Various Modeller errors

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/magic/OneDrive/Desktop/RBD with full residues.pdb"

Summary of feedback from opening C:/Users/magic/OneDrive/Desktop/RBD with full
residues.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2026-01-10T14:52:32Z  
  
Chain information for RBD with full residues.pdb #1  
---  
Chain | Description  
B | No description available  
  
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> ui tool show "Model Loops"

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

Webservices job id: 3HDF3PSNOTMDNN68  
Webservices job finished: 3HDF3PSNOTMDNN68  
Modeller job (ID 3HDF3PSNOTMDNN68) finished  
  
Modeller error output  
Traceback (most recent call last):  
File "ModellerModelling.py", line 93, in <module>  
a.make()  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make  
AutoModel.make(self, exit_stage)  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make  
atmsel = self._check_select_atoms()  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 700, in _check_select_atoms  
raise ModellerError("no atoms selected for optimization")  
_modeller.ModellerError: no atoms selected for optimization  
  
  
Modeller run output  
  
MODELLER 10.6, 2024/10/17, r12888  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.89.1.el8_10.x86_64 x86_64  
Date and time of compilation : 2024/10/17 20:43:03  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2026/01/10 05:44:25  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v6}/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 amaxsequence [B,KiB,MiB]: 344685 336.606 0.329  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 345461 337.364 0.329  
  
Read the alignment from file : alignment.ali  
  
Total number of alignment positions: 195  
  
# Code #_Res #_Segm PDB_code Name  
\-------------------------------------------------------------------------------  
1 RBD_with_ 195 1 RBD_with_fu  
2 chain_B 195 1 chain_B  
check_a_343_> >> BEGINNING OF COMMAND  
openf___224_> Open ./RBD_with_full_residues.pdb_1.pdb  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 405686 396.178
0.387  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405686 396.178 0.387  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 405857 396.345
0.387  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 406707 397.175
0.388  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 407965 398.403
0.389  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 409869 400.263
0.391  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 409869 400.263 0.391  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 409959 400.351
0.391  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 412815 403.140
0.394  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 412815 403.140 0.394  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 412950 403.271
0.394  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 417234 407.455
0.398  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 417234 407.455 0.398  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 417432 407.648
0.398  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 423858 413.924
0.404  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 423858 413.924 0.404  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 424155 414.214
0.405  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 433777 423.610
0.414  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 433777 423.610 0.414  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 434227 424.050
0.414  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 448677 438.161
0.428  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 448677 438.161 0.428  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449352 438.820
0.429  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 471010 459.971
0.449  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 470740 459.707
0.449  
  
check_ali___> Checking the sequence-structure alignment.  
  
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:  
  
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST  
\----------------------------------------------  
END OF TABLE  
check_a_344_> << END OF COMMAND  
openf___224_> Open ${LIB}/top_heav.lib  
read_to_681_> topology.submodel read from topology file: 3  
openf___224_> Open ${LIB}/par.lib  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 609992 595.695
0.582  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 611592 597.258
0.583  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 615572 601.145
0.587  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 617572 603.098
0.589  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 620572 606.027
0.592  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 625072 610.422
0.596  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 630644 615.863
0.601  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 633444 618.598
0.604  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 637644 622.699
0.608  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 643944 628.852
0.614  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 646716 631.559
0.617  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 648116 632.926
0.618  
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE  
227 561 661 112 0  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 678574 662.670 0.647  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 831650 812.158 0.793  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 855962 835.900 0.816  
  
mkilst______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1543 1587 0 0 726  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 923002 901.369 0.880  
  
patch_______> segment topology patched using RTF: 1 ; THR ; NTER  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1543 1587 2161 2571 726  
  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 987018 963.885 0.941  
patch_______> segment topology patched using RTF: 195 ; PRO ; CTER  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1588 2163 2573 727  
  
genseg______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1588 2163 2573 727  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1002962 979.455 0.956  
patch_______> segment topology patched using RTF: 4 29 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1589 2165 2576 727  
patch_______> segment topology patched using RTF: 47 100 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1590 2167 2579 727  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1003210 979.697 0.957  
patch_______> segment topology patched using RTF: 59 193 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1591 2169 2582 727  
patch_______> segment topology patched using RTF: 148 156 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 195 1544 1592 2171 2585 727  
patch_s_522_> Number of disulfides patched in MODEL: 4  
transfe_506_> MODEL is an average of all templates.  
transfe_511_> Number of templates for coordinate transfer: 1  
After transferring coordinates of the equivalent template atoms,  
there are defined, undefined atoms in MODEL: 1543 1  
openf___224_> Open chain_B.ini  
wrpdb___568_> Residues, atoms, selected atoms: 195 1544 1544  
make_re_417_> Restraint type to be calculated: stereo  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1110659 1084.628
1.059  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1118851 1092.628
1.067  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1135235 1108.628
1.083  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1168003 1140.628
1.114  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1200771 1172.628
1.145  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1266307 1236.628
1.208  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1299075 1268.628
1.239  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1331843 1300.628
1.270  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1397379 1364.628
1.333  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1528451 1492.628
1.458  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1593987 1556.628
1.520  
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.  
Added bond,angle,dihedral,improper restraints : 1592 2171 2478 716  
Total number of restraints before, now : 0 6957  
make_re_422_> Number of previous, current restraints : 0 6957  
make_re_423_> Number of previous, current selected restraints: 0 6957  
make_re_417_> Restraint type to be calculated: phi-psi_binormal  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1705773 1665.794
1.627  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 6957 7150  
make_re_423_> Number of previous, current selected restraints: 6957 7150  
make_re_417_> Restraint type to be calculated: omega_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1705789 1665.810
1.627  
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
omgdel__425_> Unselected all O C +N +CA dihedrals: 205  
(This is to avoid clashes between STEREO  
and OMEGA_DIHEDRAL restraints)  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1771325 1729.810
1.689  
make_re_422_> Number of previous, current restraints : 7150 7344  
make_re_423_> Number of previous, current selected restraints: 7150 7139  
make_re_417_> Restraint type to be calculated: chi1_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1771325 1729.810
1.689  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 7344 7512  
make_re_423_> Number of previous, current selected restraints: 7139 7307  
make_re_417_> Restraint type to be calculated: chi2_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1771325 1729.810
1.689  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 7512 7630  
make_re_423_> Number of previous, current selected restraints: 7307 7425  
make_re_417_> Restraint type to be calculated: chi3_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1771325 1729.810
1.689  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 7630 7670  
make_re_423_> Number of previous, current selected restraints: 7425 7465  
make_re_417_> Restraint type to be calculated: chi4_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1771325 1729.810
1.689  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt  
mdtrsr__446W> A potential that relies on one protein is used, yet you have at  
least one known structure available. MDT, not library, potential is used.  
getdata_643_> Protein accepted: RBD_with_full_residues.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 7670 7687  
make_re_423_> Number of previous, current selected restraints: 7465 7482  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2215961 2164.024
2.113  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2347033 2292.024
2.238  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2478105 2420.024
2.363  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2740249 2676.024
2.613  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2871321 2804.024
2.738  
make_re_422_> Number of previous, current restraints : 7687 11292  
make_re_423_> Number of previous, current selected restraints: 7482 11087  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 11292 15096  
make_re_423_> Number of previous, current selected restraints: 11087 14891  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3133465 3060.024
2.988  
make_re_422_> Number of previous, current restraints : 15096 18578  
make_re_423_> Number of previous, current selected restraints: 14891 18373  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3657753 3572.024
3.488  
make_re_422_> Number of previous, current restraints : 18578 20580  
make_re_423_> Number of previous, current selected restraints: 18373 20375  
0 atoms in HETATM/BLK residues constrained  
to protein atoms within 2.30 angstroms  
and protein CA atoms within 10.00 angstroms  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 20580 20580  
make_re_423_> Number of previous, current selected restraints: 20375 20375  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 20580 20580  
make_re_423_> Number of previous, current selected restraints: 20375 20375  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 20580 20580  
make_re_423_> Number of previous, current selected restraints: 20375 20375  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 20580 20580  
make_re_423_> Number of previous, current selected restraints: 20375 20375  
0 atoms in residues without defined topology  
constrained to be rigid bodies  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 20580 20580  
make_re_423_> Number of previous, current selected restraints: 20375 20375  
rmdupl__427_> 1169 redundant cosine dihedral restraints were unselected.  
condens_443_> Restraints marked for deletion were removed.  
Total number of restraints before, now: 20580 19206  
openf___224_> Open chain_B.rsr  
openf___224_> Open chain_B.rsr  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3862267 3771.745
3.683  
rdcsr2__307_> Number of restraints read : 19206  
Number of excluded pairs read: 0  
Number of pseudo atoms read : 0  
rdcsrs__304_> Restraints in memory, selected restraints: 19206 19206  
Explicitly excluded atom pairs in memory : 0  
Pseudo atoms in memory : 0  
  
No output models from Modeller; see log for Modeller text output.  

> close session

> open P0DTC2 fromDatabase alphafold

Summary of feedback from opening P0DTC2 fetched from alphafold  
---  
note | Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
  
Fetching url https://alphafold.ebi.ac.uk/files/AF-P0DTC2-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> open PODTC2 fromDatabase alphafold

Fetching url https://alphafold.ebi.ac.uk/files/AF-PODTC2-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> open P0DTC2 fromDatabase alphafold

Fetching url https://alphafold.ebi.ac.uk/files/AF-P0DTC2-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> alphafold fetch P0DTC2

Fetching url https://alphafold.ebi.ac.uk/files/AF-P0DTC2-F1-model_v6.cif
failed:  
HTTP Error 404: Not Found  

> ui tool show AlphaFold

No sequence chosen for AlphaFold match  

Fetching compressed P0DTC2 UniProt info from
https://www.uniprot.org/uniprot/P0DTC2.xml  

> alphafold match P0DTC2

1 UniProt id does not have an AlphaFold database model: P0DTC2 (UniProt
P0DTC2)  

No AlphaFold model with similar sequence for UniProt P0DTC2  

Opened 0 AlphaFold model  

> open "C:/Users/magic/OneDrive/Desktop/ACE2 pdb chimera.pdb"

Summary of feedback from opening C:/Users/magic/OneDrive/Desktop/ACE2 pdb
chimera.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2026-01-10T03:11:03Z  
  
Chain information for ACE2 pdb chimera.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> ui tool show "Model Loops"

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

Webservices job id: MTCUN752OU53YKYS  
Webservices job finished: MTCUN752OU53YKYS  
Modeller job (ID MTCUN752OU53YKYS) finished  
  
Modeller error output  
Traceback (most recent call last):  
File "ModellerModelling.py", line 93, in <module>  
a.make()  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make  
AutoModel.make(self, exit_stage)  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make  
atmsel = self._check_select_atoms()  
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 700, in _check_select_atoms  
raise ModellerError("no atoms selected for optimization")  
_modeller.ModellerError: no atoms selected for optimization  
  
  
Modeller run output  
  
MODELLER 10.6, 2024/10/17, r12888  
  
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS  
  
  
Copyright(c) 1989-2024 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 crick.cgl.ucsf.edu
4.18.0-553.89.1.el8_10.x86_64 x86_64  
Date and time of compilation : 2024/10/17 20:43:03  
MODELLER executable type : x86_64-intel8  
Job starting time (YY/MM/DD HH:MM:SS): 2026/01/10 06:13:49  
  
environ____W> The class 'environ' is deprecated; use 'Environ' instead  
openf___224_> Open $(LIB)/restyp.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib  
rdresgr_266_> Number of residue groups: 2  
openf___224_> Open ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/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 ${MODINSTALL10v6}/modlib/radii.lib  
  
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242  
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib  
rdwilmo_274_> Mainchain residue conformation classes: APBLE  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib  
rdclass_257_> Number of classes: 5  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib  
openf___224_> Open ${MODINSTALL10v6}/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 amaxalignment [B,KiB,MiB]: 528709 516.317
0.504  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 531089 518.642 0.506  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 533469 520.966 0.509  
  
Read the alignment from file : alignment.ali  
  
Total number of alignment positions: 596  
  
# Code #_Res #_Segm PDB_code Name  
\-------------------------------------------------------------------------------  
1 ACE2_pdb_ 596 1 ACE2_pdb_ch  
2 chain_A 596 1 chain_A  
check_a_343_> >> BEGINNING OF COMMAND  
openf___224_> Open ./ACE2_pdb_chimera.pdb_1.pdb  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 713994 697.260
0.681  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 713994 697.260 0.681  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 714165 697.427
0.681  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 715015 698.257
0.682  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 716273 699.485
0.683  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 718177 701.345
0.685  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 718177 701.345 0.685  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 718267 701.433
0.685  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 721123 704.222
0.688  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 721123 704.222 0.688  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 721258 704.354
0.688  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725542 708.537
0.692  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 725542 708.537 0.692  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725740 708.730
0.692  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732166 715.006
0.698  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 732166 715.006 0.698  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732463 715.296
0.699  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742085 724.692
0.708  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 742085 724.692 0.708  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742535 725.132
0.708  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 756985 739.243
0.722  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 756985 739.243 0.722  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 757660 739.902
0.723  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779318 761.053
0.743  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 779318 761.053 0.743  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 780326 762.037
0.744  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 812830 793.779
0.775  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 812830 793.779 0.775  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 814342 795.256
0.777  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 863098 842.869
0.823  
  
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 863098 842.869 0.823  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 865366 845.084
0.825  
  
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 938500 916.504
0.895  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 937051 915.089
0.894  
  
check_ali___> Checking the sequence-structure alignment.  
  
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:  
  
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST  
\----------------------------------------------  
END OF TABLE  
check_a_344_> << END OF COMMAND  
openf___224_> Open ${LIB}/top_heav.lib  
read_to_681_> topology.submodel read from topology file: 3  
openf___224_> Open ${LIB}/par.lib  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1076303 1051.077
1.026  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1077903 1052.640
1.028  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1081883 1056.526
1.032  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1083883 1058.479
1.034  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1086883 1061.409
1.037  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1091383 1065.804
1.041  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1096955 1071.245
1.046  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1099755 1073.979
1.049  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1103955 1078.081
1.053  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1110255 1084.233
1.059  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1113027 1086.940
1.061  
  
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1114427 1088.308
1.063  
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE  
227 561 661 112 0  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1207842 1179.533 1.152  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1686180 1646.660 1.608  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1761180 1719.902 1.680  
  
mkilst______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4862 4999 0 0 2188  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1971696 1925.484 1.880  
  
patch_______> segment topology patched using RTF: 1 ; SER ; NTER  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4862 4999 6792 8065 2188  
  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2200712 2149.133 2.099  
patch_______> segment topology patched using RTF: 596 ; ALA ; CTER  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4863 5000 6794 8067 2189  
  
genseg______> segment topology constructed from sequence and RTF:  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4863 5000 6794 8067 2189  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2250816 2198.062 2.147  
patch_______> segment topology patched using RTF: 115 123 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4863 5001 6796 8070 2189  
patch_______> segment topology patched using RTF: 326 343 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4863 5002 6798 8073 2189  
  
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2251064 2198.305 2.147  
patch_______> segment topology patched using RTF: 512 524 ; CYS CYS ; DISU  
segments residues atoms bonds angles dihedrals impropers:  
1 596 4863 5003 6800 8076 2189  
patch_s_522_> Number of disulfides patched in MODEL: 3  
transfe_506_> MODEL is an average of all templates.  
transfe_511_> Number of templates for coordinate transfer: 1  
After transferring coordinates of the equivalent template atoms,  
there are defined, undefined atoms in MODEL: 4862 1  
openf___224_> Open chain_A.ini  
wrpdb___568_> Residues, atoms, selected atoms: 596 4863 4863  
make_re_417_> Restraint type to be calculated: stereo  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2358513 2303.235
2.249  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2366705 2311.235
2.257  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2383089 2327.235
2.273  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2415857 2359.235
2.304  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2448625 2391.235
2.335  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2514161 2455.235
2.398  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2546929 2487.235
2.429  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2612465 2551.235
2.491  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2645233 2583.235
2.523  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2776305 2711.235
2.648  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2841841 2775.235
2.710  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2907377 2839.235
2.773  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3038449 2967.235
2.898  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3300593 3223.235
3.148  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3431665 3351.235
3.273  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3562737 3479.235
3.398  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3824881 3735.235
3.648  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4349169 4247.235
4.148  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4611313 4503.235
4.398  
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.  
Added bond,angle,dihedral,improper restraints : 5003 6800 7727 2162  
Total number of restraints before, now : 0 21692  
make_re_422_> Number of previous, current restraints : 0 21692  
make_re_423_> Number of previous, current selected restraints: 0 21692  
make_re_417_> Restraint type to be calculated: phi-psi_binormal  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4959854 4843.607
4.730  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 21692 22286  
make_re_423_> Number of previous, current selected restraints: 21692 22286  
make_re_417_> Restraint type to be calculated: omega_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4959870 4843.623
4.730  
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
omgdel__425_> Unselected all O C +N +CA dihedrals: 622  
(This is to avoid clashes between STEREO  
and OMEGA_DIHEDRAL restraints)  
make_re_422_> Number of previous, current restraints : 22286 22881  
make_re_423_> Number of previous, current selected restraints: 22286 22259  
make_re_417_> Restraint type to be calculated: chi1_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4959870 4843.623
4.730  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5222014 5099.623
4.980  
make_re_422_> Number of previous, current restraints : 22881 23407  
make_re_423_> Number of previous, current selected restraints: 22259 22785  
make_re_417_> Restraint type to be calculated: chi2_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 5222014 5099.623
4.980  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 23407 23828  
make_re_423_> Number of previous, current selected restraints: 22785 23206  
make_re_417_> Restraint type to be calculated: chi3_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 5222014 5099.623
4.980  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 23828 24005  
make_re_423_> Number of previous, current selected restraints: 23206 23383  
make_re_417_> Restraint type to be calculated: chi4_dihedral  
  
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 5222014 5099.623
4.980  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin  
openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt  
mdtrsr__446W> A potential that relies on one protein is used, yet you have at  
least one known structure available. MDT, not library, potential is used.  
getdata_643_> Protein accepted: ACE2_pdb_chimera.pdb_1  
getdata_289_> Proteins (all/accepted): 1 1  
make_re_422_> Number of previous, current restraints : 24005 24057  
make_re_423_> Number of previous, current selected restraints: 23383 23435  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 6622522 6467.307
6.316  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7146810 6979.307
6.816  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7671098 7491.307
7.316  
make_re_422_> Number of previous, current restraints : 24057 36613  
make_re_423_> Number of previous, current selected restraints: 23435 35991  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8719674 8515.307
8.316  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9243962 9027.307
8.816  
make_re_422_> Number of previous, current restraints : 36613 49193  
make_re_423_> Number of previous, current selected restraints: 35991 48571  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 49193 58804  
make_re_423_> Number of previous, current selected restraints: 48571 58182  
make_re_417_> Restraint type to be calculated: DISTANCE  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10292538 10051.307
9.816  
make_re_422_> Number of previous, current restraints : 58804 66116  
make_re_423_> Number of previous, current selected restraints: 58182 65494  
0 atoms in HETATM/BLK residues constrained  
to protein atoms within 2.30 angstroms  
and protein CA atoms within 10.00 angstroms  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 66116 66116  
make_re_423_> Number of previous, current selected restraints: 65494 65494  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 66116 66116  
make_re_423_> Number of previous, current selected restraints: 65494 65494  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 66116 66116  
make_re_423_> Number of previous, current selected restraints: 65494 65494  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 66116 66116  
make_re_423_> Number of previous, current selected restraints: 65494 65494  
0 atoms in residues without defined topology  
constrained to be rigid bodies  
make_re_417_> Restraint type to be calculated: DISTANCE  
make_re_422_> Number of previous, current restraints : 66116 66116  
make_re_423_> Number of previous, current selected restraints: 65494 65494  
rmdupl__427_> 3714 redundant cosine dihedral restraints were unselected.  
condens_443_> Restraints marked for deletion were removed.  
Total number of restraints before, now: 66116 61780  
openf___224_> Open chain_A.rsr  
openf___224_> Open chain_A.rsr  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10318274 10076.439
9.840  
  
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 11891138 11612.439
11.340  
rdcsr2__307_> Number of restraints read : 61780  
Number of excluded pairs read: 0  
Number of pseudo atoms read : 0  
rdcsrs__304_> Restraints in memory, selected restraints: 61780 61780  
Explicitly excluded atom pairs in memory : 0  
Pseudo atoms in memory : 0  
  
No output models from Modeller; see log for Modeller text output.  

> close session

> open "C:/Users/magic/OneDrive/Desktop/RBD with full residues.pdb"

Summary of feedback from opening C:/Users/magic/OneDrive/Desktop/RBD with full
residues.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2026-01-10T14:52:32Z  
  
Chain information for RBD with full residues.pdb #1  
---  
Chain | Description  
B | No description available  
  
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> altlocs clean

Removed alternate locations from 1 residue  

> altlocs clean

No alternate locations in 195 residues  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/B PRO 527: phi -58.3, psi none trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /B PRO 527  
Summary of feedback from adding hydrogens to RBD with full residues.pdb #1  
---  
notes | No usable SEQRES records for RBD with full residues.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 333  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /B PRO 527  
135 hydrogen bonds  
/B PRO 527 is not terminus, removing H atom from 'C'  
1463 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save "C:/Users/magic/OneDrive/Desktop/RBD GLN498.pdb" relModel #1

> close session

> open C:/Users/magic/Downloads/cluster1_1.pdb

Summary of feedback from opening C:/Users/magic/Downloads/cluster1_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_110w.pdb"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_110.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
29 messages similar to the above omitted  
  
Chain information for cluster1_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> select /A

5895 atoms, 6032 bonds, 596 residues, 1 model selected  

> select /B

1886 atoms, 1930 bonds, 195 residues, 1 model selected  

> select /A

5895 atoms, 6032 bonds, 596 residues, 1 model selected  

> color sel red

> select /B

1886 atoms, 1930 bonds, 195 residues, 1 model selected  

> color sel orange

> ui tool show H-Bonds

> hbonds intraModel false distSlop 1.0 angleSlop 30.0 intraMol false intraRes
> false reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds intraModel false distSlop 1.0 angleSlop 30.0 intraMol false intraRes
> false reveal true

0 hydrogen bonds found  

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to cluster1_1.pdb #1  
---  
notes | No usable SEQRES records for cluster1_1.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for cluster1_1.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A SER 19, /B THR 333  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 614, /B PRO 527  
771 hydrogen bonds  
/A ALA 614 is not terminus, removing H atom from 'C'  
/B PRO 527 is not terminus, removing H atom from 'C'  
4747 hydrogens added  
  

> ui tool show H-Bonds

> hbonds showDist true intraModel false distSlop 1.0 angleSlop 30.0 intraMol
> false intraRes false reveal true

0 hydrogen bonds found  

> surface sel

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> style sel stick

Changed 1886 atom styles  

> style sel sphere

Changed 1886 atom styles  

> style sel sphere

Changed 1886 atom styles  

> surface hidePatches sel

> select N487

Expected an objects specifier or a keyword  

> select :487 ,24

47 atoms, 44 bonds, 3 residues, 1 model selected  

> show sel

> style sel stick

Changed 47 atom styles  

> label sel text "{res_name} {res_num}"

> zoom 2.0

> show sel atoms

[Repeated 3 time(s)]

> style sel ball

Changed 47 atom styles  

> color byelement sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byelement sel

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color /A : 487 blue

> color /B : 24 hotpink

> color /B : 24 blue

> color (#!1 & sel) hot pink

> select :487

30 atoms, 28 bonds, 2 residues, 1 model selected  

> color (#!1 & sel) orange red

> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select :24

17 atoms, 16 bonds, 1 residue, 1 model selected  

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select :487 , 24

47 atoms, 44 bonds, 3 residues, 1 model selected  

> ui tool show Distances

Exactly two atoms must be selected!  

> select :487 , 24

47 atoms, 44 bonds, 3 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select :487

30 atoms, 28 bonds, 2 residues, 1 model selected  

> color (#!1 & sel) byelement

> select :24

17 atoms, 16 bonds, 1 residue, 1 model selected  

> color sel byelement

> select /A:24@OE1

1 atom, 1 residue, 1 model selected  

> select /B:487@ND2

1 atom, 1 residue, 1 model selected  

> show :487, 24 atoms and style :487 , 24 ball

Expected ',' or a keyword  

> select clear

[Repeated 1 time(s)]

> select ::name="ASN"

784 atoms, 730 bonds, 56 residues, 1 model selected  

> select clear

> select :487,24

47 atoms, 44 bonds, 3 residues, 1 model selected  

> show (#!1 & sel) target ab

> zoom 1.5

> select clear

> select /B:487@ND2

1 atom, 1 residue, 1 model selected  

> select add /A:24@OE1

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance /B:487@ND2 /A:24@OE1

Distance between /B ASN 487 ND2 and /A GLN 24 OE1: 5.506Å  

> distance style color #0055ff

[Repeated 2 time(s)]

> select :449,38

47 atoms, 45 bonds, 3 residues, 1 model selected  

> ui tool show "Minimize Structure"

> minimize #1

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
Swapping /A ALA 614 to ALA  
/B PRO 527: phi -59.3, psi none trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /B PRO 527  
Summary of feedback from adding hydrogens to cluster1_1.pdb #1  
---  
notes | No usable SEQRES records for cluster1_1.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for cluster1_1.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A SER 19, /B THR 333  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 614, /B PRO 527  
767 hydrogen bonds  
/A ALA 614 is not terminus, removing H atom from 'C'  
/B PRO 527 is not terminus, removing H atom from 'C'  
11 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 101, in minimize  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 173, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
Exception: Could not find typename 'N' for atom '<Atom 9504 (N) of chain 0
residue 595 (A-ALA-614)>' in list of known atom types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
Exception: Could not find typename 'N' for atom '' in list of known atom
types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
  
See log for complete Python traceback.  
  

> ui tool show "Minimize Structure"

> minimize #1

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
Swapping /A ALA 614 to ALA  
/B PRO 527: phi -59.3, psi none trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /B PRO 527  
Summary of feedback from adding hydrogens to cluster1_1.pdb #1  
---  
notes | No usable SEQRES records for cluster1_1.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for cluster1_1.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A SER 19, /B THR 333  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 614, /B PRO 527  
767 hydrogen bonds  
/A ALA 614 is not terminus, removing H atom from 'C'  
/B PRO 527 is not terminus, removing H atom from 'C'  
11 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 101, in minimize  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 107, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 173, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
Exception: Could not find typename 'N' for atom '<Atom 9504 (N) of chain 0
residue 595 (A-ALA-614)>' in list of known atom types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
Exception: Could not find typename 'N' for atom '' in list of known atom
types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
File "C:\Program Files\ChimeraX 1.11\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.5063
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_ZA.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude E5450
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,459,206,656
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-5300U CPU @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.11.12
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0