Opened 18 months ago

Closed 18 months ago

#15240 closed defect (fixed)

altloc code typo

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8rc202405102050 (2024-05-10 20:50:33 UTC)
Description
Looking at altloc.py, looks like `s` should be `alt_loc_s`.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.8rc202405102050 (2024-05-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7pe8

7pe8 title:  
cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one
protomer [more info...]  
  
Chain information for 7pe8 #1  
---  
Chain | Description | UniProt  
A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549  
C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708  
G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522  
I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409  
  
Non-standard residues in 7pe8 #1  
---  
ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> log metadata #1

Metadata for 7pe8 #1  
---  
Title | cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one protomer  
Citation | Walchli, M., Berneiser, K., Mangia, F., Imseng, S., Craigie, L.M., Stuttfeld, E., Hall, M.N., Maier, T. (2021). Regulation of human mTOR complexes by DEPTOR. Elife, 10. PMID: 34519268. DOI: 10.7554/eLife.70871  
Non-standard residues | ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
Gene source | Homo sapiens (human)  
CryoEM Map | EMDB 13348 — open map  
Experimental method | Electron microscopy  
Resolution | 3.20Å  
  
> open 13348 fromDatabase emdb

Opened emdb 13348 as #2, grid size 480,480,480, pixel 1.06, shown at level
0.185, step 2, values float32, fit PDB 7pe8  

> clipper associate #2 toModel #1

Opened emdb 13348 as #1.1.1.1, grid size 480,480,480, pixel 1.06, shown at
level 0.587, step 1, values float32  
7pe8 title:  
cryo-EM structure of DEPTOR bound to human mTOR complex 2, focussed on one
protomer [more info...]  
  
Chain information for 7pe8  
---  
Chain | Description | UniProt  
1.2/A | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 1-2549  
1.2/C | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
1.2/E | Rapamycin-insensitive companion of mTOR | RICTR_HUMAN 1-1708  
1.2/G | Target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522  
1.2/I | DEP domain-containing mTOR-interacting protein | DPTOR_HUMAN 1-409  
  
Non-standard residues in 7pe8 #1.2  
---  
ACE — acetyl group  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> clipper isolate /E,G

> clipper isolate /C,G

> select :ARG

2369 atoms, 2144 bonds, 235 residues, 1 model selected  

> select /I

795 atoms, 811 bonds, 106 residues, 1 model selected  

> clipper spotlight

> addh

Summary of feedback from adding hydrogens to 7pe8 #1.2  
---  
warnings | Not adding hydrogens to /A SER 17 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to /A ASN 18 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A VAL 19 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A SER 20 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A VAL 21 CB because it is missing heavy-atom bond
partners  
432 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A PRO 465 N; /A PRO 529 N; /A PRO 515 N; /G PRO 133 N; /A PRO
507 N; /A PRO 464 N; /A PRO 116 N; /A PRO 189 N; /A PRO 180 N; /A PRO 201 N;
/A PRO 120 N; /E PRO 27 N; /E PRO 34 N; /A PRO 397 N; /A PRO 404 N; /A PRO 453
N; /E PRO 642 N; /G PRO 134 N  
notes | Termini for 7pe8 (#1.2) chain A determined from SEQRES records  
Termini for 7pe8 (#1.2) chain C determined from SEQRES records  
Termini for 7pe8 (#1.2) chain E determined from SEQRES records  
Termini for 7pe8 (#1.2) chain G determined from SEQRES records  
Termini for 7pe8 (#1.2) chain I determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A SER 17, /A ARG 37, /A
SER 60, /A GLU 82, /A GLU 162, /A TRP 233, /A ASP 259, /A MET 304, /A LEU 356,
/A SER 386, /A THR 410, /A VAL 478, /A ILE 497, /A GLY 580, /A LEU 599, /A VAL
644, /A ASN 791, /A TYR 929, /A ILE 1263, /A LEU 1873, /A ALA 2492, /C VAL 8,
/E ASN 25, /E ILE 520, /E GLN 872, /E ASP 1423, /E SER 1479, /E THR 1510, /E
MET 1607, /G ALA 2, /G SER 84, /I CYS 304  
Chain-final residues that are actual C termini: /A TRP 2549, /C GLY 326, /I
CYS 409  
Chain-final residues that are not actual C termini: /A LYS 30, /A ARG 53, /A
LEU 74, /A LEU 156, /A ARG 223, /A ASP 246, /A ILE 289, /A THR 317, /A CYS
380, /A PRO 404, /A LYS 466, /A ARG 491, /A HIS 549, /A GLU 595, /A SER 633,
/A PRO 786, /A ILE 903, /A ARG 1238, /A ALA 1810, /A ASP 2433, /E GLN 510, /E
PRO 857, /E PRO 1005, /E LYS 1448, /E ASN 1494, /E GLN 1536, /E ALA 1694, /G
VAL 36, /G LEU 146  
Missing OXT added to C-terminal residue /A TRP 2549  
Missing OXT added to C-terminal residue /C GLY 326  
2842 hydrogen bonds  
Adding 'H' to /A SER 17  
Adding 'H' to /A ARG 37  
Adding 'H' to /A SER 60  
Adding 'H' to /A GLU 82  
Adding 'H' to /A GLU 162  
26 messages similar to the above omitted  
/E ALA 1694 is not terminus, removing H atom from 'C'  
/G LEU 146 is not terminus, removing H atom from 'C'  
28253 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 203 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> ui tool show Shell

0.01s - Debugger warning: It seems that frozen modules are being used, which
may  
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off  
0.00s - to python to disable frozen modules.  
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.  

> usage swapaa mouse

swapaa mousemode residues restypes  
— Replace residue with specified amino acid  
restypes: a collection of one of ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS,
ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, or VAL  

> swapaa mousemode /A:17 SER

> swapaa mousemode /A:18 ASN

> swapaa mousemode /A:19 VAL

> swapaa mousemode /A:20 SER

> swapaa mousemode /A:21 VAL

> swapaa mousemode /A:22 LEU

> swapaa mousemode /A:23 GLN

> swapaa mousemode /A:24 GLN

> swapaa mousemode /A:25 PHE

> swapaa mousemode /A:27 SER

> swapaa mousemode /A:29 LEU

> swapaa mousemode /A:30 LYS

> swapaa mousemode /A:37 ARG

> swapaa mousemode /A:39 LYS

> swapaa mousemode /A:42 LYS

> swapaa mousemode /A:43 GLU

> swapaa mousemode /A:44 LEU

> swapaa mousemode /A:45 GLN

> swapaa mousemode /A:46 HIS

> swapaa mousemode /A:47 TYR

> swapaa mousemode /A:48 VAL

> swapaa mousemode /A:49 THR

> swapaa mousemode /A:50 MET

> swapaa mousemode /A:51 GLU

> swapaa mousemode /A:52 LEU

> swapaa mousemode /A:53 ARG

> swapaa mousemode /A:60 SER

> swapaa mousemode /A:61 THR

> swapaa mousemode /A:62 ARG

> swapaa mousemode /A:63 PHE

> swapaa mousemode /A:64 TYR

> swapaa mousemode /A:65 ASP

> swapaa mousemode /A:66 GLN

> swapaa mousemode /A:67 LEU

> swapaa mousemode /A:68 ASN

> swapaa mousemode /A:69 HIS

> swapaa mousemode /A:70 HIS

> swapaa mousemode /A:71 ILE

> swapaa mousemode /A:72 PHE

> swapaa mousemode /A:73 GLU

> swapaa mousemode /A:74 LEU

> swapaa mousemode /A:82 GLU

> swapaa mousemode /A:83 ARG

> swapaa mousemode /A:84 LYS

> swapaa mousemode /A:87 ILE

> swapaa mousemode /A:88 LEU

> swapaa mousemode /A:90 ILE

> swapaa mousemode /A:92 SER

> swapaa mousemode /A:93 LEU

> swapaa mousemode /A:94 ILE

> swapaa mousemode /A:96 VAL

> swapaa mousemode /A:97 GLU

> swapaa mousemode /A:100 ASN

> swapaa mousemode /A:102 THR

> swapaa mousemode /A:103 ARG

> swapaa mousemode /A:104 ILE

> swapaa mousemode /A:106 ARG

> swapaa mousemode /A:107 PHE

> swapaa mousemode /A:109 ASN

> swapaa mousemode /A:110 TYR

> swapaa mousemode /A:111 LEU

> swapaa mousemode /A:112 ARG

> swapaa mousemode /A:113 ASN

> swapaa mousemode /A:114 LEU

> swapaa mousemode /A:115 LEU

> swapaa mousemode /A:116 PRO

> swapaa mousemode /A:117 SER

> swapaa mousemode /A:118 ASN

> swapaa mousemode /A:119 ASP

> swapaa mousemode /A:120 PRO

> swapaa mousemode /A:121 VAL

> swapaa mousemode /A:122 VAL

> swapaa mousemode /A:123 MET

> swapaa mousemode /A:124 GLU

> swapaa mousemode /A:125 MET

> swapaa mousemode /A:127 SER

> swapaa mousemode /A:128 LYS

> swapaa mousemode /A:130 ILE

> swapaa mousemode /A:132 ARG

> swapaa mousemode /A:133 LEU

> swapaa mousemode /A:135 MET

> swapaa mousemode /A:138 ASP

> swapaa mousemode /A:139 THR

> swapaa mousemode /A:140 PHE

> swapaa mousemode /A:141 THR

> swapaa mousemode /A:143 GLU

> swapaa mousemode /A:144 TYR

> swapaa mousemode /A:145 VAL

> swapaa mousemode /A:146 GLU

> swapaa mousemode /A:147 PHE

> swapaa mousemode /A:148 GLU

> swapaa mousemode /A:149 VAL

> swapaa mousemode /A:150 LYS

> swapaa mousemode /A:151 ARG

> swapaa mousemode /A:153 LEU

> swapaa mousemode /A:154 GLU

> swapaa mousemode /A:155 TRP

> swapaa mousemode /A:156 LEU

> swapaa mousemode /A:162 GLU

> swapaa mousemode /A:164 ARG

> swapaa mousemode /A:165 ARG

> swapaa mousemode /A:166 HIS

> swapaa mousemode /A:169 VAL

> swapaa mousemode /A:170 LEU

> swapaa mousemode /A:171 VAL

> swapaa mousemode /A:172 LEU

> swapaa mousemode /A:173 ARG

> swapaa mousemode /A:174 GLU

> swapaa mousemode /A:175 LEU

> swapaa mousemode /A:177 ILE

> swapaa mousemode /A:178 SER

> swapaa mousemode /A:179 VAL

> swapaa mousemode /A:180 PRO

> swapaa mousemode /A:181 THR

> swapaa mousemode /A:182 PHE

> swapaa mousemode /A:183 PHE

> swapaa mousemode /A:184 PHE

> swapaa mousemode /A:185 GLN

> swapaa mousemode /A:186 GLN

> swapaa mousemode /A:187 VAL

> swapaa mousemode /A:188 GLN

> swapaa mousemode /A:189 PRO

> swapaa mousemode /A:190 PHE

> swapaa mousemode /A:191 PHE

> swapaa mousemode /A:192 ASP

> swapaa mousemode /A:193 ASN

> swapaa mousemode /A:194 ILE

> swapaa mousemode /A:195 PHE

> swapaa mousemode /A:196 VAL

> swapaa mousemode /A:198 VAL

> swapaa mousemode /A:199 TRP

> swapaa mousemode /A:200 ASP

> swapaa mousemode /A:201 PRO

> swapaa mousemode /A:202 LYS

> swapaa mousemode /A:203 GLN

> swapaa mousemode /A:205 ILE

> swapaa mousemode /A:206 ARG

> swapaa mousemode /A:207 GLU

> swapaa mousemode /A:210 VAL

> swapaa mousemode /A:213 LEU

> swapaa mousemode /A:214 ARG

> swapaa mousemode /A:216 CYS

> swapaa mousemode /A:217 LEU

> swapaa mousemode /A:218 ILE

> swapaa mousemode /A:219 LEU

> swapaa mousemode /A:220 THR

> swapaa mousemode /A:221 THR

> swapaa mousemode /A:222 GLN

> swapaa mousemode /A:223 ARG

> swapaa mousemode /A:233 TRP

> swapaa mousemode /A:234 TYR

> swapaa mousemode /A:235 ARG

> swapaa mousemode /A:236 HIS

> swapaa mousemode /A:237 THR

> swapaa mousemode /A:238 PHE

> swapaa mousemode /A:239 GLU

> swapaa mousemode /A:240 GLU

> swapaa mousemode /A:242 GLU

> swapaa mousemode /A:243 LYS

> swapaa mousemode /A:245 PHE

> swapaa mousemode /A:246 ASP

> swapaa mousemode /A:259 ASP

> swapaa mousemode /A:260 ARG

> swapaa mousemode /A:261 ILE

> swapaa mousemode /A:262 HIS

> swapaa mousemode /A:265 LEU

> swapaa mousemode /A:266 LEU

> swapaa mousemode /A:267 ILE

> swapaa mousemode /A:268 LEU

> swapaa mousemode /A:269 ASN

> swapaa mousemode /A:270 GLU

> swapaa mousemode /A:271 LEU

> swapaa mousemode /A:272 VAL

> swapaa mousemode /A:273 ARG

> swapaa mousemode /A:274 ILE

> swapaa mousemode /A:275 SER

> swapaa mousemode /A:276 SER

> swapaa mousemode /A:277 MET

> swapaa mousemode /A:278 GLU

> swapaa mousemode /A:280 GLU

> swapaa mousemode /A:281 ARG

> swapaa mousemode /A:282 LEU

> swapaa mousemode /A:283 ARG

> swapaa mousemode /A:284 GLU

> swapaa mousemode /A:285 GLU

> swapaa mousemode /A:286 MET

> swapaa mousemode /A:287 GLU

> swapaa mousemode /A:288 GLU

> swapaa mousemode /A:289 ILE

> swapaa mousemode /A:317 THR

> swapaa mousemode /A:356 LEU

> swapaa mousemode /A:357 VAL

> swapaa mousemode /A:358 GLU

> swapaa mousemode /A:359 SER

> swapaa mousemode /A:360 ARG

> swapaa mousemode /A:361 CYS

> swapaa mousemode /A:362 CYS

> swapaa mousemode /A:363 ARG

> swapaa mousemode /A:364 ASP

> swapaa mousemode /A:365 LEU

> swapaa mousemode /A:366 MET

> swapaa mousemode /A:367 GLU

> swapaa mousemode /A:368 GLU

> swapaa mousemode /A:369 LYS

> swapaa mousemode /A:370 PHE

> swapaa mousemode /A:371 ASP

> swapaa mousemode /A:372 GLN

> swapaa mousemode /A:373 VAL

> swapaa mousemode /A:374 CYS

> swapaa mousemode /A:375 GLN

> swapaa mousemode /A:376 TRP

> swapaa mousemode /A:377 VAL

> swapaa mousemode /A:378 LEU

> swapaa mousemode /A:379 LYS

> swapaa mousemode /A:380 CYS

> swapaa mousemode /A:386 SER

> swapaa mousemode /A:387 LEU

> swapaa mousemode /A:388 ILE

> swapaa mousemode /A:389 GLN

> swapaa mousemode /A:390 MET

> swapaa mousemode /A:391 THR

> swapaa mousemode /A:392 ILE

> swapaa mousemode /A:393 LEU

> swapaa mousemode /A:394 ASN

> swapaa mousemode /A:395 LEU

> swapaa mousemode /A:396 LEU

> swapaa mousemode /A:397 PRO

> swapaa mousemode /A:398 ARG

> swapaa mousemode /A:399 LEU

> swapaa mousemode /A:402 PHE

> swapaa mousemode /A:403 ARG

> swapaa mousemode /A:404 PRO

> swapaa mousemode /A:410 THR

> swapaa mousemode /A:411 GLN

> swapaa mousemode /A:412 TYR

> swapaa mousemode /A:413 LEU

> swapaa mousemode /A:414 GLN

> swapaa mousemode /A:415 ASP

> swapaa mousemode /A:416 THR

> swapaa mousemode /A:417 MET

> swapaa mousemode /A:418 ASN

> swapaa mousemode /A:419 HIS

> swapaa mousemode /A:420 VAL

> swapaa mousemode /A:421 LEU

> swapaa mousemode /A:422 SER

> swapaa mousemode /A:423 CYS

> swapaa mousemode /A:424 VAL

> swapaa mousemode /A:425 LYS

> swapaa mousemode /A:426 LYS

> swapaa mousemode /A:427 GLU

> swapaa mousemode /A:428 LYS

> swapaa mousemode /A:429 GLU

> swapaa mousemode /A:430 ARG

> swapaa mousemode /A:431 THR

> swapaa mousemode /A:434 PHE

> swapaa mousemode /A:435 GLN

> swapaa mousemode /A:437 LEU

> swapaa mousemode /A:439 LEU

> swapaa mousemode /A:440 LEU

> swapaa mousemode /A:441 SER

> swapaa mousemode /A:442 VAL

> swapaa mousemode /A:444 VAL

> swapaa mousemode /A:445 ARG

> swapaa mousemode /A:446 SER

> swapaa mousemode /A:447 GLU

> swapaa mousemode /A:448 PHE

> swapaa mousemode /A:449 LYS

> swapaa mousemode /A:450 VAL

> swapaa mousemode /A:451 TYR

> swapaa mousemode /A:452 LEU

> swapaa mousemode /A:453 PRO

> swapaa mousemode /A:454 ARG

> swapaa mousemode /A:455 VAL

> swapaa mousemode /A:456 LEU

> swapaa mousemode /A:457 ASP

> swapaa mousemode /A:458 ILE

> swapaa mousemode /A:459 ILE

> swapaa mousemode /A:460 ARG

> swapaa mousemode /A:463 LEU

> swapaa mousemode /A:464 PRO

> swapaa mousemode /A:465 PRO

> swapaa mousemode /A:466 LYS

> swapaa mousemode /A:478 VAL

> swapaa mousemode /A:479 ASP

> swapaa mousemode /A:481 THR

> swapaa mousemode /A:482 VAL

> swapaa mousemode /A:483 PHE

> swapaa mousemode /A:484 THR

> swapaa mousemode /A:485 CYS

> swapaa mousemode /A:486 ILE

> swapaa mousemode /A:487 SER

> swapaa mousemode /A:488 MET

> swapaa mousemode /A:489 LEU

> swapaa mousemode /A:491 ARG

> swapaa mousemode /A:497 ILE

> swapaa mousemode /A:498 GLN

> swapaa mousemode /A:499 GLN

> swapaa mousemode /A:500 ASP

> swapaa mousemode /A:501 ILE

> swapaa mousemode /A:502 LYS

> swapaa mousemode /A:503 GLU

> swapaa mousemode /A:504 LEU

> swapaa mousemode /A:505 LEU

> swapaa mousemode /A:506 GLU

> swapaa mousemode /A:507 PRO

> swapaa mousemode /A:508 MET

> swapaa mousemode /A:509 LEU

> swapaa mousemode /A:511 VAL

> swapaa mousemode /A:513 LEU

> swapaa mousemode /A:514 SER

> swapaa mousemode /A:515 PRO

> swapaa mousemode /A:517 LEU

> swapaa mousemode /A:518 THR

> swapaa mousemode /A:520 VAL

> swapaa mousemode /A:521 LEU

> swapaa mousemode /A:522 TYR

> swapaa mousemode /A:523 ASP

> swapaa mousemode /A:524 LEU

> swapaa mousemode /A:525 SER

> swapaa mousemode /A:526 ARG

> swapaa mousemode /A:527 GLN

> swapaa mousemode /A:528 ILE

> swapaa mousemode /A:529 PRO

> swapaa mousemode /A:530 GLN

> swapaa mousemode /A:531 LEU

> swapaa mousemode /A:532 LYS

> swapaa mousemode /A:533 LYS

> swapaa mousemode /A:534 ASP

> swapaa mousemode /A:535 ILE

> swapaa mousemode /A:536 GLN

> swapaa mousemode /A:537 ASP

> swapaa mousemode /A:539 LEU

> swapaa mousemode /A:540 LEU

> swapaa mousemode /A:541 LYS

> swapaa mousemode /A:542 MET

> swapaa mousemode /A:543 LEU

> swapaa mousemode /A:544 SER

> swapaa mousemode /A:545 LEU

> swapaa mousemode /A:546 VAL

> swapaa mousemode /A:547 LEU

> swapaa mousemode /A:548 MET

> swapaa mousemode /A:549 HIS

> swapaa mousemode /A:593 GLU

> swapaa mousemode /A:829 GLN

> swapaa mousemode /A:830 ASP

> swapaa mousemode /A:831 SER

> swapaa mousemode /A:832 SER

> swapaa mousemode /A:833 LEU

> swapaa mousemode /A:834 LEU

> swapaa mousemode /A:836 LYS

> swapaa mousemode /A:962 GLN

> swapaa mousemode /A:963 SER

> swapaa mousemode /A:1273 ARG

> swapaa mousemode /A:1730 HIS

> swapaa mousemode /A:1732 ILE

> swapaa mousemode /A:1734 THR

> swapaa mousemode /A:1735 GLU

> swapaa mousemode /A:1736 ASP

> swapaa mousemode /A:1737 GLN

> swapaa mousemode /C:162 ASN

> swapaa mousemode /E:25 ASN

> swapaa mousemode /E:26 VAL

> swapaa mousemode /E:27 PRO

> swapaa mousemode /E:28 LEU

> swapaa mousemode /E:29 ASP

> swapaa mousemode /E:30 LEU

> swapaa mousemode /E:31 THR

> swapaa mousemode /E:32 ARG

> swapaa mousemode /E:33 GLU

> swapaa mousemode /E:34 PRO

> swapaa mousemode /E:267 ASP

> swapaa mousemode /E:640 MET

> swapaa mousemode /E:641 LYS

> swapaa mousemode /E:642 PRO

> swapaa mousemode /E:643 GLU

> swapaa mousemode /E:644 ARG

> swapaa mousemode /E:645 SER

> swapaa mousemode /G:97 ARG

> swapaa mousemode /G:98 GLN

> swapaa mousemode /G:99 ASN

> swapaa mousemode /G:100 GLN

> swapaa mousemode /G:101 ILE

> swapaa mousemode /G:102 LYS

> swapaa mousemode /G:109 LYS

> swapaa mousemode /G:110 GLU

> swapaa mousemode /G:111 ARG

> swapaa mousemode /G:112 ASN

> swapaa mousemode /G:113 SER

> swapaa mousemode /G:114 LYS

> swapaa mousemode /G:115 GLN

> swapaa mousemode /G:116 SER

> swapaa mousemode /G:118 GLN

> swapaa mousemode /G:119 GLU

> swapaa mousemode /G:120 LEU

> swapaa mousemode /G:121 LYS

> swapaa mousemode /G:122 SER

> swapaa mousemode /G:123 LEU

> swapaa mousemode /G:124 PHE

> swapaa mousemode /G:125 GLU

> swapaa mousemode /G:126 LYS

> swapaa mousemode /G:127 LYS

> swapaa mousemode /G:128 SER

> swapaa mousemode /G:129 LEU

> swapaa mousemode /G:130 LYS

> swapaa mousemode /G:131 GLU

> swapaa mousemode /G:132 LYS

> swapaa mousemode /G:133 PRO

> swapaa mousemode /G:134 PRO

> swapaa mousemode /G:135 ILE

> swapaa mousemode /G:136 SER

> swapaa mousemode /G:138 LYS

> swapaa mousemode /G:139 GLN

> swapaa mousemode /G:140 SER

> swapaa mousemode /G:141 ILE

> swapaa mousemode /G:142 LEU

> swapaa mousemode /G:143 SER

> swapaa mousemode /G:144 VAL

> swapaa mousemode /G:145 ARG

> swapaa mousemode /G:146 LEU

> select clear

> select /C

4825 atoms, 4883 bonds, 319 residues, 1 model selected  

> isolde sim start /C

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select ~sel & ##selected

Nothing selected  

> select /C|/G:104-200

5561 atoms, 5623 bonds, 362 residues, 1 model selected  

> isolde sim start /C/G:104-146

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim resume

> isolde pepflip /G:138

[Repeated 1 time(s)]

> isolde pepflip /G:139

[Repeated 1 time(s)]

> isolde pepflip /G:137

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> open "C:/Users/Tristan
> Croll/Documents/Structures/RAPTOR/6zwo/6zwo_working.pdb"

Chain information for 6zwo_working.pdb #2  
---  
Chain | Description  
B | No description available  
D | No description available  
F | No description available  
H | No description available  
  

> matchmaker #2 to #1/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7pe8, chain C (#1.2) with 6zwo_working.pdb, chain D (#2), sequence
alignment score = 1648.1  
RMSD between 302 pruned atom pairs is 0.646 angstroms; (across all 319 pairs:
1.320)  
  

> show #2

> select #1/G:110-130

358 atoms, 358 bonds, 21 residues, 1 model selected  

> isolde sim start #1.2/G:110-130

ISOLDE: started sim  

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde restrain distances "#1/G:101-200","#1/C" templateAtoms "#2/H","#2/D"
> displayThreshold 0.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]RMSD between 356 pruned atom pairs is 1.171 angstroms;
(across all 365 pairs: 1.639)  
RMSD between 4 pruned atom pairs is 3.599 angstroms; (across all 9 pairs:
27.504)  
RMSD between 3 pruned atom pairs is 2.096 angstroms; (across all 5 pairs:
11.533)  

> isolde restrain torsions #1/G:110-300 templateResidues #2/H

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> isolde restrain torsions #1/C templateResidues #2/D

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> select /C|/G:104-200

5561 atoms, 5623 bonds, 362 residues, 1 model selected  

> hide #!2 models

> isolde sim start #1.2/C/G:104-146

ISOLDE: started sim  

> select clear

> select #1

61882 atoms, 62484 bonds, 31 pseudobonds, 3835 residues, 23 models selected  

> ra

> select clear

> isolde pepflip #1.2/C:119

> isolde pepflip #1.2/C:121

> isolde pepflip #1.2/C:122

> isolde pepflip #1.2/C:118

[Repeated 1 time(s)]

> isolde pepflip #1.2/C:119

[Repeated 1 time(s)]

> isolde pepflip #1.2/C:117

> isolde pepflip #1.2/C:116

> select clear

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/G:601

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> cd "C:/Users/Tristan Croll/Documents/Structures/RAPTOR/7pe8"

Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\RAPTOR\7pe8  

> save 7pe8_working.cxs

> select #1/G:100-300|#1/C

5630 atoms, 5692 bonds, 366 residues, 1 model selected  

> save lst8_sin1_from_7pe8.pdb #1 selectedOnly true

> clipper isolate #1/C,G

> save 7pe8_CG_rebuilt.cxs

> close

> open 3wf7 structureFactors true

Summary of feedback from opening 3wf7 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 3wf7 from http://files.rcsb.org/download/3wf7.cif  
Fetching CCD FS9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/FS9/FS9.cif  
Fetching compressed 3wf7 structure factors from
http://files.rcsb.org/download/3wf7-sf.cif  
Resolution: 1.7396317635646323  
Launching live xmap mgr took 1.5464694499969482 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 44,44,44, pixel
0.579,0.579,0.569, shown at level 0.594, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 44,44,44, pixel
0.579,0.579,0.569, shown at level -0.13,0.13, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_19 as #1.1.1.4, grid size 44,44,44, pixel
0.579,0.579,0.569, shown at level 0.175, step 1, values float32  
3wf7 title:  
Crystal structure of S6K1 kinase domain in complex with a purine derivative
1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide [more
info...]  
  
Chain information for 3wf7  
---  
Chain | Description | UniProt  
1.2/A | Ribosomal protein S6 kinase beta-1 | KS6B1_HUMAN 78-399  
  
Non-standard residues in 3wf7 #1.2  
---  
FS9 — 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> addh

Summary of feedback from adding hydrogens to 3wf7 #1.2  
---  
warnings | Not adding hydrogens to /A ARG 132 CD because it is missing heavy-atom bond partners  
Not adding hydrogens to /A LYS 135 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ILE 244 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 364 CG because it is missing heavy-atom bond
partners  
notes | Termini for 3wf7 (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 83, /A THR 250  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASP 246, /A GLN 374  
910 hydrogen bonds  
Adding 'H' to /A THR 250  
/A GLN 374 is not terminus, removing H atom from 'C'  
2808 hydrogens added  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 44,44,44, pixel
0.579,0.579,0.569, shown at level 0.455, step 1, values float32  
Loading residue template for FS9 from internal database  
Loading residue template for GOL from internal database  
Deleted the following atoms from residue TPO A252: O  

> view :FS9

> delete sel

> select #1

5368 atoms, 5195 bonds, 5 pseudobonds, 518 residues, 30 models selected  

> isolde sim start /A

ISOLDE: started sim  

> select clear

> isolde pepflip /A:245

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> swapaa mousemode sel ILE

> select #1

5380 atoms, 5207 bonds, 5 pseudobonds, 518 residues, 35 models selected  

> isolde sim start /A

ISOLDE: started sim  

> select clear

> isolde sim pause

> select clear

> st

[Repeated 1 time(s)]

> delete :HOH

Sim termination reason: coord length mismatch  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> st

[Repeated 1 time(s)]

> select clear

> st

[Repeated 1 time(s)]

> aw

> isolde sim start /A:88,404

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> altlocs show #1

Removed all altlocs in #1.2.Occupancies for all affected atoms have been reset
to 1.  

> close #1.2.12

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 301, in _models_closed_cb  
self.destroy()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy  
s._alt_loc_changes_handler.remove()  
^  
NameError: name 's' is not defined  
  
Error processing trigger "remove models":  
NameError: name 's' is not defined  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\std_commands\altlocs.py", line 172, in destroy  
s._alt_loc_changes_handler.remove()  
^  
  
See log for complete Python traceback.  
  

> select clear




OpenGL version: 3.3.0 NVIDIA 552.22
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

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    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
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    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8rc202405102050
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.1
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8rc1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.3.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
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    pynmrstar: 3.3.4
    pynrrd: 1.0.0
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    PyOpenGL-accelerate: 3.1.7
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    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
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    snowballstemmer: 2.2.0
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    soupsieve: 2.5
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    stack-data: 0.6.3
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    tcia-utils: 1.5.1
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    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → altloc code typo

comment:2 by Eric Pettersen, 18 months ago

Resolution: → fixed
Status: accepted → closed

Fixed. Thanks!

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