    8526 > isolde sim stop
    8527 
    8528 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8529 chains... 
    8530 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8531 standards. 
    8532 ISOLDE: stopped sim 
    8533 
    8534 > ui tool show "Ramachandran Plot"
    8535 
    8536 [Repeated 1 time(s)]
    8537 
    8538 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8539 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.cxs
    8540 
    8541 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8542 
    8543 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8544 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8545 > KSRP.pdb
    8546 
    8547 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8548 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.pdb
    8549 
    8550 > isolde sim start sel
    8551 
    8552 ISOLDE: started sim 
    8553 
    8554 > isolde sim stop discardTo start
    8555 
    8556 reverting to start 
    8557 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8558 chains... 
    8559 ISOLDE: stopped sim 
    8560 
    8561 > isolde sim start sel
    8562 
    8563 ISOLDE: started sim 
    8564 
    8565 > isolde pepflip sel
    8566 
    8567 Flipping the peptide bond for 1 residues 
    8568 
    8569 > isolde pepflip sel
    8570 
    8571 Flipping the peptide bond for 1 residues 
    8572 
    8573 > select clear
    8574 
    8575 > ui tool show "Ramachandran Plot"
    8576 
    8577 [Repeated 1 time(s)]
    8578 
    8579 > isolde sim pause
    8580 
    8581 > ui tool show "Ramachandran Plot"
    8582 
    8583 > isolde sim resume
    8584 
    8585 > ui tool show "Ramachandran Plot"
    8586 
    8587 > isolde pepflip sel
    8588 
    8589 Flipping the peptide bond for 1 residues 
    8590 
    8591 > isolde pepflip sel
    8592 
    8593 Flipping the peptide bond for 1 residues 
    8594 
    8595 > select clear
    8596 
    8597 > isolde pepflip sel
    8598 
    8599 Flipping the peptide bond for 1 residues 
    8600 
    8601 > isolde pepflip sel
    8602 
    8603 Flipping the peptide bond for 1 residues 
    8604 
    8605 > isolde sim stop
    8606 
    8607 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8608 chains... 
    8609 ISOLDE: stopped sim 
    8610 
    8611 > isolde sim start sel
    8612 
    8613 ISOLDE: started sim 
    8614 
    8615 > select clear
    8616 
    8617 > ui tool show "Ramachandran Plot"
    8618 
    8619 [Repeated 2 time(s)]
    8620 
    8621 > isolde pepflip sel
    8622 
    8623 Flipping the peptide bond for 1 residues 
    8624 
    8625 > ui tool show "Ramachandran Plot"
    8626 
    8627 [Repeated 1 time(s)]
    8628 
    8629 > select clear
    8630 
    8631 > ui tool show "Ramachandran Plot"
    8632 
    8633 > isolde sim stop
    8634 
    8635 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8636 chains... 
    8637 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8638 standards. 
    8639 ISOLDE: stopped sim 
    8640 
    8641 > isolde sim start sel
    8642 
    8643 ISOLDE: started sim 
    8644 
    8645 > ui tool show "Ramachandran Plot"
    8646 
    8647 > select clear
    8648 
    8649 > ui tool show "Ramachandran Plot"
    8650 
    8651 > select clear
    8652 
    8653 > ui tool show "Ramachandran Plot"
    8654 
    8655 > select clear
    8656 
    8657 > ui tool show "Ramachandran Plot"
    8658 
    8659 [Repeated 1 time(s)]
    8660 
    8661 > isolde sim stop
    8662 
    8663 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8664 chains... 
    8665 ISOLDE: stopped sim 
    8666 
    8667 > ui tool show "Ramachandran Plot"
    8668 
    8669 > isolde sim start sel
    8670 
    8671 ISOLDE: started sim 
    8672 
    8673 > ui tool show "Ramachandran Plot"
    8674 
    8675 > select clear
    8676 
    8677 [Repeated 1 time(s)]
    8678 
    8679 > isolde pepflip sel
    8680 
    8681 Flipping the peptide bond for 1 residues 
    8682 
    8683 > select clear
    8684 
    8685 > ui tool show "Ramachandran Plot"
    8686 
    8687 > isolde sim stop
    8688 
    8689 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8690 chains... 
    8691 ISOLDE: stopped sim 
    8692 
    8693 > ui tool show "Ramachandran Plot"
    8694 
    8695 > isolde sim start sel
    8696 
    8697 ISOLDE: started sim 
    8698 
    8699 > ui tool show "Ramachandran Plot"
    8700 
    8701 [Repeated 1 time(s)]
    8702 
    8703 > isolde sim stop
    8704 
    8705 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8706 chains... 
    8707 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8708 standards. 
    8709 ISOLDE: stopped sim 
    8710 
    8711 > isolde sim start sel
    8712 
    8713 ISOLDE: started sim 
    8714 
    8715 > select clear
    8716 
    8717 [Repeated 2 time(s)]
    8718 
    8719 > isolde pepflip sel
    8720 
    8721 Flipping the peptide bond for 1 residues 
    8722 
    8723 > isolde pepflip sel
    8724 
    8725 Flipping the peptide bond for 1 residues 
    8726 
    8727 > isolde pepflip sel
    8728 
    8729 Flipping the peptide bond for 1 residues 
    8730 
    8731 > isolde pepflip sel
    8732 
    8733 Flipping the peptide bond for 1 residues 
    8734 
    8735 > ui tool show "Ramachandran Plot"
    8736 
    8737 > isolde pepflip sel
    8738 
    8739 Flipping the peptide bond for 1 residues 
    8740 
    8741 > select clear
    8742 
    8743 > isolde pepflip sel
    8744 
    8745 Flipping the peptide bond for 1 residues 
    8746 
    8747 > isolde pepflip sel
    8748 
    8749 Flipping the peptide bond for 1 residues 
    8750 
    8751 > select clear
    8752 
    8753 [Repeated 1 time(s)]
    8754 
    8755 > isolde pepflip sel
    8756 
    8757 Flipping the peptide bond for 1 residues 
    8758 
    8759 > ui tool show "Ramachandran Plot"
    8760 
    8761 > select clear
    8762 
    8763 > ui tool show "Ramachandran Plot"
    8764 
    8765 [Repeated 1 time(s)]
    8766 
    8767 > isolde sim stop
    8768 
    8769 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8770 chains... 
    8771 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8772 standards. 
    8773 ISOLDE: stopped sim 
    8774 
    8775 > ui tool show "Ramachandran Plot"
    8776 
    8777 > isolde sim start sel
    8778 
    8779 ISOLDE: started sim 
    8780 
    8781 > ui tool show "Ramachandran Plot"
    8782 
    8783 > select clear
    8784 
    8785 > isolde sim stop
    8786 
    8787 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8788 chains... 
    8789 ISOLDE: stopped sim 
    8790 
    8791 > ui tool show "Ramachandran Plot"
    8792 
    8793 > isolde sim start sel
    8794 
    8795 ISOLDE: started sim 
    8796 
    8797 > isolde pepflip sel
    8798 
    8799 Flipping the peptide bond for 1 residues 
    8800 
    8801 > select clear
    8802 
    8803 > isolde pepflip sel
    8804 
    8805 Flipping the peptide bond for 1 residues 
    8806 
    8807 > select clear
    8808 
    8809 > isolde pepflip sel
    8810 
    8811 Flipping the peptide bond for 1 residues 
    8812 
    8813 > isolde pepflip sel
    8814 
    8815 Flipping the peptide bond for 1 residues 
    8816 
    8817 > select clear
    8818 
    8819 > ui tool show "Ramachandran Plot"
    8820 
    8821 > select clear
    8822 
    8823 [Repeated 2 time(s)]
    8824 
    8825 > ui tool show "Ramachandran Plot"
    8826 
    8827 > isolde pepflip sel
    8828 
    8829 Flipping the peptide bond for 1 residues 
    8830 
    8831 > isolde pepflip sel
    8832 
    8833 Flipping the peptide bond for 1 residues 
    8834 
    8835 > ui tool show "Ramachandran Plot"
    8836 
    8837 > select clear
    8838 
    8839 > isolde sim stop
    8840 
    8841 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8842 chains... 
    8843 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8844 standards. 
    8845 ISOLDE: stopped sim 
    8846 
    8847 > ui tool show "Ramachandran Plot"
    8848 
    8849 [Repeated 1 time(s)]
    8850 
    8851 > isolde sim start sel
    8852 
    8853 ISOLDE: started sim 
    8854 
    8855 > select clear
    8856 
    8857 > ui tool show "Ramachandran Plot"
    8858 
    8859 [Repeated 1 time(s)]
    8860 
    8861 > view #1/d:155
    8862 
    8863 > select clear
    8864 
    8865 > isolde sim stop
    8866 
    8867 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8868 chains... 
    8869 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8870 standards. 
    8871 ISOLDE: stopped sim 
    8872 
    8873 > ui tool show "Ramachandran Plot"
    8874 
    8875 > isolde sim start sel
    8876 
    8877 ISOLDE: started sim 
    8878 
    8879 > isolde pepflip sel
    8880 
    8881 Flipping the peptide bond for 1 residues 
    8882 
    8883 > ui tool show "Ramachandran Plot"
    8884 
    8885 > select clear
    8886 
    8887 > isolde sim pause
    8888 
    8889 > isolde sim resume
    8890 
    8891 > ui tool show "Ramachandran Plot"
    8892 
    8893 > isolde sim stop
    8894 
    8895 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8896 chains... 
    8897 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8898 standards. 
    8899 ISOLDE: stopped sim 
    8900 
    8901 > ui tool show "Ramachandran Plot"
    8902 
    8903 > isolde sim start sel
    8904 
    8905 ISOLDE: started sim 
    8906 
    8907 > isolde pepflip sel
    8908 
    8909 Flipping the peptide bond for 1 residues 
    8910 
    8911 > isolde pepflip sel
    8912 
    8913 Flipping the peptide bond for 1 residues 
    8914 
    8915 > isolde pepflip sel
    8916 
    8917 Flipping the peptide bond for 1 residues 
    8918 
    8919 > isolde pepflip sel
    8920 
    8921 Flipping the peptide bond for 1 residues 
    8922 
    8923 > isolde pepflip sel
    8924 
    8925 Flipping the peptide bond for 1 residues 
    8926 
    8927 > select clear
    8928 
    8929 > isolde pepflip sel
    8930 
    8931 Flipping the peptide bond for 1 residues 
    8932 
    8933 > isolde pepflip sel
    8934 
    8935 Flipping the peptide bond for 1 residues 
    8936 
    8937 > isolde pepflip sel
    8938 
    8939 Flipping the peptide bond for 1 residues 
    8940 
    8941 > isolde pepflip sel
    8942 
    8943 Flipping the peptide bond for 1 residues 
    8944 
    8945 > select clear
    8946 
    8947 > ui tool show "Ramachandran Plot"
    8948 
    8949 > isolde sim pause
    8950 
    8951 > isolde sim resume
    8952 
    8953 > ui tool show "Ramachandran Plot"
    8954 
    8955 > isolde sim stop
    8956 
    8957 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8958 chains... 
    8959 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8960 standards. 
    8961 ISOLDE: stopped sim 
    8962 
    8963 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8964 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    8965 > step20-1.cxs
    8966 
    8967 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8968 
    8969 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8970 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    8971 > step20-1.pdb
    8972 
    8973 > ui tool show "Ramachandran Plot"
    8974 
    8975 > isolde sim start sel
    8976 
    8977 ISOLDE: started sim 
    8978 
    8979 > select clear
    8980 
    8981 > ui tool show "Ramachandran Plot"
    8982 
    8983 > select clear
    8984 
    8985 > isolde sim stop
    8986 
    8987 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8988 chains... 
    8989 ISOLDE: stopped sim 
    8990 
    8991 > ui tool show "Ramachandran Plot"
    8992 
    8993 > isolde sim start sel
    8994 
    8995 ISOLDE: started sim 
    8996 
    8997 > ui tool show "Ramachandran Plot"
    8998 
    8999 > select clear
    9000 
    9001 > ui tool show "Ramachandran Plot"
    9002 
    9003 > isolde pepflip sel
    9004 
    9005 Flipping the peptide bond for 1 residues 
    9006 
    9007 > select clear
    9008 
    9009 > isolde pepflip sel
    9010 
    9011 Flipping the peptide bond for 1 residues 
    9012 
    9013 > select clear
    9014 
    9015 > ui tool show "Ramachandran Plot"
    9016 
    9017 > select clear
    9018 
    9019 [Repeated 1 time(s)]
    9020 
    9021 > view #1/q:29
    9022 
    9023 > isolde sim pause
    9024 
    9025 > ui tool show "Ramachandran Plot"
    9026 
    9027 Traceback (most recent call last): 
    9028 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9029 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9030 func(*args, **kwargs) 
    9031 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9032 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9033 on_resize 
    9034 c.draw() 
    9035 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9036 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9037 self.figure.draw(self.renderer) 
    9038 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9039 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9040 result = draw(artist, renderer, *args, **kwargs) 
    9041 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9042 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9043 return draw(artist, renderer) 
    9044 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9045 packages/matplotlib/figure.py", line 2796, in draw 
    9046 artists = self._get_draw_artists(renderer) 
    9047 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9048 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9049 ax.apply_aspect() 
    9050 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9051 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9052 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9053 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9054 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9055 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9056 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9057 
    9058 > ui tool show "Ramachandran Plot"
    9059 
    9060 [Repeated 1 time(s)]Traceback (most recent call last): 
    9061 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9062 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9063 func(*args, **kwargs) 
    9064 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9065 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9066 on_resize 
    9067 c.draw() 
    9068 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9069 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9070 self.figure.draw(self.renderer) 
    9071 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9072 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9073 result = draw(artist, renderer, *args, **kwargs) 
    9074 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9075 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9076 return draw(artist, renderer) 
    9077 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9078 packages/matplotlib/figure.py", line 2796, in draw 
    9079 artists = self._get_draw_artists(renderer) 
    9080 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9081 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9082 ax.apply_aspect() 
    9083 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9084 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9085 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9086 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9087 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9088 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9089 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9090 
    9091 > isolde sim resume
    9092 
    9093 > isolde sim pause
    9094 
    9095 > isolde sim resume
    9096 
    9097 > select clear
    9098 
    9099 > isolde pepflip sel
    9100 
    9101 Flipping the peptide bond for 1 residues 
    9102 
    9103 > select clear
    9104 
    9105 > isolde sim pause
    9106 
    9107 > isolde sim resume
    9108 
    9109 > select clear
    9110 
    9111 > isolde pepflip sel
    9112 
    9113 Flipping the peptide bond for 1 residues 
    9114 
    9115 > isolde pepflip sel
    9116 
    9117 Flipping the peptide bond for 1 residues 
    9118 
    9119 > select clear
    9120 
    9121 > ui tool show "Ramachandran Plot"
    9122 
    9123 > select clear
    9124 
    9125 > isolde sim pause
    9126 
    9127 > ui tool show "Ramachandran Plot"
    9128 
    9129 > isolde sim resume
    9130 
    9131 > select clear
    9132 
    9133 > isolde pepflip sel
    9134 
    9135 Flipping the peptide bond for 1 residues 
    9136 
    9137 > isolde pepflip sel
    9138 
    9139 Flipping the peptide bond for 1 residues 
    9140 
    9141 > isolde pepflip sel
    9142 
    9143 Flipping the peptide bond for 1 residues 
    9144 
    9145 > isolde pepflip sel
    9146 
    9147 Flipping the peptide bond for 1 residues 
    9148 
    9149 > isolde pepflip sel
    9150 
    9151 Flipping the peptide bond for 1 residues 
    9152 
    9153 > isolde pepflip sel
    9154 
    9155 Flipping the peptide bond for 1 residues 
    9156 
    9157 > ui tool show "Ramachandran Plot"
    9158 
    9159 > select clear
    9160 
    9161 > isolde sim pause
    9162 
    9163 > ui tool show "Ramachandran Plot"
    9164 
    9165 > select clear
    9166 
    9167 > isolde sim resume
    9168 
    9169 > isolde pepflip sel
    9170 
    9171 Flipping the peptide bond for 1 residues 
    9172 
    9173 > select clear
    9174 
    9175 > isolde pepflip sel
    9176 
    9177 Flipping the peptide bond for 1 residues 
    9178 
    9179 > ui tool show "Ramachandran Plot"
    9180 
    9181 > select clear
    9182 
    9183 > isolde sim pause
    9184 
    9185 > isolde sim resume
    9186 
    9187 > ui tool show "Ramachandran Plot"
    9188 
    9189 [Repeated 2 time(s)]
    9190 
    9191 > select clear
    9192 
    9193 > isolde pepflip sel
    9194 
    9195 Flipping the peptide bond for 1 residues 
    9196 
    9197 > ui tool show "Ramachandran Plot"
    9198 
    9199 > select clear
    9200 
    9201 [Repeated 2 time(s)]
    9202 
    9203 > ui tool show "Ramachandran Plot"
    9204 
    9205 > select clear
    9206 
    9207 > ui tool show "Ramachandran Plot"
    9208 
    9209 Traceback (most recent call last): 
    9210 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9211 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9212 func(*args, **kwargs) 
    9213 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9214 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9215 on_resize 
    9216 c.draw() 
    9217 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9218 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9219 self.figure.draw(self.renderer) 
    9220 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9221 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9222 result = draw(artist, renderer, *args, **kwargs) 
    9223 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9224 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9225 return draw(artist, renderer) 
    9226 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9227 packages/matplotlib/figure.py", line 2796, in draw 
    9228 artists = self._get_draw_artists(renderer) 
    9229 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9230 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9231 ax.apply_aspect() 
    9232 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9233 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9234 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9235 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9236 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9237 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9238 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9239 
    9240 > select clear
    9241 
    9242 > ui tool show "Ramachandran Plot"
    9243 
    9244 > select clear
    9245 
    9246 > ui tool show "Ramachandran Plot"
    9247 
    9248 > style #1/q:34|/q:39 sphere
    9249 
    9250 Changed 38 atom styles 
    9251 
    9252 > style #1/q:34|/q:39 stick
    9253 
    9254 Changed 38 atom styles 
    9255 
    9256 > ui tool show "Ramachandran Plot"
    9257 
    9258 > select clear
    9259 
    9260 > isolde sim pause
    9261 
    9262 > style #1/q:34|/q:39|/q:32 sphere
    9263 
    9264 Changed 57 atom styles 
    9265 
    9266 > style #1/q:34|/q:39|/q:32 stick
    9267 
    9268 Changed 57 atom styles 
    9269 
    9270 > ui tool show "Ramachandran Plot"
    9271 
    9272 > isolde sim resume
    9273 
    9274 > isolde sim stop
    9275 
    9276 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9277 chains... 
    9278 ISOLDE: stopped sim 
    9279 
    9280 > isolde sim start sel
    9281 
    9282 ISOLDE: started sim 
    9283 
    9284 > select clear
    9285 
    9286 > isolde pepflip sel
    9287 
    9288 Flipping the peptide bond for 1 residues 
    9289 
    9290 > isolde pepflip sel
    9291 
    9292 Flipping the peptide bond for 1 residues 
    9293 
    9294 > isolde pepflip sel
    9295 
    9296 Flipping the peptide bond for 1 residues 
    9297 
    9298 > isolde pepflip sel
    9299 
    9300 Flipping the peptide bond for 1 residues 
    9301 
    9302 > isolde pepflip sel
    9303 
    9304 Flipping the peptide bond for 1 residues 
    9305 
    9306 > isolde pepflip sel
    9307 
    9308 Flipping the peptide bond for 1 residues 
    9309 
    9310 > isolde pepflip sel
    9311 
    9312 Flipping the peptide bond for 1 residues 
    9313 
    9314 > isolde sim pause
    9315 
    9316 > isolde sim resume
    9317 
    9318 > ui tool show "Ramachandran Plot"
    9319 
    9320 [Repeated 1 time(s)]
    9321 
    9322 > select clear
    9323 
    9324 [Repeated 2 time(s)]
    9325 
    9326 > ui tool show "Ramachandran Plot"
    9327 
    9328 [Repeated 2 time(s)]
    9329 
    9330 > isolde pepflip sel
    9331 
    9332 Flipping the peptide bond for 1 residues 
    9333 
    9334 > select clear
    9335 
    9336 > isolde pepflip sel
    9337 
    9338 Flipping the peptide bond for 1 residues 
    9339 
    9340 > isolde pepflip sel
    9341 
    9342 Flipping the peptide bond for 1 residues 
    9343 
    9344 > select clear
    9345 
    9346 [Repeated 2 time(s)]
    9347 
    9348 > style #1/q:23-24 sphere
    9349 
    9350 Changed 35 atom styles 
    9351 
    9352 > style #1/q:23-24 stick
    9353 
    9354 Changed 35 atom styles 
    9355 
    9356 > ui tool show "Ramachandran Plot"
    9357 
    9358 > select clear
    9359 
    9360 > ui tool show "Ramachandran Plot"
    9361 
    9362 > select clear
    9363 
    9364 [Repeated 2 time(s)]
    9365 
    9366 > isolde sim pause
    9367 
    9368 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9369 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9370 > step20-2.pdb
    9371 
    9372 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9373 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9374 > step20-2.cxs
    9375 
    9376 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    9377 
    9378 > isolde sim resume
    9379 
    9380 > ui tool show "Ramachandran Plot"
    9381 
    9382 Traceback (most recent call last): 
    9383 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9384 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9385 func(*args, **kwargs) 
    9386 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9387 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9388 on_resize 
    9389 c.draw() 
    9390 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9391 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9392 self.figure.draw(self.renderer) 
    9393 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9394 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9395 result = draw(artist, renderer, *args, **kwargs) 
    9396 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9397 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9398 return draw(artist, renderer) 
    9399 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9400 packages/matplotlib/figure.py", line 2796, in draw 
    9401 artists = self._get_draw_artists(renderer) 
    9402 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9403 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9404 ax.apply_aspect() 
    9405 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9406 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9407 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9408 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9409 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9410 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9411 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9412 
    9413 > isolde sim pause
    9414 
    9415 > view #1/q:24
    9416 
    9417 > isolde sim resume
    9418 
    9419 > select clear
    9420 
    9421 [Repeated 2 time(s)]
    9422 
    9423 > isolde pepflip sel
    9424 
    9425 Flipping the peptide bond for 1 residues 
    9426 
    9427 > select clear
    9428 
    9429 [Repeated 4 time(s)]
    9430 
    9431 > ui tool show "Ramachandran Plot"
    9432 
    9433 > style #1/i:23-24|/n:68 sphere
    9434 
    9435 Changed 53 atom styles 
    9436 
    9437 > style #1/i:23-24|/n:68 stick]
    9438 
    9439 Expected a keyword 
    9440 
    9441 > style #1/i:23-24|/n:68 stick
    9442 
    9443 Changed 53 atom styles 
    9444 
    9445 > style #1/q:23-24|/n:68 sphere
    9446 
    9447 Changed 59 atom styles 
    9448 
    9449 > style #1/q:23-24|/n:68 stick
    9450 
    9451 Changed 59 atom styles 
    9452 
    9453 > ui tool show "Ramachandran Plot"
    9454 
    9455 > isolde sim stop
    9456 
    9457 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9458 chains... 
    9459 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9460 standards. 
    9461 ISOLDE: stopped sim 
    9462 
    9463 > view #1/q:41
    9464 
    9465 > select #1/q:41
    9466 
    9467 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9468 
    9469 > isolde sim start sel
    9470 
    9471 ISOLDE: started sim 
    9472 
    9473 > ui tool show "Ramachandran Plot"
    9474 
    9475 > select clear
    9476 
    9477 > isolde sim stop
    9478 
    9479 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9480 chains... 
    9481 ISOLDE: stopped sim 
    9482 
    9483 > isolde sim start sel
    9484 
    9485 ISOLDE: started sim 
    9486 
    9487 > ui tool show "Ramachandran Plot"
    9488 
    9489 > select clear
    9490 
    9491 [Repeated 1 time(s)]
    9492 
    9493 > isolde pepflip sel
    9494 
    9495 Flipping the peptide bond for 1 residues 
    9496 
    9497 > isolde pepflip sel
    9498 
    9499 Flipping the peptide bond for 1 residues 
    9500 
    9501 > isolde pepflip sel
    9502 
    9503 Flipping the peptide bond for 1 residues 
    9504 
    9505 > isolde sim stop discardTo start
    9506 
    9507 reverting to start 
    9508 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9509 chains... 
    9510 ISOLDE: stopped sim 
    9511 
    9512 > isolde sim start sel
    9513 
    9514 ISOLDE: started sim 
    9515 
    9516 > ui tool show "Ramachandran Plot"
    9517 
    9518 > select clear
    9519 
    9520 > isolde pepflip sel
    9521 
    9522 Flipping the peptide bond for 1 residues 
    9523 
    9524 > select clear
    9525 
    9526 > isolde pepflip sel
    9527 
    9528 Flipping the peptide bond for 1 residues 
    9529 
    9530 > isolde pepflip sel
    9531 
    9532 Flipping the peptide bond for 1 residues 
    9533 
    9534 > select clear
    9535 
    9536 > isolde pepflip sel
    9537 
    9538 Flipping the peptide bond for 1 residues 
    9539 
    9540 > isolde pepflip sel
    9541 
    9542 Flipping the peptide bond for 1 residues 
    9543 
    9544 > isolde pepflip sel
    9545 
    9546 Flipping the peptide bond for 1 residues 
    9547 
    9548 > isolde pepflip sel
    9549 
    9550 Flipping the peptide bond for 1 residues 
    9551 
    9552 > isolde pepflip sel
    9553 
    9554 Flipping the peptide bond for 1 residues 
    9555 
    9556 > select clear
    9557 
    9558 > ui tool show "Ramachandran Plot"
    9559 
    9560 [Repeated 1 time(s)]
    9561 
    9562 > isolde sim stop
    9563 
    9564 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9565 chains... 
    9566 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    9567 standards. 
    9568 ISOLDE: stopped sim 
    9569 
    9570 > view #1/q:41
    9571 
    9572 > select #1/q:41
    9573 
    9574 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9575 
    9576 > isolde sim start sel
    9577 
    9578 ISOLDE: started sim 
    9579 
    9580 > ui tool show "Ramachandran Plot"
    9581 
    9582 > select clear
    9583 
    9584 > isolde sim stop
    9585 
    9586 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9587 chains... 
    9588 ISOLDE: stopped sim 
    9589 
    9590 > ui tool show "Ramachandran Plot"
    9591 
    9592 > isolde sim start sel
    9593 
    9594 ISOLDE: started sim 
    9595 
    9596 > isolde pepflip sel
    9597 
    9598 Flipping the peptide bond for 1 residues 
    9599 
    9600 > isolde pepflip sel
    9601 
    9602 Flipping the peptide bond for 1 residues 
    9603 
    9604 > select clear
    9605 
    9606 > ui tool show "Ramachandran Plot"
    9607 
    9608 > isolde pepflip sel
    9609 
    9610 Flipping the peptide bond for 1 residues 
    9611 
    9612 > select clear
    9613 
    9614 > ui tool show "Ramachandran Plot"
    9615 
    9616 > select clear
    9617 
    9618 [Repeated 1 time(s)]
    9619 
    9620 > isolde sim stop
    9621 
    9622 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9623 chains... 
    9624 ISOLDE: stopped sim 
    9625 
    9626 > ui tool show "Ramachandran Plot"
    9627 
    9628 > isolde sim start sel
    9629 
    9630 ISOLDE: started sim 
    9631 
    9632 > ui tool show "Ramachandran Plot"
    9633 
    9634 > select clear
    9635 
    9636 > isolde sim stop
    9637 
    9638 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9639 chains... 
    9640 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9641 standards. 
    9642 ISOLDE: stopped sim 
    9643 
    9644 > ui tool show "Ramachandran Plot"
    9645 
    9646 > isolde sim start sel
    9647 
    9648 ISOLDE: started sim 
    9649 
    9650 > ui tool show "Ramachandran Plot"
    9651 
    9652 > select clear
    9653 
    9654 > ui tool show "Ramachandran Plot"
    9655 
    9656 > isolde sim stop
    9657 
    9658 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9659 chains... 
    9660 ISOLDE: stopped sim 
    9661 
    9662 > ui tool show "Ramachandran Plot"
    9663 
    9664 > isolde sim start sel
    9665 
    9666 ISOLDE: started sim 
    9667 
    9668 > ui tool show "Ramachandran Plot"
    9669 
    9670 > isolde pepflip sel
    9671 
    9672 Flipping the peptide bond for 1 residues 
    9673 
    9674 > isolde pepflip sel
    9675 
    9676 Flipping the peptide bond for 1 residues 
    9677 
    9678 > isolde pepflip sel
    9679 
    9680 Flipping the peptide bond for 1 residues 
    9681 
    9682 > isolde pepflip sel
    9683 
    9684 Flipping the peptide bond for 1 residues 
    9685 
    9686 > select clear
    9687 
    9688 [Repeated 1 time(s)]
    9689 
    9690 > isolde pepflip sel
    9691 
    9692 Flipping the peptide bond for 1 residues 
    9693 
    9694 > select clear
    9695 
    9696 [Repeated 1 time(s)]
    9697 
    9698 > ui tool show "Ramachandran Plot"
    9699 
    9700 > select clear
    9701 
    9702 > ui tool show "Ramachandran Plot"
    9703 
    9704 > select clear
    9705 
    9706 > isolde pepflip sel
    9707 
    9708 Flipping the peptide bond for 1 residues 
    9709 
    9710 > select clear
    9711 
    9712 [Repeated 2 time(s)]
    9713 
    9714 > ui tool show "Ramachandran Plot"
    9715 
    9716 > select clear
    9717 
    9718 > isolde sim stop
    9719 
    9720 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9721 chains... 
    9722 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9723 standards. 
    9724 ISOLDE: stopped sim 
    9725 
    9726 > ui tool show "Ramachandran Plot"
    9727 
    9728 > isolde sim start sel
    9729 
    9730 ISOLDE: started sim 
    9731 
    9732 > isolde pepflip sel
    9733 
    9734 Flipping the peptide bond for 1 residues 
    9735 
    9736 > isolde pepflip sel
    9737 
    9738 Flipping the peptide bond for 1 residues 
    9739 
    9740 > isolde pepflip sel
    9741 
    9742 Flipping the peptide bond for 1 residues 
    9743 
    9744 > select clear
    9745 
    9746 > isolde pepflip sel
    9747 
    9748 Flipping the peptide bond for 1 residues 
    9749 
    9750 > isolde pepflip sel
    9751 
    9752 Flipping the peptide bond for 1 residues 
    9753 
    9754 > select clear
    9755 
    9756 > isolde pepflip sel
    9757 
    9758 Flipping the peptide bond for 1 residues 
    9759 
    9760 > isolde pepflip sel
    9761 
    9762 Flipping the peptide bond for 1 residues 
    9763 
    9764 > select clear
    9765 
    9766 [Repeated 1 time(s)]
    9767 
    9768 > ui tool show "Ramachandran Plot"
    9769 
    9770 > select clear
    9771 
    9772 > isolde pepflip sel
    9773 
    9774 Flipping the peptide bond for 1 residues 
    9775 
    9776 > select clear
    9777 
    9778 [Repeated 2 time(s)]
    9779 
    9780 > ui tool show "Ramachandran Plot"
    9781 
    9782 > select clear
    9783 
    9784 [Repeated 2 time(s)]
    9785 
    9786 > isolde pepflip sel
    9787 
    9788 Flipping the peptide bond for 1 residues 
    9789 
    9790 > select clear
    9791 
    9792 [Repeated 1 time(s)]
    9793 
    9794 > isolde pepflip sel
    9795 
    9796 Flipping the peptide bond for 1 residues 
    9797 
    9798 > isolde pepflip sel
    9799 
    9800 Flipping the peptide bond for 1 residues 
    9801 
    9802 > isolde pepflip sel
    9803 
    9804 Flipping the peptide bond for 1 residues 
    9805 
    9806 > select clear
    9807 
    9808 > isolde sim pause
    9809 
    9810 > isolde sim resume
    9811 
    9812 > isolde sim stop
    9813 
    9814 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9815 chains... 
    9816 ISOLDE: stopped sim 
    9817 
    9818 > select #1/o:74-81|/o:12
    9819 
    9820 140 atoms, 138 bonds, 9 residues, 1 model selected 
    9821 
    9822 > isolde sim start sel
    9823 
    9824 ISOLDE: started sim 
    9825 
    9826 > isolde pepflip sel
    9827 
    9828 Flipping the peptide bond for 1 residues 
    9829 
    9830 Multiple residues selected! Going to the first... 
    9831 
    9832 > view #1/o:74
    9833 
    9834 > select clear
    9835 
    9836 [Repeated 3 time(s)]
    9837 
    9838 > ui tool show "Ramachandran Plot"
    9839 
    9840 > isolde pepflip sel
    9841 
    9842 Flipping the peptide bond for 1 residues 
    9843 
    9844 > isolde pepflip sel
    9845 
    9846 Flipping the peptide bond for 1 residues 
    9847 
    9848 > select clear
    9849 
    9850 > isolde pepflip sel
    9851 
    9852 Flipping the peptide bond for 1 residues 
    9853 
    9854 > select clear
    9855 
    9856 > ui tool show "Ramachandran Plot"
    9857 
    9858 > view #1/o:74
    9859 
    9860 > select clear
    9861 
    9862 > ui tool show "Ramachandran Plot"
    9863 
    9864 > select clear
    9865 
    9866 [Repeated 1 time(s)]Traceback (most recent call last): 
    9867 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9868 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9869 func(*args, **kwargs) 
    9870 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9871 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9872 on_resize 
    9873 c.draw() 
    9874 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9875 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9876 self.figure.draw(self.renderer) 
    9877 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9878 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9879 result = draw(artist, renderer, *args, **kwargs) 
    9880 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9881 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9882 return draw(artist, renderer) 
    9883 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9884 packages/matplotlib/figure.py", line 2796, in draw 
    9885 artists = self._get_draw_artists(renderer) 
    9886 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9887 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9888 ax.apply_aspect() 
    9889 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9890 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9891 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9892 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9893 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9894 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9895 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9896 
    9897 > select clear
    9898 
    9899 > isolde pepflip sel
    9900 
    9901 Flipping the peptide bond for 1 residues 
    9902 
    9903 > isolde pepflip sel
    9904 
    9905 Flipping the peptide bond for 1 residues 
    9906 
    9907 > select clear
    9908 
    9909 [Repeated 1 time(s)]
    9910 
    9911 > view #1/o:74
    9912 
    9913 > isolde sim pause
    9914 
    9915 > ui tool show "Ramachandran Plot"
    9916 
    9917 > isolde sim resume
    9918 
    9919 > ui tool show "Ramachandran Plot"
    9920 
    9921 > select clear
    9922 
    9923 > ui tool show "Ramachandran Plot"
    9924 
    9925 > isolde sim pause
    9926 
    9927 > ui tool show "Ramachandran Plot"
    9928 
    9929 > view #1/o:74
    9930 
    9931 > isolde sim resume
    9932 
    9933 > ui tool show "Ramachandran Plot"
    9934 
    9935 > isolde sim pause
    9936 
    9937 > isolde sim stop
    9938 
    9939 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9940 chains... 
    9941 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9942 standards. 
    9943 ISOLDE: stopped sim 
    9944 
    9945 > isolde sim start sel
    9946 
    9947 ISOLDE: started sim 
    9948 
    9949 > ui tool show "Ramachandran Plot"
    9950 
    9951 > select clear
    9952 
    9953 > isolde sim stop
    9954 
    9955 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9956 chains... 
    9957 ISOLDE: stopped sim 
    9958 
    9959 > view #1/o:74
    9960 
    9961 > view #1/o:74-81|/o:12
    9962 
    9963 > select #1/o:74-81|/o:12
    9964 
    9965 140 atoms, 138 bonds, 9 residues, 1 model selected 
    9966 
    9967 > isolde sim start sel
    9968 
    9969 ISOLDE: started sim 
    9970 
    9971 > ui tool show "Ramachandran Plot"
    9972 
    9973 > select clear
    9974 
    9975 > isolde sim stop
    9976 
    9977 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9978 chains... 
    9979 ISOLDE: stopped sim 
    9980 
    9981 > select #1/o:74
    9982 
    9983 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9984 
    9985 > view #1/o:74
    9986 
    9987 > isolde sim start sel
    9988 
    9989 ISOLDE: started sim 
    9990 
    9991 > ui tool show "Ramachandran Plot"
    9992 
    9993 [Repeated 1 time(s)]
    9994 
    9995 > select clear
    9996 
    9997 > ui tool show "Ramachandran Plot"
    9998 
    9999 > isolde sim stop
    10000 
    10001 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10002 chains... 
    10003 ISOLDE: stopped sim 
    10004 
    10005 > ui tool show "Ramachandran Plot"
    10006 
    10007 > isolde sim start sel
    10008 
    10009 ISOLDE: started sim 
    10010 
    10011 > ui tool show "Ramachandran Plot"
    10012 
    10013 > select clear
    10014 
    10015 > ui tool show "Ramachandran Plot"
    10016 
    10017 [Repeated 1 time(s)]
    10018 
    10019 > isolde sim stop
    10020 
    10021 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10022 chains... 
    10023 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10024 standards. 
    10025 ISOLDE: stopped sim 
    10026 
    10027 > ui tool show "Ramachandran Plot"
    10028 
    10029 > isolde sim start sel
    10030 
    10031 ISOLDE: started sim 
    10032 
    10033 > select clear
    10034 
    10035 > ui tool show "Ramachandran Plot"
    10036 
    10037 > isolde sim pause
    10038 
    10039 > isolde sim resume
    10040 
    10041 > isolde pepflip sel
    10042 
    10043 Flipping the peptide bond for 1 residues 
    10044 
    10045 > isolde pepflip sel
    10046 
    10047 Flipping the peptide bond for 1 residues 
    10048 
    10049 > isolde pepflip sel
    10050 
    10051 Flipping the peptide bond for 1 residues 
    10052 
    10053 > isolde pepflip sel
    10054 
    10055 Flipping the peptide bond for 1 residues 
    10056 
    10057 > select clear
    10058 
    10059 > isolde pepflip sel
    10060 
    10061 Flipping the peptide bond for 1 residues 
    10062 
    10063 > isolde pepflip sel
    10064 
    10065 Flipping the peptide bond for 1 residues 
    10066 
    10067 > select clear
    10068 
    10069 [Repeated 2 time(s)]
    10070 
    10071 > ui tool show "Ramachandran Plot"
    10072 
    10073 > select clear
    10074 
    10075 [Repeated 1 time(s)]
    10076 
    10077 > view #1/l:33
    10078 
    10079 > select clear
    10080 
    10081 [Repeated 1 time(s)]
    10082 
    10083 > isolde pepflip sel
    10084 
    10085 Flipping the peptide bond for 1 residues 
    10086 
    10087 > select clear
    10088 
    10089 > ui tool show "Ramachandran Plot"
    10090 
    10091 > select clear
    10092 
    10093 > isolde sim pause
    10094 
    10095 > isolde sim resume
    10096 
    10097 > ui tool show "Ramachandran Plot"
    10098 
    10099 > isolde sim pause
    10100 
    10101 > isolde sim stop
    10102 
    10103 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10104 chains... 
    10105 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    10106 standards. 
    10107 ISOLDE: stopped sim 
    10108 
    10109 > isolde sim start sel
    10110 
    10111 ISOLDE: started sim 
    10112 
    10113 > ui tool show "Ramachandran Plot"
    10114 
    10115 > select clear
    10116 
    10117 > isolde sim pause
    10118 
    10119 > isolde sim resume
    10120 
    10121 > ui tool show "Ramachandran Plot"
    10122 
    10123 > select clear
    10124 
    10125 > isolde pepflip sel
    10126 
    10127 Flipping the peptide bond for 1 residues 
    10128 
    10129 > isolde pepflip sel
    10130 
    10131 Flipping the peptide bond for 1 residues 
    10132 
    10133 > isolde pepflip sel
    10134 
    10135 Flipping the peptide bond for 1 residues 
    10136 
    10137 > ui tool show "Ramachandran Plot"
    10138 
    10139 > select clear
    10140 
    10141 > ui tool show "Ramachandran Plot"
    10142 
    10143 > select clear
    10144 
    10145 > isolde pepflip sel
    10146 
    10147 Flipping the peptide bond for 1 residues 
    10148 
    10149 > isolde pepflip sel
    10150 
    10151 Flipping the peptide bond for 1 residues 
    10152 
    10153 > ui tool show "Ramachandran Plot"
    10154 
    10155 > select clear
    10156 
    10157 [Repeated 1 time(s)]
    10158 
    10159 > isolde sim stop
    10160 
    10161 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10162 chains... 
    10163 ISOLDE: stopped sim 
    10164 
    10165 > view #1/l:33
    10166 
    10167 > select #1/l:33
    10168 
    10169 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10170 
    10171 > isolde sim start sel
    10172 
    10173 ISOLDE: started sim 
    10174 
    10175 > ui tool show "Ramachandran Plot"
    10176 
    10177 > select clear
    10178 
    10179 > ui tool show "Ramachandran Plot"
    10180 
    10181 > isolde sim stop
    10182 
    10183 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10184 chains... 
    10185 ISOLDE: stopped sim 
    10186 
    10187 > isolde sim start sel
    10188 
    10189 ISOLDE: started sim 
    10190 
    10191 > select clear
    10192 
    10193 > ui tool show "Ramachandran Plot"
    10194 
    10195 > isolde pepflip sel
    10196 
    10197 Flipping the peptide bond for 1 residues 
    10198 
    10199 > select clear
    10200 
    10201 [Repeated 2 time(s)]
    10202 
    10203 > ui tool show "Ramachandran Plot"
    10204 
    10205 [Repeated 2 time(s)]
    10206 
    10207 > select clear
    10208 
    10209 > ui tool show "Ramachandran Plot"
    10210 
    10211 > isolde sim pause
    10212 
    10213 > isolde sim resume
    10214 
    10215 > ui tool show "Ramachandran Plot"
    10216 
    10217 > isolde sim stop
    10218 
    10219 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10220 chains... 
    10221 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10222 standards. 
    10223 ISOLDE: stopped sim 
    10224 
    10225 > view #1/l:33
    10226 
    10227 > select #1/l:33
    10228 
    10229 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10230 
    10231 > isolde sim start sel
    10232 
    10233 ISOLDE: started sim 
    10234 
    10235 > ui tool show "Ramachandran Plot"
    10236 
    10237 > select clear
    10238 
    10239 > ui tool show "Ramachandran Plot"
    10240 
    10241 > isolde sim stop
    10242 
    10243 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10244 chains... 
    10245 ISOLDE: stopped sim 
    10246 
    10247 > ui tool show "Ramachandran Plot"
    10248 
    10249 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10250 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10251 > step20-3-afterStep1d2.cxs
    10252 
    10253 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    10254 
    10255 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10256 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10257 > step20-3-afterStep1d2.pdb
    10258 
    10259 > ui tool show "Ramachandran Plot"
    10260 
    10261 > isolde sim start sel
    10262 
    10263 ISOLDE: started sim 
    10264 
    10265 > select clear
    10266 
    10267 > isolde sim pause
    10268 
    10269 > select clear
    10270 
    10271 > isolde sim resume
    10272 
    10273 > select clear
    10274 
    10275 > ui tool show "Ramachandran Plot"
    10276 
    10277 > select clear
    10278 
    10279 > isolde sim pause
    10280 
    10281 > isolde sim resume
    10282 
    10283 > ui tool show "Ramachandran Plot"
     4925
     4926[had to delete part of log to fit within ticket limits]
    102844927
    102854928> isolde sim stop