[Chimera-users] Structure superimposition - RMSD

[Suda Parimala Ravindran]

Hi Elaine..

Thanks a lot for your reply. I have run even the Match-> Align along with
iteration. After running, the alignment window does show up, I have checked
the reply log. But can't find the overall RMSD value for some runs. I have
attached the entire reply log file along for which i didn't find the
overall value. So can you please help me locate the overall RMSD value? I
can only find the pairwise RMSD values.

Also, I want to know on how to choose a reference structure. Say for
example, i have 10 structures to superimpose and among them 5 belong to
(eg) bacterial species (my query/study of interest) and the remaining 5
belong to varied organisms of different hierarchy. So how do i choose my
reference structure among the 5 from my query. what I thought was to run
the superimposition 5 times choosing each bacterial strcuture as a
reference each time, calculate the overall RMSD and then choose the least
RMSD one as reference? Can i proceed this way or are there any other better
option to choose a reference structure?

PLease help.

Thanks,

-Suda
**







On Wed, Nov 16, 2011 at 11:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Suda,
> Matchmaker does pairwise superpositions to the reference, so even if you
> chose to match structures B,C,D to A, it will perform pairwise matches and
> report pairwise RMSD for A-B, A-C, and A-D.  All of those should be in the
> Reply Log, but there is various other stuff between them such as parameters
> listings, so you would need to scroll up to see them.
>
> However, to get an overall RMSD of more than two structures, after you run
> MatchMaker you would run Match->Align to make a multiple sequence alignment
> (instead of the pairwise ones created by MatchMaker).  Match->Align is in
> the menu under Tools... Structure Comparison.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
> >
>
> Besides overall RMSD it will also give you other measures of structural
> similarity (SDM, Q-score), and in the output sequence alignment there will
> be an RMSD histogram above sequences showing the per-column values.
>
> HOWEVER, be aware it will take a pretty long time to run Match->Align on
> 10 structures, especially with iteration.  I would try it without iteration
> first (which still might take a pretty long time, many minutes) and see if
> the resulting sequence alignment looks good enough.
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
>
> > Hi all,
> >
> > I have a set of protein structures (about 10) that I need to
> superimpose. I have used Matchmaker and superimposed by choosing a
> reference structure. I want to know how to calculate the overall RMSD of
> the superimposed structures? Where do I lokk out for it? I have checked the
> Reply log window, but it gets displayed only for some, whereas for others
> it does not. Please help..
> >
> > Thanks,
> >
> > -Suda
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20111117/c96ff22f/attachment.html>
-------------- next part --------------
The following problems occurred while reading PDB file for Asterina pectinifera-YET.pdb
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 3
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 5
warning:  Ignored bad PDB record found on line 6
warning:  Ignored bad PDB record found on line 7
warning:  Ignored bad PDB record found on line 8
warning:  Ignored bad PDB record found on line 9
warning:  Ignored bad PDB record found on line 10
warning:  Ignored bad PDB record found on line 11
warning:  Ignored bad PDB record found on line 12
warning:  Ignored bad PDB record found on line 13
warning:  Ignored bad PDB record found on line 15
Model 0 (Asterina pectinifera-YET.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Culex quinquefasciatus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 2150
warning:  Ignored bad PDB record found on line 2151
warning:  Ignored bad PDB record found on line 2152
warning:  Ignored bad PDB record found on line 2153
warning:  Ignored bad PDB record found on line 2154
warning:  Ignored bad PDB record found on line 2155
warning:  Ignored bad PDB record found on line 2156
warning:  Ignored bad PDB record found on line 2157
warning:  Ignored bad PDB record found on line 2158
warning:  Ignored bad PDB record found on line 2159
warning:  Ignored bad PDB record found on line 2160
warning:  Ignored bad PDB record found on line 2161
warning:  Ignored bad PDB record found on line 2162
warning:  Ignored bad PDB record found on line 2163
warning:  Ignored bad PDB record found on line 2164
warning:  Ignored bad PDB record found on line 2165
warning:  Ignored bad PDB record found on line 2166
warning:  Ignored bad PDB record found on line 2167
warning:  Ignored bad PDB record found on line 2168
warning:  Ignored bad PDB record found on line 2169
warning:  Ignored bad PDB record found on line 2170
warning:  Ignored bad PDB record found on line 2171
warning:  Ignored bad PDB record found on line 2172
warning:  Ignored bad PDB record found on line 2173
warning:  Ignored bad PDB record found on line 2174
warning:  Ignored bad PDB record found on line 2175
warning:  Ignored bad PDB record found on line 2176
warning:  Ignored bad PDB record found on line 2177
warning:  Ignored bad PDB record found on line 2178
warning:  Ignored bad PDB record found on line 2179
warning:  Ignored bad PDB record found on line 2180
warning:  Ignored bad PDB record found on line 2181
warning:  Ignored bad PDB record found on line 2182
warning:  Ignored bad PDB record found on line 2183
warning:  Ignored bad PDB record found on line 2184
warning:  Ignored bad PDB record found on line 2185
warning:  Ignored bad PDB record found on line 2186
warning:  Ignored bad PDB record found on line 2187
warning:  Ignored bad PDB record found on line 2188
warning:  Ignored bad PDB record found on line 2189
warning:  Ignored bad PDB record found on line 2190
warning:  Ignored bad PDB record found on line 2191
warning:  Ignored bad PDB record found on line 2192
warning:  Ignored bad PDB record found on line 2193
warning:  Ignored bad PDB record found on line 2194
warning:  Ignored bad PDB record found on line 2195
warning:  Ignored bad PDB record found on line 2196
warning:  Ignored bad PDB record found on line 2197
warning:  Ignored bad PDB record found on line 2198
warning:  Ignored bad PDB record found on line 2199
warning:  Ignored bad PDB record found on line 2200
warning:  Ignored bad PDB record found on line 2201
warning:  Ignored bad PDB record found on line 2202
warning:  Ignored bad PDB record found on line 2203
warning:  Ignored bad PDB record found on line 2204
warning:  Ignored bad PDB record found on line 2205
warning:  Ignored bad PDB record found on line 2206
warning:  Ignored bad PDB record found on line 2207
warning:  Ignored bad PDB record found on line 2208
warning:  Ignored bad PDB record found on line 2209
warning:  Ignored bad PDB record found on line 2210
warning:  Ignored bad PDB record found on line 2211
warning:  Ignored bad PDB record found on line 2212
warning:  Ignored bad PDB record found on line 2213
warning:  Ignored bad PDB record found on line 2214
warning:  Ignored bad PDB record found on line 2215
warning:  Ignored bad PDB record found on line 2216
warning:  Ignored bad PDB record found on line 2217
warning:  Ignored bad PDB record found on line 2218
warning:  Ignored bad PDB record found on line 2219
warning:  Ignored bad PDB record found on line 2220
warning:  Ignored bad PDB record found on line 2221
warning:  Ignored bad PDB record found on line 2222
warning:  Ignored bad PDB record found on line 2223
warning:  Ignored bad PDB record found on line 2224
warning:  Ignored bad PDB record found on line 2225
warning:  Ignored bad PDB record found on line 2226
warning:  Ignored bad PDB record found on line 2227
warning:  Ignored bad PDB record found on line 2228
warning:  Ignored bad PDB record found on line 2229
warning:  Ignored bad PDB record found on line 2230
warning:  Ignored bad PDB record found on line 2231
warning:  Ignored bad PDB record found on line 2232
warning:  Ignored bad PDB record found on line 2233
warning:  Ignored bad PDB record found on line 2234
warning:  Ignored bad PDB record found on line 2235
warning:  Ignored bad PDB record found on line 2236
warning:  Ignored bad PDB record found on line 2237
warning:  Ignored bad PDB record found on line 2238
warning:  Ignored bad PDB record found on line 2239
warning:  Ignored bad PDB record found on line 2240
warning:  Ignored bad PDB record found on line 2241
warning:  Ignored bad PDB record found on line 2242
warning:  Ignored bad PDB record found on line 2243
warning:  Ignored bad PDB record found on line 2244
warning:  Ignored bad PDB record found on line 2245
warning:  Ignored bad PDB record found on line 2246
warning:  Ignored bad PDB record found on line 2247
Model 1 (Culex quinquefasciatus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Heloderma horridum horridum.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 372
warning:  Ignored bad PDB record found on line 373
warning:  Ignored bad PDB record found on line 374
warning:  Ignored bad PDB record found on line 375
warning:  Ignored bad PDB record found on line 376
warning:  Ignored bad PDB record found on line 377
warning:  Ignored bad PDB record found on line 378
warning:  Ignored bad PDB record found on line 379
warning:  Ignored bad PDB record found on line 380
warning:  Ignored bad PDB record found on line 381
warning:  Ignored bad PDB record found on line 382
warning:  Ignored bad PDB record found on line 383
warning:  Ignored bad PDB record found on line 384
warning:  Ignored bad PDB record found on line 385
warning:  Ignored bad PDB record found on line 386
warning:  Ignored bad PDB record found on line 387
warning:  Ignored bad PDB record found on line 388
warning:  Ignored bad PDB record found on line 389
warning:  Ignored bad PDB record found on line 390
warning:  Ignored bad PDB record found on line 391
warning:  Ignored bad PDB record found on line 392
warning:  Ignored bad PDB record found on line 393
warning:  Ignored bad PDB record found on line 394
warning:  Ignored bad PDB record found on line 395
warning:  Ignored bad PDB record found on line 396
warning:  Ignored bad PDB record found on line 397
warning:  Ignored bad PDB record found on line 398
warning:  Ignored bad PDB record found on line 399
warning:  Ignored bad PDB record found on line 400
warning:  Ignored bad PDB record found on line 401
warning:  Ignored bad PDB record found on line 402
Model 2 (Heloderma horridum horridum.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Mesobuthus tamulus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 1699
warning:  Ignored bad PDB record found on line 1700
warning:  Ignored bad PDB record found on line 1701
warning:  Ignored bad PDB record found on line 1702
warning:  Ignored bad PDB record found on line 1703
warning:  Ignored bad PDB record found on line 1704
warning:  Ignored bad PDB record found on line 1705
warning:  Ignored bad PDB record found on line 1706
warning:  Ignored bad PDB record found on line 1707
warning:  Ignored bad PDB record found on line 1708
warning:  Ignored bad PDB record found on line 1709
warning:  Ignored bad PDB record found on line 1710
warning:  Ignored bad PDB record found on line 1711
warning:  Ignored bad PDB record found on line 1712
warning:  Ignored bad PDB record found on line 1713
warning:  Ignored bad PDB record found on line 1714
warning:  Ignored bad PDB record found on line 1715
warning:  Ignored bad PDB record found on line 1716
warning:  Ignored bad PDB record found on line 1717
warning:  Ignored bad PDB record found on line 1718
warning:  Ignored bad PDB record found on line 1719
warning:  Ignored bad PDB record found on line 1720
warning:  Ignored bad PDB record found on line 1721
warning:  Ignored bad PDB record found on line 1722
warning:  Ignored bad PDB record found on line 1723
warning:  Ignored bad PDB record found on line 1724
warning:  Ignored bad PDB record found on line 1725
warning:  Ignored bad PDB record found on line 1726
warning:  Ignored bad PDB record found on line 1727
warning:  Ignored bad PDB record found on line 1728
warning:  Ignored bad PDB record found on line 1729
warning:  Ignored bad PDB record found on line 1730
warning:  Ignored bad PDB record found on line 1731
warning:  Ignored bad PDB record found on line 1732
warning:  Ignored bad PDB record found on line 1733
warning:  Ignored bad PDB record found on line 1734
warning:  Ignored bad PDB record found on line 1735
warning:  Ignored bad PDB record found on line 1736
warning:  Ignored bad PDB record found on line 1737
warning:  Ignored bad PDB record found on line 1738
warning:  Ignored bad PDB record found on line 1739
warning:  Ignored bad PDB record found on line 1740
warning:  Ignored bad PDB record found on line 1741
warning:  Ignored bad PDB record found on line 1742
warning:  Ignored bad PDB record found on line 1743
warning:  Ignored bad PDB record found on line 1744
warning:  Ignored bad PDB record found on line 1745
warning:  Ignored bad PDB record found on line 1746
warning:  Ignored bad PDB record found on line 1747
warning:  Ignored bad PDB record found on line 1748
warning:  Ignored bad PDB record found on line 1749
warning:  Ignored bad PDB record found on line 1750
warning:  Ignored bad PDB record found on line 1751
warning:  Ignored bad PDB record found on line 1752
warning:  Ignored bad PDB record found on line 1753
warning:  Ignored bad PDB record found on line 1754
warning:  Ignored bad PDB record found on line 1755
warning:  Ignored bad PDB record found on line 1756
warning:  Ignored bad PDB record found on line 1757
warning:  Ignored bad PDB record found on line 1758
warning:  Ignored bad PDB record found on line 1759
warning:  Ignored bad PDB record found on line 1760
warning:  Ignored bad PDB record found on line 1761
warning:  Ignored bad PDB record found on line 1762
warning:  Ignored bad PDB record found on line 1763
warning:  Ignored bad PDB record found on line 1764
warning:  Ignored bad PDB record found on line 1765
warning:  Ignored bad PDB record found on line 1766
warning:  Ignored bad PDB record found on line 1767
warning:  Ignored bad PDB record found on line 1768
warning:  Ignored bad PDB record found on line 1769
warning:  Ignored bad PDB record found on line 1770
warning:  Ignored bad PDB record found on line 1771
warning:  Ignored bad PDB record found on line 1772
warning:  Ignored bad PDB record found on line 1773
warning:  Ignored bad PDB record found on line 1774
warning:  Ignored bad PDB record found on line 1775
warning:  Ignored bad PDB record found on line 1776
warning:  Ignored bad PDB record found on line 1777
warning:  Ignored bad PDB record found on line 1778
warning:  Ignored bad PDB record found on line 1779
warning:  Ignored bad PDB record found on line 1780
warning:  Ignored bad PDB record found on line 1781
Model 4 (Mesobuthus tamulus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Mirabilis jalapa.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 834
warning:  Ignored bad PDB record found on line 835
warning:  Ignored bad PDB record found on line 836
warning:  Ignored bad PDB record found on line 837
warning:  Ignored bad PDB record found on line 838
warning:  Ignored bad PDB record found on line 839
warning:  Ignored bad PDB record found on line 840
warning:  Ignored bad PDB record found on line 841
warning:  Ignored bad PDB record found on line 842
warning:  Ignored bad PDB record found on line 843
warning:  Ignored bad PDB record found on line 844
warning:  Ignored bad PDB record found on line 845
warning:  Ignored bad PDB record found on line 846
warning:  Ignored bad PDB record found on line 847
warning:  Ignored bad PDB record found on line 848
warning:  Ignored bad PDB record found on line 849
warning:  Ignored bad PDB record found on line 850
warning:  Ignored bad PDB record found on line 851
warning:  Ignored bad PDB record found on line 852
warning:  Ignored bad PDB record found on line 853
warning:  Ignored bad PDB record found on line 854
warning:  Ignored bad PDB record found on line 855
warning:  Ignored bad PDB record found on line 856
warning:  Ignored bad PDB record found on line 857
warning:  Ignored bad PDB record found on line 858
warning:  Ignored bad PDB record found on line 859
warning:  Ignored bad PDB record found on line 860
warning:  Ignored bad PDB record found on line 861
warning:  Ignored bad PDB record found on line 862
warning:  Ignored bad PDB record found on line 863
warning:  Ignored bad PDB record found on line 864
warning:  Ignored bad PDB record found on line 865
warning:  Ignored bad PDB record found on line 866
warning:  Ignored bad PDB record found on line 867
warning:  Ignored bad PDB record found on line 868
warning:  Ignored bad PDB record found on line 869
warning:  Ignored bad PDB record found on line 870
warning:  Ignored bad PDB record found on line 871
warning:  Ignored bad PDB record found on line 872
warning:  Ignored bad PDB record found on line 873
warning:  Ignored bad PDB record found on line 874
warning:  Ignored bad PDB record found on line 875
warning:  Ignored bad PDB record found on line 876
warning:  Ignored bad PDB record found on line 877
warning:  Ignored bad PDB record found on line 878
warning:  Ignored bad PDB record found on line 879
warning:  Ignored bad PDB record found on line 880
warning:  Ignored bad PDB record found on line 881
warning:  Ignored bad PDB record found on line 882
warning:  Ignored bad PDB record found on line 883
warning:  Ignored bad PDB record found on line 884
warning:  Ignored bad PDB record found on line 885
Model 5 (Mirabilis jalapa.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Schizosaccharomyces japonicus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 4363
warning:  Ignored bad PDB record found on line 4364
warning:  Ignored bad PDB record found on line 4365
warning:  Ignored bad PDB record found on line 4366
warning:  Ignored bad PDB record found on line 4367
warning:  Ignored bad PDB record found on line 4368
warning:  Ignored bad PDB record found on line 4369
warning:  Ignored bad PDB record found on line 4370
warning:  Ignored bad PDB record found on line 4371
warning:  Ignored bad PDB record found on line 4372
warning:  Ignored bad PDB record found on line 4373
warning:  Ignored bad PDB record found on line 4374
warning:  Ignored bad PDB record found on line 4375
warning:  Ignored bad PDB record found on line 4376
warning:  Ignored bad PDB record found on line 4377
warning:  Ignored bad PDB record found on line 4378
warning:  Ignored bad PDB record found on line 4379
warning:  Ignored bad PDB record found on line 4380
warning:  Ignored bad PDB record found on line 4381
warning:  Ignored bad PDB record found on line 4382
warning:  Ignored bad PDB record found on line 4383
warning:  Ignored bad PDB record found on line 4384
warning:  Ignored bad PDB record found on line 4385
warning:  Ignored bad PDB record found on line 4386
warning:  Ignored bad PDB record found on line 4387
warning:  Ignored bad PDB record found on line 4388
warning:  Ignored bad PDB record found on line 4389
warning:  Ignored bad PDB record found on line 4390
warning:  Ignored bad PDB record found on line 4391
warning:  Ignored bad PDB record found on line 4392
warning:  Ignored bad PDB record found on line 4393
warning:  Ignored bad PDB record found on line 4394
warning:  Ignored bad PDB record found on line 4395
warning:  Ignored bad PDB record found on line 4396
warning:  Ignored bad PDB record found on line 4397
warning:  Ignored bad PDB record found on line 4398
warning:  Ignored bad PDB record found on line 4399
warning:  Ignored bad PDB record found on line 4400
warning:  Ignored bad PDB record found on line 4401
warning:  Ignored bad PDB record found on line 4402
warning:  Ignored bad PDB record found on line 4403
warning:  Ignored bad PDB record found on line 4404
warning:  Ignored bad PDB record found on line 4405
warning:  Ignored bad PDB record found on line 4406
warning:  Ignored bad PDB record found on line 4407
warning:  Ignored bad PDB record found on line 4408
warning:  Ignored bad PDB record found on line 4409
warning:  Ignored bad PDB record found on line 4410
warning:  Ignored bad PDB record found on line 4411
warning:  Ignored bad PDB record found on line 4412
warning:  Ignored bad PDB record found on line 4413
warning:  Ignored bad PDB record found on line 4414
warning:  Ignored bad PDB record found on line 4415
warning:  Ignored bad PDB record found on line 4416
warning:  Ignored bad PDB record found on line 4417
warning:  Ignored bad PDB record found on line 4418
warning:  Ignored bad PDB record found on line 4419
warning:  Ignored bad PDB record found on line 4420
warning:  Ignored bad PDB record found on line 4421
warning:  Ignored bad PDB record found on line 4422
warning:  Ignored bad PDB record found on line 4423
warning:  Ignored bad PDB record found on line 4424
warning:  Ignored bad PDB record found on line 4425
warning:  Ignored bad PDB record found on line 4426
warning:  Ignored bad PDB record found on line 4427
warning:  Ignored bad PDB record found on line 4428
warning:  Ignored bad PDB record found on line 4429
warning:  Ignored bad PDB record found on line 4430
warning:  Ignored bad PDB record found on line 4431
warning:  Ignored bad PDB record found on line 4432
warning:  Ignored bad PDB record found on line 4433
warning:  Ignored bad PDB record found on line 4434
warning:  Ignored bad PDB record found on line 4435
warning:  Ignored bad PDB record found on line 4436
warning:  Ignored bad PDB record found on line 4437
warning:  Ignored bad PDB record found on line 4438
warning:  Ignored bad PDB record found on line 4439
warning:  Ignored bad PDB record found on line 4440
warning:  Ignored bad PDB record found on line 4441
warning:  Ignored bad PDB record found on line 4442
warning:  Ignored bad PDB record found on line 4443
warning:  Ignored bad PDB record found on line 4444
warning:  Ignored bad PDB record found on line 4445
warning:  Ignored bad PDB record found on line 4446
warning:  Ignored bad PDB record found on line 4447
warning:  Ignored bad PDB record found on line 4448
warning:  Ignored bad PDB record found on line 4449
warning:  Ignored bad PDB record found on line 4450
warning:  Ignored bad PDB record found on line 4451
warning:  Ignored bad PDB record found on line 4452
warning:  Ignored bad PDB record found on line 4453
warning:  Ignored bad PDB record found on line 4454
warning:  Ignored bad PDB record found on line 4455
warning:  Ignored bad PDB record found on line 4456
warning:  Ignored bad PDB record found on line 4457
warning:  Ignored bad PDB record found on line 4458
warning:  Ignored bad PDB record found on line 4459
warning:  Ignored bad PDB record found on line 4460
warning:  Ignored bad PDB record found on line 4461
warning:  Ignored bad PDB record found on line 4462
warning:  Ignored bad PDB record found on line 4463
warning:  Ignored bad PDB record found on line 4464
warning:  Ignored bad PDB record found on line 4465
warning:  Ignored bad PDB record found on line 4466
warning:  Ignored bad PDB record found on line 4467
warning:  Ignored bad PDB record found on line 4468
warning:  Ignored bad PDB record found on line 4469
warning:  Ignored bad PDB record found on line 4470
warning:  Ignored bad PDB record found on line 4471
warning:  Ignored bad PDB record found on line 4472
warning:  Ignored bad PDB record found on line 4473
warning:  Ignored bad PDB record found on line 4474
warning:  Ignored bad PDB record found on line 4475
warning:  Ignored bad PDB record found on line 4476
warning:  Ignored bad PDB record found on line 4477
warning:  Ignored bad PDB record found on line 4478
warning:  Ignored bad PDB record found on line 4479
warning:  Ignored bad PDB record found on line 4480
warning:  Ignored bad PDB record found on line 4481
warning:  Ignored bad PDB record found on line 4482
warning:  Ignored bad PDB record found on line 4483
warning:  Ignored bad PDB record found on line 4484
warning:  Ignored bad PDB record found on line 4485
warning:  Ignored bad PDB record found on line 4486
warning:  Ignored bad PDB record found on line 4487
warning:  Ignored bad PDB record found on line 4488
warning:  Ignored bad PDB record found on line 4489
warning:  Ignored bad PDB record found on line 4490
warning:  Ignored bad PDB record found on line 4491
warning:  Ignored bad PDB record found on line 4492
warning:  Ignored bad PDB record found on line 4493
warning:  Ignored bad PDB record found on line 4494
warning:  Ignored bad PDB record found on line 4495
warning:  Ignored bad PDB record found on line 4496
warning:  Ignored bad PDB record found on line 4497
warning:  Ignored bad PDB record found on line 4498
warning:  Ignored bad PDB record found on line 4499
warning:  Ignored bad PDB record found on line 4500
warning:  Ignored bad PDB record found on line 4501
warning:  Ignored bad PDB record found on line 4502
warning:  Ignored bad PDB record found on line 4503
warning:  Ignored bad PDB record found on line 4504
warning:  Ignored bad PDB record found on line 4505
warning:  Ignored bad PDB record found on line 4506
warning:  Ignored bad PDB record found on line 4507
warning:  Ignored bad PDB record found on line 4508
warning:  Ignored bad PDB record found on line 4509
warning:  Ignored bad PDB record found on line 4510
warning:  Ignored bad PDB record found on line 4511
warning:  Ignored bad PDB record found on line 4512
warning:  Ignored bad PDB record found on line 4513
warning:  Ignored bad PDB record found on line 4514
warning:  Ignored bad PDB record found on line 4515
warning:  Ignored bad PDB record found on line 4516
warning:  Ignored bad PDB record found on line 4517
warning:  Ignored bad PDB record found on line 4518
warning:  Ignored bad PDB record found on line 4519
warning:  Ignored bad PDB record found on line 4520
warning:  Ignored bad PDB record found on line 4521
warning:  Ignored bad PDB record found on line 4522
warning:  Ignored bad PDB record found on line 4523
warning:  Ignored bad PDB record found on line 4524
warning:  Ignored bad PDB record found on line 4525
warning:  Ignored bad PDB record found on line 4526
warning:  Ignored bad PDB record found on line 4527
warning:  Ignored bad PDB record found on line 4528
warning:  Ignored bad PDB record found on line 4529
warning:  Ignored bad PDB record found on line 4530
warning:  Ignored bad PDB record found on line 4531
warning:  Ignored bad PDB record found on line 4532
warning:  Ignored bad PDB record found on line 4533
warning:  Ignored bad PDB record found on line 4534
warning:  Ignored bad PDB record found on line 4535
warning:  Ignored bad PDB record found on line 4536
warning:  Ignored bad PDB record found on line 4537
warning:  Ignored bad PDB record found on line 4538
warning:  Ignored bad PDB record found on line 4539
warning:  Ignored bad PDB record found on line 4540
warning:  Ignored bad PDB record found on line 4541
warning:  Ignored bad PDB record found on line 4542
warning:  Ignored bad PDB record found on line 4543
warning:  Ignored bad PDB record found on line 4544
warning:  Ignored bad PDB record found on line 4545
warning:  Ignored bad PDB record found on line 4546
warning:  Ignored bad PDB record found on line 4547
warning:  Ignored bad PDB record found on line 4548
warning:  Ignored bad PDB record found on line 4549
warning:  Ignored bad PDB record found on line 4550
warning:  Ignored bad PDB record found on line 4551
Model 6 (Schizosaccharomyces japonicus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Streptomyces violaceoruber.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 1515
warning:  Ignored bad PDB record found on line 1516
warning:  Ignored bad PDB record found on line 1517
warning:  Ignored bad PDB record found on line 1518
warning:  Ignored bad PDB record found on line 1519
warning:  Ignored bad PDB record found on line 1520
warning:  Ignored bad PDB record found on line 1521
warning:  Ignored bad PDB record found on line 1522
warning:  Ignored bad PDB record found on line 1523
warning:  Ignored bad PDB record found on line 1524
warning:  Ignored bad PDB record found on line 1525
warning:  Ignored bad PDB record found on line 1526
warning:  Ignored bad PDB record found on line 1527
warning:  Ignored bad PDB record found on line 1528
warning:  Ignored bad PDB record found on line 1529
warning:  Ignored bad PDB record found on line 1530
warning:  Ignored bad PDB record found on line 1531
warning:  Ignored bad PDB record found on line 1532
warning:  Ignored bad PDB record found on line 1533
warning:  Ignored bad PDB record found on line 1534
warning:  Ignored bad PDB record found on line 1535
warning:  Ignored bad PDB record found on line 1536
warning:  Ignored bad PDB record found on line 1537
warning:  Ignored bad PDB record found on line 1538
warning:  Ignored bad PDB record found on line 1539
warning:  Ignored bad PDB record found on line 1540
warning:  Ignored bad PDB record found on line 1541
warning:  Ignored bad PDB record found on line 1542
warning:  Ignored bad PDB record found on line 1543
warning:  Ignored bad PDB record found on line 1544
warning:  Ignored bad PDB record found on line 1545
warning:  Ignored bad PDB record found on line 1546
warning:  Ignored bad PDB record found on line 1547
warning:  Ignored bad PDB record found on line 1548
warning:  Ignored bad PDB record found on line 1549
warning:  Ignored bad PDB record found on line 1550
warning:  Ignored bad PDB record found on line 1551
warning:  Ignored bad PDB record found on line 1552
warning:  Ignored bad PDB record found on line 1553
warning:  Ignored bad PDB record found on line 1554
warning:  Ignored bad PDB record found on line 1555
warning:  Ignored bad PDB record found on line 1556
warning:  Ignored bad PDB record found on line 1557
warning:  Ignored bad PDB record found on line 1558
warning:  Ignored bad PDB record found on line 1559
warning:  Ignored bad PDB record found on line 1560
warning:  Ignored bad PDB record found on line 1561
warning:  Ignored bad PDB record found on line 1562
warning:  Ignored bad PDB record found on line 1563
warning:  Ignored bad PDB record found on line 1564
warning:  Ignored bad PDB record found on line 1565
warning:  Ignored bad PDB record found on line 1566
warning:  Ignored bad PDB record found on line 1567
warning:  Ignored bad PDB record found on line 1568
warning:  Ignored bad PDB record found on line 1569
warning:  Ignored bad PDB record found on line 1570
warning:  Ignored bad PDB record found on line 1571
warning:  Ignored bad PDB record found on line 1572
warning:  Ignored bad PDB record found on line 1573
warning:  Ignored bad PDB record found on line 1574
warning:  Ignored bad PDB record found on line 1575
warning:  Ignored bad PDB record found on line 1576
warning:  Ignored bad PDB record found on line 1577
warning:  Ignored bad PDB record found on line 1578
warning:  Ignored bad PDB record found on line 1579
warning:  Ignored bad PDB record found on line 1580
warning:  Ignored bad PDB record found on line 1581
warning:  Ignored bad PDB record found on line 1582
warning:  Ignored bad PDB record found on line 1583
warning:  Ignored bad PDB record found on line 1584
warning:  Ignored bad PDB record found on line 1585
warning:  Ignored bad PDB record found on line 1586
warning:  Ignored bad PDB record found on line 1587
warning:  Ignored bad PDB record found on line 1588
warning:  Ignored bad PDB record found on line 1589
warning:  Ignored bad PDB record found on line 1590
warning:  Ignored bad PDB record found on line 1591
Model 7 (Streptomyces violaceoruber.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Struthio camelus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 242
warning:  Ignored bad PDB record found on line 243
warning:  Ignored bad PDB record found on line 244
warning:  Ignored bad PDB record found on line 245
warning:  Ignored bad PDB record found on line 246
warning:  Ignored bad PDB record found on line 247
warning:  Ignored bad PDB record found on line 248
warning:  Ignored bad PDB record found on line 249
warning:  Ignored bad PDB record found on line 250
warning:  Ignored bad PDB record found on line 251
warning:  Ignored bad PDB record found on line 252
warning:  Ignored bad PDB record found on line 253
warning:  Ignored bad PDB record found on line 254
warning:  Ignored bad PDB record found on line 255
warning:  Ignored bad PDB record found on line 256
warning:  Ignored bad PDB record found on line 257
warning:  Ignored bad PDB record found on line 258
warning:  Ignored bad PDB record found on line 259
warning:  Ignored bad PDB record found on line 260
warning:  Ignored bad PDB record found on line 261
warning:  Ignored bad PDB record found on line 262
warning:  Ignored bad PDB record found on line 263
warning:  Ignored bad PDB record found on line 264
warning:  Ignored bad PDB record found on line 265
warning:  Ignored bad PDB record found on line 266
warning:  Ignored bad PDB record found on line 267
Model 8 (Struthio camelus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Trichoderma koningii.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 5628
warning:  Ignored bad PDB record found on line 5629
warning:  Ignored bad PDB record found on line 5630
warning:  Ignored bad PDB record found on line 5631
warning:  Ignored bad PDB record found on line 5632
warning:  Ignored bad PDB record found on line 5633
warning:  Ignored bad PDB record found on line 5634
warning:  Ignored bad PDB record found on line 5635
warning:  Ignored bad PDB record found on line 5636
warning:  Ignored bad PDB record found on line 5637
warning:  Ignored bad PDB record found on line 5638
warning:  Ignored bad PDB record found on line 5639
warning:  Ignored bad PDB record found on line 5640
warning:  Ignored bad PDB record found on line 5641
warning:  Ignored bad PDB record found on line 5642
warning:  Ignored bad PDB record found on line 5643
warning:  Ignored bad PDB record found on line 5644
warning:  Ignored bad PDB record found on line 5645
warning:  Ignored bad PDB record found on line 5646
warning:  Ignored bad PDB record found on line 5647
warning:  Ignored bad PDB record found on line 5648
warning:  Ignored bad PDB record found on line 5649
warning:  Ignored bad PDB record found on line 5650
warning:  Ignored bad PDB record found on line 5651
warning:  Ignored bad PDB record found on line 5652
warning:  Ignored bad PDB record found on line 5653
warning:  Ignored bad PDB record found on line 5654
warning:  Ignored bad PDB record found on line 5655
warning:  Ignored bad PDB record found on line 5656
warning:  Ignored bad PDB record found on line 5657
warning:  Ignored bad PDB record found on line 5658
warning:  Ignored bad PDB record found on line 5659
warning:  Ignored bad PDB record found on line 5660
warning:  Ignored bad PDB record found on line 5661
warning:  Ignored bad PDB record found on line 5662
warning:  Ignored bad PDB record found on line 5663
warning:  Ignored bad PDB record found on line 5664
warning:  Ignored bad PDB record found on line 5665
warning:  Ignored bad PDB record found on line 5666
warning:  Ignored bad PDB record found on line 5667
warning:  Ignored bad PDB record found on line 5668
warning:  Ignored bad PDB record found on line 5669
warning:  Ignored bad PDB record found on line 5670
warning:  Ignored bad PDB record found on line 5671
warning:  Ignored bad PDB record found on line 5672
warning:  Ignored bad PDB record found on line 5673
warning:  Ignored bad PDB record found on line 5674
warning:  Ignored bad PDB record found on line 5675
warning:  Ignored bad PDB record found on line 5676
warning:  Ignored bad PDB record found on line 5677
warning:  Ignored bad PDB record found on line 5678
warning:  Ignored bad PDB record found on line 5679
warning:  Ignored bad PDB record found on line 5680
warning:  Ignored bad PDB record found on line 5681
warning:  Ignored bad PDB record found on line 5682
warning:  Ignored bad PDB record found on line 5683
warning:  Ignored bad PDB record found on line 5684
warning:  Ignored bad PDB record found on line 5685
warning:  Ignored bad PDB record found on line 5686
warning:  Ignored bad PDB record found on line 5687
warning:  Ignored bad PDB record found on line 5688
warning:  Ignored bad PDB record found on line 5689
warning:  Ignored bad PDB record found on line 5690
warning:  Ignored bad PDB record found on line 5691
warning:  Ignored bad PDB record found on line 5692
warning:  Ignored bad PDB record found on line 5693
warning:  Ignored bad PDB record found on line 5694
warning:  Ignored bad PDB record found on line 5695
warning:  Ignored bad PDB record found on line 5696
warning:  Ignored bad PDB record found on line 5697
warning:  Ignored bad PDB record found on line 5698
warning:  Ignored bad PDB record found on line 5699
warning:  Ignored bad PDB record found on line 5700
warning:  Ignored bad PDB record found on line 5701
warning:  Ignored bad PDB record found on line 5702
warning:  Ignored bad PDB record found on line 5703
warning:  Ignored bad PDB record found on line 5704
warning:  Ignored bad PDB record found on line 5705
warning:  Ignored bad PDB record found on line 5706
warning:  Ignored bad PDB record found on line 5707
warning:  Ignored bad PDB record found on line 5708
warning:  Ignored bad PDB record found on line 5709
warning:  Ignored bad PDB record found on line 5710
warning:  Ignored bad PDB record found on line 5711
warning:  Ignored bad PDB record found on line 5712
warning:  Ignored bad PDB record found on line 5713
warning:  Ignored bad PDB record found on line 5714
warning:  Ignored bad PDB record found on line 5715
warning:  Ignored bad PDB record found on line 5716
warning:  Ignored bad PDB record found on line 5717
warning:  Ignored bad PDB record found on line 5718
warning:  Ignored bad PDB record found on line 5719
warning:  Ignored bad PDB record found on line 5720
warning:  Ignored bad PDB record found on line 5721
warning:  Ignored bad PDB record found on line 5722
warning:  Ignored bad PDB record found on line 5723
warning:  Ignored bad PDB record found on line 5724
warning:  Ignored bad PDB record found on line 5725
warning:  Ignored bad PDB record found on line 5726
warning:  Ignored bad PDB record found on line 5727
warning:  Ignored bad PDB record found on line 5728
warning:  Ignored bad PDB record found on line 5729
warning:  Ignored bad PDB record found on line 5730
warning:  Ignored bad PDB record found on line 5731
warning:  Ignored bad PDB record found on line 5732
warning:  Ignored bad PDB record found on line 5733
warning:  Ignored bad PDB record found on line 5734
warning:  Ignored bad PDB record found on line 5735
warning:  Ignored bad PDB record found on line 5736
warning:  Ignored bad PDB record found on line 5737
warning:  Ignored bad PDB record found on line 5738
warning:  Ignored bad PDB record found on line 5739
warning:  Ignored bad PDB record found on line 5740
warning:  Ignored bad PDB record found on line 5741
warning:  Ignored bad PDB record found on line 5742
warning:  Ignored bad PDB record found on line 5743
warning:  Ignored bad PDB record found on line 5744
warning:  Ignored bad PDB record found on line 5745
warning:  Ignored bad PDB record found on line 5746
warning:  Ignored bad PDB record found on line 5747
warning:  Ignored bad PDB record found on line 5748
warning:  Ignored bad PDB record found on line 5749
warning:  Ignored bad PDB record found on line 5750
warning:  Ignored bad PDB record found on line 5751
warning:  Ignored bad PDB record found on line 5752
warning:  Ignored bad PDB record found on line 5753
warning:  Ignored bad PDB record found on line 5754
warning:  Ignored bad PDB record found on line 5755
warning:  Ignored bad PDB record found on line 5756
warning:  Ignored bad PDB record found on line 5757
warning:  Ignored bad PDB record found on line 5758
warning:  Ignored bad PDB record found on line 5759
warning:  Ignored bad PDB record found on line 5760
warning:  Ignored bad PDB record found on line 5761
warning:  Ignored bad PDB record found on line 5762
warning:  Ignored bad PDB record found on line 5763
warning:  Ignored bad PDB record found on line 5764
warning:  Ignored bad PDB record found on line 5765
warning:  Ignored bad PDB record found on line 5766
warning:  Ignored bad PDB record found on line 5767
warning:  Ignored bad PDB record found on line 5768
warning:  Ignored bad PDB record found on line 5769
warning:  Ignored bad PDB record found on line 5770
warning:  Ignored bad PDB record found on line 5771
warning:  Ignored bad PDB record found on line 5772
warning:  Ignored bad PDB record found on line 5773
warning:  Ignored bad PDB record found on line 5774
warning:  Ignored bad PDB record found on line 5775
warning:  Ignored bad PDB record found on line 5776
warning:  Ignored bad PDB record found on line 5777
warning:  Ignored bad PDB record found on line 5778
warning:  Ignored bad PDB record found on line 5779
warning:  Ignored bad PDB record found on line 5780
warning:  Ignored bad PDB record found on line 5781
warning:  Ignored bad PDB record found on line 5782
warning:  Ignored bad PDB record found on line 5783
warning:  Ignored bad PDB record found on line 5784
warning:  Ignored bad PDB record found on line 5785
warning:  Ignored bad PDB record found on line 5786
warning:  Ignored bad PDB record found on line 5787
warning:  Ignored bad PDB record found on line 5788
warning:  Ignored bad PDB record found on line 5789
warning:  Ignored bad PDB record found on line 5790
warning:  Ignored bad PDB record found on line 5791
warning:  Ignored bad PDB record found on line 5792
warning:  Ignored bad PDB record found on line 5793
warning:  Ignored bad PDB record found on line 5794
warning:  Ignored bad PDB record found on line 5795
warning:  Ignored bad PDB record found on line 5796
warning:  Ignored bad PDB record found on line 5797
warning:  Ignored bad PDB record found on line 5798
warning:  Ignored bad PDB record found on line 5799
warning:  Ignored bad PDB record found on line 5800
warning:  Ignored bad PDB record found on line 5801
warning:  Ignored bad PDB record found on line 5802
warning:  Ignored bad PDB record found on line 5803
warning:  Ignored bad PDB record found on line 5804
warning:  Ignored bad PDB record found on line 5805
warning:  Ignored bad PDB record found on line 5806
warning:  Ignored bad PDB record found on line 5807
warning:  Ignored bad PDB record found on line 5808
warning:  Ignored bad PDB record found on line 5809
warning:  Ignored bad PDB record found on line 5810
warning:  Ignored bad PDB record found on line 5811
warning:  Ignored bad PDB record found on line 5812
warning:  Ignored bad PDB record found on line 5813
warning:  Ignored bad PDB record found on line 5814
warning:  Ignored bad PDB record found on line 5815
warning:  Ignored bad PDB record found on line 5816
warning:  Ignored bad PDB record found on line 5817
warning:  Ignored bad PDB record found on line 5818
warning:  Ignored bad PDB record found on line 5819
warning:  Ignored bad PDB record found on line 5820
warning:  Ignored bad PDB record found on line 5821
warning:  Ignored bad PDB record found on line 5822
warning:  Ignored bad PDB record found on line 5823
warning:  Ignored bad PDB record found on line 5824
warning:  Ignored bad PDB record found on line 5825
warning:  Ignored bad PDB record found on line 5826
warning:  Ignored bad PDB record found on line 5827
warning:  Ignored bad PDB record found on line 5828
warning:  Ignored bad PDB record found on line 5829
warning:  Ignored bad PDB record found on line 5830
warning:  Ignored bad PDB record found on line 5831
warning:  Ignored bad PDB record found on line 5832
warning:  Ignored bad PDB record found on line 5833
warning:  Ignored bad PDB record found on line 5834
warning:  Ignored bad PDB record found on line 5835
warning:  Ignored bad PDB record found on line 5836
warning:  Ignored bad PDB record found on line 5837
warning:  Ignored bad PDB record found on line 5838
warning:  Ignored bad PDB record found on line 5839
warning:  Ignored bad PDB record found on line 5840
warning:  Ignored bad PDB record found on line 5841
warning:  Ignored bad PDB record found on line 5842
warning:  Ignored bad PDB record found on line 5843
warning:  Ignored bad PDB record found on line 5844
warning:  Ignored bad PDB record found on line 5845
warning:  Ignored bad PDB record found on line 5846
warning:  Ignored bad PDB record found on line 5847
warning:  Ignored bad PDB record found on line 5848
warning:  Ignored bad PDB record found on line 5849
warning:  Ignored bad PDB record found on line 5850
warning:  Ignored bad PDB record found on line 5851
warning:  Ignored bad PDB record found on line 5852
warning:  Ignored bad PDB record found on line 5853
warning:  Ignored bad PDB record found on line 5854
warning:  Ignored bad PDB record found on line 5855
warning:  Ignored bad PDB record found on line 5856
warning:  Ignored bad PDB record found on line 5857
warning:  Ignored bad PDB record found on line 5858
warning:  Ignored bad PDB record found on line 5859
warning:  Ignored bad PDB record found on line 5860
warning:  Ignored bad PDB record found on line 5861
warning:  Ignored bad PDB record found on line 5862
warning:  Ignored bad PDB record found on line 5863
warning:  Ignored bad PDB record found on line 5864
warning:  Ignored bad PDB record found on line 5865
warning:  Ignored bad PDB record found on line 5866
warning:  Ignored bad PDB record found on line 5867
warning:  Ignored bad PDB record found on line 5868
warning:  Ignored bad PDB record found on line 5869
warning:  Ignored bad PDB record found on line 5870
warning:  Ignored bad PDB record found on line 5871
warning:  Ignored bad PDB record found on line 5872
warning:  Ignored bad PDB record found on line 5873
Model 9 (Trichoderma koningii.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Zea mayS.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 1581
warning:  Ignored bad PDB record found on line 1582
warning:  Ignored bad PDB record found on line 1583
warning:  Ignored bad PDB record found on line 1584
warning:  Ignored bad PDB record found on line 1585
warning:  Ignored bad PDB record found on line 1586
warning:  Ignored bad PDB record found on line 1587
warning:  Ignored bad PDB record found on line 1588
warning:  Ignored bad PDB record found on line 1589
warning:  Ignored bad PDB record found on line 1590
warning:  Ignored bad PDB record found on line 1591
warning:  Ignored bad PDB record found on line 1592
warning:  Ignored bad PDB record found on line 1593
warning:  Ignored bad PDB record found on line 1594
warning:  Ignored bad PDB record found on line 1595
warning:  Ignored bad PDB record found on line 1596
warning:  Ignored bad PDB record found on line 1597
warning:  Ignored bad PDB record found on line 1598
warning:  Ignored bad PDB record found on line 1599
warning:  Ignored bad PDB record found on line 1600
warning:  Ignored bad PDB record found on line 1601
warning:  Ignored bad PDB record found on line 1602
warning:  Ignored bad PDB record found on line 1603
warning:  Ignored bad PDB record found on line 1604
warning:  Ignored bad PDB record found on line 1605
warning:  Ignored bad PDB record found on line 1606
warning:  Ignored bad PDB record found on line 1607
warning:  Ignored bad PDB record found on line 1608
warning:  Ignored bad PDB record found on line 1609
warning:  Ignored bad PDB record found on line 1610
warning:  Ignored bad PDB record found on line 1611
warning:  Ignored bad PDB record found on line 1612
warning:  Ignored bad PDB record found on line 1613
warning:  Ignored bad PDB record found on line 1614
warning:  Ignored bad PDB record found on line 1615
warning:  Ignored bad PDB record found on line 1616
warning:  Ignored bad PDB record found on line 1617
warning:  Ignored bad PDB record found on line 1618
warning:  Ignored bad PDB record found on line 1619
warning:  Ignored bad PDB record found on line 1620
warning:  Ignored bad PDB record found on line 1621
warning:  Ignored bad PDB record found on line 1622
warning:  Ignored bad PDB record found on line 1623
warning:  Ignored bad PDB record found on line 1624
warning:  Ignored bad PDB record found on line 1625
warning:  Ignored bad PDB record found on line 1626
warning:  Ignored bad PDB record found on line 1627
warning:  Ignored bad PDB record found on line 1628
warning:  Ignored bad PDB record found on line 1629
warning:  Ignored bad PDB record found on line 1630
warning:  Ignored bad PDB record found on line 1631
warning:  Ignored bad PDB record found on line 1632
warning:  Ignored bad PDB record found on line 1633
warning:  Ignored bad PDB record found on line 1634
warning:  Ignored bad PDB record found on line 1635
warning:  Ignored bad PDB record found on line 1636
warning:  Ignored bad PDB record found on line 1637
warning:  Ignored bad PDB record found on line 1638
warning:  Ignored bad PDB record found on line 1639
warning:  Ignored bad PDB record found on line 1640
warning:  Ignored bad PDB record found on line 1641
warning:  Ignored bad PDB record found on line 1642
warning:  Ignored bad PDB record found on line 1643
warning:  Ignored bad PDB record found on line 1644
warning:  Ignored bad PDB record found on line 1645
warning:  Ignored bad PDB record found on line 1646
warning:  Ignored bad PDB record found on line 1647
warning:  Ignored bad PDB record found on line 1648
warning:  Ignored bad PDB record found on line 1649
warning:  Ignored bad PDB record found on line 1650
warning:  Ignored bad PDB record found on line 1651
warning:  Ignored bad PDB record found on line 1652
warning:  Ignored bad PDB record found on line 1653
warning:  Ignored bad PDB record found on line 1654
warning:  Ignored bad PDB record found on line 1655
warning:  Ignored bad PDB record found on line 1656
warning:  Ignored bad PDB record found on line 1657
warning:  Ignored bad PDB record found on line 1658
warning:  Ignored bad PDB record found on line 1659
warning:  Ignored bad PDB record found on line 1660
warning:  Ignored bad PDB record found on line 1661
warning:  Ignored bad PDB record found on line 1662
warning:  Ignored bad PDB record found on line 1663
warning:  Ignored bad PDB record found on line 1664
Model 10 (Zea mayS.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Model 11 (Bitis gabonica.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Model 12 (Bothrops jararaca.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Model 13 (Cerrophidion godmani.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Model 14 (Echis carinatus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Micrurus corallinus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 1436
warning:  Ignored bad PDB record found on line 1437
warning:  Ignored bad PDB record found on line 1438
warning:  Ignored bad PDB record found on line 1439
warning:  Ignored bad PDB record found on line 1440
warning:  Ignored bad PDB record found on line 1441
warning:  Ignored bad PDB record found on line 1442
warning:  Ignored bad PDB record found on line 1443
warning:  Ignored bad PDB record found on line 1444
warning:  Ignored bad PDB record found on line 1445
warning:  Ignored bad PDB record found on line 1446
warning:  Ignored bad PDB record found on line 1447
warning:  Ignored bad PDB record found on line 1448
warning:  Ignored bad PDB record found on line 1449
warning:  Ignored bad PDB record found on line 1450
warning:  Ignored bad PDB record found on line 1451
warning:  Ignored bad PDB record found on line 1452
warning:  Ignored bad PDB record found on line 1453
warning:  Ignored bad PDB record found on line 1454
warning:  Ignored bad PDB record found on line 1455
warning:  Ignored bad PDB record found on line 1456
warning:  Ignored bad PDB record found on line 1457
warning:  Ignored bad PDB record found on line 1458
warning:  Ignored bad PDB record found on line 1459
warning:  Ignored bad PDB record found on line 1460
warning:  Ignored bad PDB record found on line 1461
warning:  Ignored bad PDB record found on line 1462
warning:  Ignored bad PDB record found on line 1463
warning:  Ignored bad PDB record found on line 1464
warning:  Ignored bad PDB record found on line 1465
warning:  Ignored bad PDB record found on line 1466
warning:  Ignored bad PDB record found on line 1467
warning:  Ignored bad PDB record found on line 1468
warning:  Ignored bad PDB record found on line 1469
warning:  Ignored bad PDB record found on line 1470
warning:  Ignored bad PDB record found on line 1471
warning:  Ignored bad PDB record found on line 1472
warning:  Ignored bad PDB record found on line 1473
warning:  Ignored bad PDB record found on line 1474
warning:  Ignored bad PDB record found on line 1475
warning:  Ignored bad PDB record found on line 1476
warning:  Ignored bad PDB record found on line 1477
warning:  Ignored bad PDB record found on line 1478
warning:  Ignored bad PDB record found on line 1479
warning:  Ignored bad PDB record found on line 1480
warning:  Ignored bad PDB record found on line 1481
warning:  Ignored bad PDB record found on line 1482
warning:  Ignored bad PDB record found on line 1483
warning:  Ignored bad PDB record found on line 1484
warning:  Ignored bad PDB record found on line 1485
warning:  Ignored bad PDB record found on line 1486
warning:  Ignored bad PDB record found on line 1487
warning:  Ignored bad PDB record found on line 1488
warning:  Ignored bad PDB record found on line 1489
warning:  Ignored bad PDB record found on line 1490
warning:  Ignored bad PDB record found on line 1491
warning:  Ignored bad PDB record found on line 1492
warning:  Ignored bad PDB record found on line 1493
warning:  Ignored bad PDB record found on line 1494
warning:  Ignored bad PDB record found on line 1495
warning:  Ignored bad PDB record found on line 1496
warning:  Ignored bad PDB record found on line 1497
warning:  Ignored bad PDB record found on line 1498
warning:  Ignored bad PDB record found on line 1499
warning:  Ignored bad PDB record found on line 1500
warning:  Ignored bad PDB record found on line 1501
warning:  Ignored bad PDB record found on line 1502
warning:  Ignored bad PDB record found on line 1503
warning:  Ignored bad PDB record found on line 1504
warning:  Ignored bad PDB record found on line 1505
warning:  Ignored bad PDB record found on line 1506
warning:  Ignored bad PDB record found on line 1507
warning:  Ignored bad PDB record found on line 1508
warning:  Ignored bad PDB record found on line 1509
warning:  Ignored bad PDB record found on line 1510
Model 15 (Micrurus corallinus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Notechis scutatus scutatus.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 1419
warning:  Ignored bad PDB record found on line 1420
warning:  Ignored bad PDB record found on line 1421
warning:  Ignored bad PDB record found on line 1422
warning:  Ignored bad PDB record found on line 1423
warning:  Ignored bad PDB record found on line 1424
warning:  Ignored bad PDB record found on line 1425
warning:  Ignored bad PDB record found on line 1426
warning:  Ignored bad PDB record found on line 1427
warning:  Ignored bad PDB record found on line 1428
warning:  Ignored bad PDB record found on line 1429
warning:  Ignored bad PDB record found on line 1430
warning:  Ignored bad PDB record found on line 1431
warning:  Ignored bad PDB record found on line 1432
warning:  Ignored bad PDB record found on line 1433
warning:  Ignored bad PDB record found on line 1434
warning:  Ignored bad PDB record found on line 1435
warning:  Ignored bad PDB record found on line 1436
warning:  Ignored bad PDB record found on line 1437
warning:  Ignored bad PDB record found on line 1438
warning:  Ignored bad PDB record found on line 1439
warning:  Ignored bad PDB record found on line 1440
warning:  Ignored bad PDB record found on line 1441
warning:  Ignored bad PDB record found on line 1442
warning:  Ignored bad PDB record found on line 1443
warning:  Ignored bad PDB record found on line 1444
warning:  Ignored bad PDB record found on line 1445
warning:  Ignored bad PDB record found on line 1446
warning:  Ignored bad PDB record found on line 1447
warning:  Ignored bad PDB record found on line 1448
warning:  Ignored bad PDB record found on line 1449
warning:  Ignored bad PDB record found on line 1450
warning:  Ignored bad PDB record found on line 1451
warning:  Ignored bad PDB record found on line 1452
warning:  Ignored bad PDB record found on line 1453
warning:  Ignored bad PDB record found on line 1454
warning:  Ignored bad PDB record found on line 1455
warning:  Ignored bad PDB record found on line 1456
warning:  Ignored bad PDB record found on line 1457
warning:  Ignored bad PDB record found on line 1458
warning:  Ignored bad PDB record found on line 1459
warning:  Ignored bad PDB record found on line 1460
warning:  Ignored bad PDB record found on line 1461
warning:  Ignored bad PDB record found on line 1462
warning:  Ignored bad PDB record found on line 1463
warning:  Ignored bad PDB record found on line 1464
warning:  Ignored bad PDB record found on line 1465
warning:  Ignored bad PDB record found on line 1466
warning:  Ignored bad PDB record found on line 1467
warning:  Ignored bad PDB record found on line 1468
warning:  Ignored bad PDB record found on line 1469
warning:  Ignored bad PDB record found on line 1470
warning:  Ignored bad PDB record found on line 1471
warning:  Ignored bad PDB record found on line 1472
warning:  Ignored bad PDB record found on line 1473
warning:  Ignored bad PDB record found on line 1474
warning:  Ignored bad PDB record found on line 1475
warning:  Ignored bad PDB record found on line 1476
warning:  Ignored bad PDB record found on line 1477
warning:  Ignored bad PDB record found on line 1478
warning:  Ignored bad PDB record found on line 1479
warning:  Ignored bad PDB record found on line 1480
warning:  Ignored bad PDB record found on line 1481
warning:  Ignored bad PDB record found on line 1482
warning:  Ignored bad PDB record found on line 1483
warning:  Ignored bad PDB record found on line 1484
warning:  Ignored bad PDB record found on line 1485
warning:  Ignored bad PDB record found on line 1486
warning:  Ignored bad PDB record found on line 1487
warning:  Ignored bad PDB record found on line 1488
warning:  Ignored bad PDB record found on line 1489
warning:  Ignored bad PDB record found on line 1490
warning:  Ignored bad PDB record found on line 1491
warning:  Ignored bad PDB record found on line 1492
warning:  Ignored bad PDB record found on line 1493
Model 17 (Notechis scutatus scutatus.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Ophiophagus hannah.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 1459
warning:  Ignored bad PDB record found on line 1460
warning:  Ignored bad PDB record found on line 1461
warning:  Ignored bad PDB record found on line 1462
warning:  Ignored bad PDB record found on line 1463
warning:  Ignored bad PDB record found on line 1464
warning:  Ignored bad PDB record found on line 1465
warning:  Ignored bad PDB record found on line 1466
warning:  Ignored bad PDB record found on line 1467
warning:  Ignored bad PDB record found on line 1468
warning:  Ignored bad PDB record found on line 1469
warning:  Ignored bad PDB record found on line 1470
warning:  Ignored bad PDB record found on line 1471
warning:  Ignored bad PDB record found on line 1472
warning:  Ignored bad PDB record found on line 1473
warning:  Ignored bad PDB record found on line 1474
warning:  Ignored bad PDB record found on line 1475
warning:  Ignored bad PDB record found on line 1476
warning:  Ignored bad PDB record found on line 1477
warning:  Ignored bad PDB record found on line 1478
warning:  Ignored bad PDB record found on line 1479
warning:  Ignored bad PDB record found on line 1480
warning:  Ignored bad PDB record found on line 1481
warning:  Ignored bad PDB record found on line 1482
warning:  Ignored bad PDB record found on line 1483
warning:  Ignored bad PDB record found on line 1484
warning:  Ignored bad PDB record found on line 1485
warning:  Ignored bad PDB record found on line 1486
warning:  Ignored bad PDB record found on line 1487
warning:  Ignored bad PDB record found on line 1488
warning:  Ignored bad PDB record found on line 1489
warning:  Ignored bad PDB record found on line 1490
warning:  Ignored bad PDB record found on line 1491
warning:  Ignored bad PDB record found on line 1492
warning:  Ignored bad PDB record found on line 1493
warning:  Ignored bad PDB record found on line 1494
warning:  Ignored bad PDB record found on line 1495
warning:  Ignored bad PDB record found on line 1496
warning:  Ignored bad PDB record found on line 1497
warning:  Ignored bad PDB record found on line 1498
warning:  Ignored bad PDB record found on line 1499
warning:  Ignored bad PDB record found on line 1500
warning:  Ignored bad PDB record found on line 1501
warning:  Ignored bad PDB record found on line 1502
warning:  Ignored bad PDB record found on line 1503
warning:  Ignored bad PDB record found on line 1504
warning:  Ignored bad PDB record found on line 1505
warning:  Ignored bad PDB record found on line 1506
warning:  Ignored bad PDB record found on line 1507
warning:  Ignored bad PDB record found on line 1508
warning:  Ignored bad PDB record found on line 1509
warning:  Ignored bad PDB record found on line 1510
warning:  Ignored bad PDB record found on line 1511
warning:  Ignored bad PDB record found on line 1512
warning:  Ignored bad PDB record found on line 1513
warning:  Ignored bad PDB record found on line 1514
warning:  Ignored bad PDB record found on line 1515
warning:  Ignored bad PDB record found on line 1516
warning:  Ignored bad PDB record found on line 1517
warning:  Ignored bad PDB record found on line 1518
warning:  Ignored bad PDB record found on line 1519
warning:  Ignored bad PDB record found on line 1520
warning:  Ignored bad PDB record found on line 1521
warning:  Ignored bad PDB record found on line 1522
warning:  Ignored bad PDB record found on line 1523
warning:  Ignored bad PDB record found on line 1524
warning:  Ignored bad PDB record found on line 1525
warning:  Ignored bad PDB record found on line 1526
warning:  Ignored bad PDB record found on line 1527
warning:  Ignored bad PDB record found on line 1528
warning:  Ignored bad PDB record found on line 1529
warning:  Ignored bad PDB record found on line 1530
warning:  Ignored bad PDB record found on line 1531
warning:  Ignored bad PDB record found on line 1532
warning:  Ignored bad PDB record found on line 1533
warning:  Ignored bad PDB record found on line 1534
warning:  Ignored bad PDB record found on line 1535
warning:  Ignored bad PDB record found on line 1536
Model 18 (Ophiophagus hannah.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
The following problems occurred while reading PDB file for Trimeresurus elegans.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 1381
warning:  Ignored bad PDB record found on line 1382
warning:  Ignored bad PDB record found on line 1383
warning:  Ignored bad PDB record found on line 1384
warning:  Ignored bad PDB record found on line 1385
warning:  Ignored bad PDB record found on line 1386
warning:  Ignored bad PDB record found on line 1387
warning:  Ignored bad PDB record found on line 1388
warning:  Ignored bad PDB record found on line 1389
warning:  Ignored bad PDB record found on line 1390
warning:  Ignored bad PDB record found on line 1391
warning:  Ignored bad PDB record found on line 1392
warning:  Ignored bad PDB record found on line 1393
warning:  Ignored bad PDB record found on line 1394
warning:  Ignored bad PDB record found on line 1395
warning:  Ignored bad PDB record found on line 1396
warning:  Ignored bad PDB record found on line 1397
warning:  Ignored bad PDB record found on line 1398
warning:  Ignored bad PDB record found on line 1399
warning:  Ignored bad PDB record found on line 1400
warning:  Ignored bad PDB record found on line 1401
warning:  Ignored bad PDB record found on line 1402
warning:  Ignored bad PDB record found on line 1403
warning:  Ignored bad PDB record found on line 1404
warning:  Ignored bad PDB record found on line 1405
warning:  Ignored bad PDB record found on line 1406
warning:  Ignored bad PDB record found on line 1407
warning:  Ignored bad PDB record found on line 1408
warning:  Ignored bad PDB record found on line 1409
warning:  Ignored bad PDB record found on line 1410
warning:  Ignored bad PDB record found on line 1411
warning:  Ignored bad PDB record found on line 1412
warning:  Ignored bad PDB record found on line 1413
warning:  Ignored bad PDB record found on line 1414
warning:  Ignored bad PDB record found on line 1415
warning:  Ignored bad PDB record found on line 1416
warning:  Ignored bad PDB record found on line 1417
warning:  Ignored bad PDB record found on line 1418
warning:  Ignored bad PDB record found on line 1419
warning:  Ignored bad PDB record found on line 1420
warning:  Ignored bad PDB record found on line 1421
warning:  Ignored bad PDB record found on line 1422
warning:  Ignored bad PDB record found on line 1423
warning:  Ignored bad PDB record found on line 1424
warning:  Ignored bad PDB record found on line 1425
warning:  Ignored bad PDB record found on line 1426
warning:  Ignored bad PDB record found on line 1427
warning:  Ignored bad PDB record found on line 1428
warning:  Ignored bad PDB record found on line 1429
warning:  Ignored bad PDB record found on line 1430
warning:  Ignored bad PDB record found on line 1431
warning:  Ignored bad PDB record found on line 1432
warning:  Ignored bad PDB record found on line 1433
warning:  Ignored bad PDB record found on line 1434
warning:  Ignored bad PDB record found on line 1435
warning:  Ignored bad PDB record found on line 1436
warning:  Ignored bad PDB record found on line 1437
warning:  Ignored bad PDB record found on line 1438
warning:  Ignored bad PDB record found on line 1439
warning:  Ignored bad PDB record found on line 1440
warning:  Ignored bad PDB record found on line 1441
warning:  Ignored bad PDB record found on line 1442
warning:  Ignored bad PDB record found on line 1443
warning:  Ignored bad PDB record found on line 1444
warning:  Ignored bad PDB record found on line 1445
warning:  Ignored bad PDB record found on line 1446
warning:  Ignored bad PDB record found on line 1447
warning:  Ignored bad PDB record found on line 1448
warning:  Ignored bad PDB record found on line 1449
warning:  Ignored bad PDB record found on line 1450
warning:  Ignored bad PDB record found on line 1451
Model 19 (Trimeresurus elegans.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Match?Align cutoff: 5.0, in column if within cutoff of: any
Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures
Match?Align cutoff: 5.0, in column if within cutoff of: any
Cannot generate alignment with Bitis gabonica.pdb principal chain because it is not superimposed on the other structures
Computing secondary structure assignments for model(s) #11, #0
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #1
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #2
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #3
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #4
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #5
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #6
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #7
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #8
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #9
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #10
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #12
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #13
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #14
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #15
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #16
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #17
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #18
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Computing secondary structure assignments for model(s) #19
using ksdssp (Kabsch and Sander Define Secondary Structure
of Proteins) with the parameters:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
match Bitis gabonica.pdb (#11) with Homo sapiens.pdb, chain A (#3), score = 399.8

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 85 atom pairs is 0.998 angstroms

match Bitis gabonica.pdb (#11) with Streptomyces violaceoruber.pdb (#7), score = 98.2

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 9 atom pairs is 1.646 angstroms

match Bitis gabonica.pdb (#11) with Bothrops jararaca.pdb (#12), score = 545

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 89 atom pairs is 0.850 angstroms

match Bitis gabonica.pdb (#11) with Mirabilis jalapa.pdb (#5), score = 158.8

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 35 atom pairs is 0.530 angstroms

match Bitis gabonica.pdb (#11) with Schizosaccharomyces japonicus.pdb, chain A (#6), score = 102.9

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 8 atom pairs is 1.453 angstroms

match Bitis gabonica.pdb (#11) with Micrurus corallinus.pdb (#15), score = 394.3

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 93 atom pairs is 0.782 angstroms

match Bitis gabonica.pdb (#11) with Zea mayS.pdb, chain A (#10), score = 178.8

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 22 atom pairs is 0.426 angstroms

match Bitis gabonica.pdb (#11) with Trichoderma koningii.pdb, chain A (#9), score = 75.5

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 4 atom pairs is 1.272 angstroms

match Bitis gabonica.pdb (#11) with Struthio camelus.pdb (#8), score = 41.8

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 13 atom pairs is 1.051 angstroms

match Bitis gabonica.pdb (#11) with Culex quinquefasciatus.pdb, chain A (#1), score = 162.7

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 27 atom pairs is 0.536 angstroms

match Bitis gabonica.pdb (#11) with Ophiophagus hannah.pdb (#18), score = 408.9

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 89 atom pairs is 0.747 angstroms

match Bitis gabonica.pdb (#11) with Trimeresurus elegans.pdb (#19), score = 518.4

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 96 atom pairs is 0.832 angstroms

match Bitis gabonica.pdb (#11) with Asterina pectinifera-YET.pdb, chain A (#0), score = 409.3

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 86 atom pairs is 0.909 angstroms

match Bitis gabonica.pdb (#11) with Echis carinatus.pdb (#14), score = 519.9

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 102 atom pairs is 0.792 angstroms

match Bitis gabonica.pdb (#11) with Notechis scutatus scutatus.pdb (#17), score = 424.4

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 84 atom pairs is 0.750 angstroms

match Bitis gabonica.pdb (#11) with Mesobuthus tamulus.pdb, chain A (#4), score = 182.4

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 32 atom pairs is 0.688 angstroms

match Bitis gabonica.pdb (#11) with Naja naja.pdb, chain A (#16), score = 463.6

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 89 atom pairs is 0.710 angstroms

match Bitis gabonica.pdb (#11) with Cerrophidion godmani.pdb (#13), score = 535.2

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 100 atom pairs is 0.633 angstroms

match Bitis gabonica.pdb (#11) with Heloderma horridum horridum.pdb (#2), score = 101

with these parameters:
	chain pairing: bb
	Needleman-Wunsch using BLOSUM-30
	ss fraction: 0.3
	gap open (HH/SS/other) 18/18/6, extend 1
	ss matrix:  (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4
	iteration cutoff: 2
RMSD between 19 atom pairs is 0.784 angstroms

Match?Align cutoff: 5.0, in column if within cutoff of: any
0 fully populated columns