Modeller: Number of residues in the alignment and pdb files are different

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109212024 (2021-09-21 20:24:53 UTC)
Description
open 1maz
open uniprot:bclx_human
sequence associate /A bclx_human:1
modeller refine bclx_human:1:all-missing numModels 5 fast false adjacentFlexible 1 protocol standard

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

executed startup.cxc  
UCSF ChimeraX version: 1.3.dev202109212024 (2021-09-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1maz

1maz title:  
X-ray structure of BCL-XL, an inhibitor of programmed cell death [more
info...]  
  
Chain information for 1maz #1  
---  
Chain | Description | UniProt  
A | Bcl-2-like protein 1 | BCLX_HUMAN  
  

> open uniprot:bclx_human

Summary of feedback from opening bclx_human fetched from uniprot  
---  
notes | UniProt identifier bclx_human maps to entry Q07817  
Alignment identifier is bclx_human  
  
Opened UniProt bclx_human  

> sequence associate /A bclx_human:1

Associated 1maz chain A to bclx_human with 12 mismatches and/or gaps  

> ui tool show "Model Loops"

> modeller refine bclx_human:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard

Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service  
Opal job id: appModeller9v8Service16323456707651186954005  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16323456707651186954005  
stdout.txt = standard output  
stderr.txt = standard error  
Modeller job ID appModeller9v8Service16323456707651186954005 finished  
  
Modeller error output  
Traceback (most recent call last):  
File "/usr/local/opal-local/bin/modeller9v8.py", line 332, in <module>  
main()  
File "/usr/local/opal-local/bin/modeller9v8.py", line 24, in main  
VersionMap[cf["version"]](cf)  
File "/usr/local/opal-local/bin/modeller9v8.py", line 34, in v2_run  
execfile(fn)  
File "ModellerModelling.py", line 88, in <module>  
a.make()  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py",
line 42, in make  
AutoModel.make(self, exit_stage)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 141, in make  
self.homcsr(exit_stage)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 625, in homcsr  
self.check_alignment(aln)  
File "/usr/lib64/python2.7/site-packages/modeller/automodel/automodel.py",
line 578, in check_alignment  
aln.check()  
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 213, in
check  
self.check_structure_structure(io=io)  
File "/usr/lib64/python2.7/site-packages/modeller/alignment.py", line 222, in
check_structure_structure  
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)  
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and
pdb files are different: 143 291 For alignment entry: 1 1maz_1  
  
  
Modeller run output  
**** IGNORE FOLLOWING LICENSE KEY MESSAGE ****  
check_lice_E> Invalid license key: xxx  
Go to https://salilab.org/modeller/ to get a license key,  
and then set the 'license' variable to it in the file  
/usr/lib/modeller10.1/modlib/modeller/config.py  
  
**** END IGNORED MESSAGE ****  
  
MODELLER 10.1, 2021/03/12, r12156  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2021 Andrej Sali  
All Rights Reserved  
  
Written by A. Sali  
with help from  
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,  
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,  
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,  
F. Melo, J.P. Overington, E. Feyfant  
University of California, San Francisco, USA  
Rockefeller University, New York, USA  
Harvard University, Cambridge, USA  
Imperial Cancer Research Fund, London, UK  
Birkbeck College, University of London, London, UK  
  
  
Kind, OS, HostName, Kernel, Processor: 4, Linux franklin.cgl.ucsf.edu
3.10.0-1160.36.2.el7.x86_64 x86_64  
Date and time of compilation : 2021/03/12 00:18:43  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2021/09/22 14:21:10  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v1}/modlib/sstruc.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183  
openf___224_> Open ${MODINSTALL10v1}/modlib/resdih.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230  
rdrdih__263_> Number of dihedral angle types : 9  
Maximal number of dihedral angle optima: 3  
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5  
openf___224_> Open ${MODINSTALL10v1}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v1}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v1}/modlib/xs4.mat  
rdrrwgh_268_> Number of residue types: 21  
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead  
openf___224_> Open alignment.ali  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328  
  
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406077 396.560 0.387  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406957 397.419 0.388  
  
Read the alignment from file : alignment.ali  
  
Total number of alignment positions: 221  
  
# Code #_Res #_Segm PDB_code Name  
\-------------------------------------------------------------------------------  
1 1maz_1 143 1 1maz_1  
2 bclx_huma 221 1 bclx_human  
check_a_343_> >> BEGINNING OF COMMAND  
openf___224_> Open ./1maz_1.pdb  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 451582 440.998
0.431  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 451582 440.998 0.431  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 451753 441.165
0.431  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 452603 441.995
0.432  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453861 443.224
0.433  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 455765 445.083
0.435  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 455765 445.083 0.435  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 455855 445.171
0.435  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 458711 447.960
0.437  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 458711 447.960 0.437  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 458846 448.092
0.438  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463130 452.275
0.442  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 463130 452.275 0.442  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463328 452.469
0.442  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 469754 458.744
0.448  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 469754 458.744 0.448  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 470051 459.034
0.448  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 479673 468.431
0.457  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 479673 468.431 0.457  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480123 468.870
0.458  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 494573 482.981
0.472  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 494573 482.981 0.472  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495248 483.641
0.472  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495248 483.641 0.472  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496256 484.625
0.473  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 517914 505.775
0.494  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 562492 549.309
0.536  
read_te_290E> Number of residues in the alignment and pdb files are different:
143 291  
For alignment entry: 1 1maz_1  
x (mismatch at alignment position 144)  
Alignment HLEPWIQENGGWDTFVELYG/  
PDB HLEPWIQENGGWDTFVELYG-wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww  
Match ********************  
  
Please check your alignment file header to be sure you correctly specified  
the starting and ending residue numbers and chains. The alignment sequence  
must match that from the atom file exactly.  
  
Another possibility is that some residues in the atom file are missing,  
perhaps because they could not be resolved experimentally. (Note that Modeller  
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)  
In this case, simply replace the section of your alignment corresponding  
to these missing residues with gaps.  
read_te_288W> Protein not accepted: 1 1maz_1  
  
No output models from Modeller; see log for Modeller text output.  




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[Eric Pettersen]

Neither sequence is a subset of the other, which is undoubtedly where I'm getting tripped up in preparing the input for Modeller.

[Eric Pettersen]

Also 1r2d

[Elaine Meng]

I'm getting this error for everything I try to loop-model today: now for 6g2e, a totally different protein than those previously mentioned in this ticket. 

[Eric Pettersen]

Okay, fixed the "error for everything" part of this ticket. These structures now work off their chain sequences and most of them off their UniProt sequences. 1maz still doesn't work off its UniProt sequence, which is a separate problem and why this ticket is remaining open.