Find Cavities crash

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202502060317 (2025-02-06 03:17:41 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow

Thread 0x0000513c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000a9c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 622 in wait
  File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\tqdm\_monitor.py", line 60 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x00004e8c (most recent call first):
  File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\pyKVFinder\grid.py", line 961 in detect
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\kvfinder\cmd.py", line 56 in cmd_kvfinder
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\kvfinder\tool.py", line 136 in find_cavities
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\rmatusiak\PROTEON PHARMACEUTICALS S.A\Projekt Booster -
> Dokumenty\04 Bioinformatics_data\Proteins_models\212EcolP5.cxs" format
> session

> view name session-start

opened ChimeraX session  

> ui tool show "Similar Structures"

> foldseek #2/A

Not saving entity_poly_seq for non-authoritative sequences  

Found 335 similar structures to 212Ecol018PP_DKPHSRRH_CDS_0005.pdb #2/A in pdb
database using foldseek, name fs1  

> similarstructures ligands

> similarstructures traces

335 backbone traces  

> close #3

> similarstructures cluster #2/A:379,427,383,348,325 clusterDistance 1.5

Installing umap-learn package from PyPi  

> pip install umap-learn

C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\sklearn\utils\deprecation.py:151: FutureWarning: 'force_all_finite'
was renamed to 'ensure_all_finite' in 1.6 and will be removed in 1.8.  
warnings.warn(  
Clustered 188 of 335 hits that have the specified 5 residues into 3 groups  
335 backbone traces  

> close #3

> open 3gw6

Summary of feedback from opening 3gw6 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3gw6 from http://files.rcsb.org/download/3gw6.cif  
Fetching CCD BR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BR/BR.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif  
Fetching CCD TAM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/TAM/TAM.cif  
  
3gw6 title:  
Intramolecular Chaperone [more info...]  
  
Chain information for 3gw6 #3  
---  
Chain | Description | UniProt  
A B C D E F | Endo-N-acetylneuraminidase | Q858B1_BPK1F 790-1064  
  
Non-standard residues in 3gw6 #3  
---  
BR — bromide ion  
CA — calcium ion  
CL — chloride ion  
PEG — di(hydroxyethyl)ether  
TAM — tris(hydroxyethyl)aminomethane  
  
3gw6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
Deleted 5 extra chains, 1 C-terminal residues, 310 non-polymer residues more
than 3.0 Angstroms away.  
Alignment of 3gw6 chain A to query has RMSD 0.907 using 123 of 208 paired
residues within cutoff distance 2.0  

> select add #3

2114 atoms, 2110 bonds, 2 pseudobonds, 304 residues, 3 models selected  

> similarstructures ligands

Fetching compressed mmCIF 3gvj from http://files.rcsb.org/download/3gvj.cif  
Fetching compressed mmCIF 3gvk from http://files.rcsb.org/download/3gvk.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
Fetching compressed mmCIF 4hiz from http://files.rcsb.org/download/4hiz.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
Fetching CCD FRU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/FRU/FRU.cif  
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching compressed mmCIF 1mz6 from http://files.rcsb.org/download/1mz6.cif  
Fetching CCD DAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/DAN/DAN.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
Fetching compressed mmCIF 7lbv from http://files.rcsb.org/download/7lbv.cif  
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif  
Fetching compressed mmCIF 1n1t from http://files.rcsb.org/download/1n1t.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
Fetching compressed mmCIF 2ags from http://files.rcsb.org/download/2ags.cif  
Fetching CCD FKD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FKD/FKD.cif  
Fetching compressed mmCIF 7a54 from http://files.rcsb.org/download/7a54.cif  
Fetching compressed mmCIF 1mz5 from http://files.rcsb.org/download/1mz5.cif  
Fetching compressed mmCIF 2ya7 from http://files.rcsb.org/download/2ya7.cif  
Fetching CCD ZMR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/ZMR/ZMR.cif  
Fetching compressed mmCIF 6qzh from http://files.rcsb.org/download/6qzh.cif  
Fetching CCD JLW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/JLW/JLW.cif  
Fetching CCD PGE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif  
Fetching CCD TAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/TAR/TAR.cif  
Fetching compressed mmCIF 3gud from http://files.rcsb.org/download/3gud.cif  
Fetching compressed mmCIF 1eus from http://files.rcsb.org/download/1eus.cif  
Fetching compressed mmCIF 3h6j from http://files.rcsb.org/download/3h6j.cif  
Fetching compressed mmCIF 4xma from http://files.rcsb.org/download/4xma.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
Fetching CCD OPX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/OPX/OPX.cif  
Fetching compressed mmCIF 4j9t from http://files.rcsb.org/download/4j9t.cif  
Fetching CCD ARS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/ARS/ARS.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
Fetching compressed mmCIF 4q6k from http://files.rcsb.org/download/4q6k.cif  
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif  
Fetching compressed mmCIF 2w38 from http://files.rcsb.org/download/2w38.cif  
Fetching compressed mmCIF 8du5 from http://files.rcsb.org/download/8du5.cif  
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif  
Fetching CCD FUC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/FUC/FUC.cif  
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif  
Fetching compressed mmCIF 2f11 from http://files.rcsb.org/download/2f11.cif  
Fetching CCD IEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/IEM/IEM.cif  
Fetching compressed mmCIF 4x49 from http://files.rcsb.org/download/4x49.cif  
Fetching CCD G39 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/G39/G39.cif  
Fetching compressed mmCIF 3sli from http://files.rcsb.org/download/3sli.cif  
Fetching CCD SKD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/SKD/SKD.cif  
Fetching compressed mmCIF 2bzd from http://files.rcsb.org/download/2bzd.cif  
Fetching CCD GAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif  
Fetching compressed mmCIF 1wcq from http://files.rcsb.org/download/1wcq.cif  
Fetching compressed mmCIF 4irt from http://files.rcsb.org/download/4irt.cif  
Fetching compressed mmCIF 2ber from http://files.rcsb.org/download/2ber.cif  
Fetching compressed mmCIF 6eks from http://files.rcsb.org/download/6eks.cif  
Fetching compressed mmCIF 5nop from http://files.rcsb.org/download/5nop.cif  
Fetching compressed mmCIF 6eku from http://files.rcsb.org/download/6eku.cif  
Fetching compressed mmCIF 8k80 from http://files.rcsb.org/download/8k80.cif  
Fetching compressed mmCIF 2f13 from http://files.rcsb.org/download/2f13.cif  
Fetching CCD DYM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/DYM/DYM.cif  
Fetching compressed mmCIF 1w8n from http://files.rcsb.org/download/1w8n.cif  
Fetching compressed mmCIF 7zei from http://files.rcsb.org/download/7zei.cif  
Fetching CCD MES from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/MES/MES.cif  
Fetching CCD TRS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TRS/TRS.cif  
Fetching compressed mmCIF 4u6b from http://files.rcsb.org/download/4u6b.cif  
Fetching CCD ACY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ACY/ACY.cif  
Fetching compressed mmCIF 7esn from http://files.rcsb.org/download/7esn.cif  
Fetching CCD BDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/BDP/BDP.cif  
Fetching CCD RAM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/RAM/RAM.cif  
Fetching compressed mmCIF 6nw9 from http://files.rcsb.org/download/6nw9.cif  
Fetching CCD CO3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/CO3/CO3.cif  
Fetching compressed mmCIF 8g3m from http://files.rcsb.org/download/8g3m.cif  
Fetching compressed mmCIF 6p2k from http://files.rcsb.org/download/6p2k.cif  
Fetching CCD ACT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif  
Fetching CCD PE3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/PE3/PE3.cif  
Fetching compressed mmCIF 5mxc from http://files.rcsb.org/download/5mxc.cif  
Fetching CCD MFU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/MFU/MFU.cif  
Fetching compressed mmCIF 7drq from http://files.rcsb.org/download/7drq.cif  
Fetching compressed mmCIF 7dc3 from http://files.rcsb.org/download/7dc3.cif  
Fetching compressed mmCIF 6br5 from http://files.rcsb.org/download/6br5.cif  
Fetching CCD GYG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/GYG/GYG.cif  
Fetching compressed mmCIF 7pi2 from http://files.rcsb.org/download/7pi2.cif  
Fetching compressed mmCIF 4gzs from http://files.rcsb.org/download/4gzs.cif  
Fetching CCD EPE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif  
Fetching compressed mmCIF 7esk from http://files.rcsb.org/download/7esk.cif  
Fetching compressed mmCIF 5y31 from http://files.rcsb.org/download/5y31.cif  
Fetching compressed mmCIF 4qqs from http://files.rcsb.org/download/4qqs.cif  
Fetching compressed mmCIF 6q20 from http://files.rcsb.org/download/6q20.cif  
Fetching compressed mmCIF 8hcj from http://files.rcsb.org/download/8hcj.cif  
Fetching compressed mmCIF 6xn1 from http://files.rcsb.org/download/6xn1.cif  
Fetching CCD XYP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XYP/XYP.cif  
Fetching compressed mmCIF 6n4d from http://files.rcsb.org/download/6n4d.cif  
Fetching compressed mmCIF 7u4g from http://files.rcsb.org/download/7u4g.cif  
Fetching compressed mmCIF 6eui from http://files.rcsb.org/download/6eui.cif  
Fetching compressed mmCIF 1eut from http://files.rcsb.org/download/1eut.cif  
Fetching compressed mmCIF 7ukj from http://files.rcsb.org/download/7ukj.cif  
Fetching compressed mmCIF 4h53 from http://files.rcsb.org/download/4h53.cif  
Fetching compressed mmCIF 4urr from http://files.rcsb.org/download/4urr.cif  
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif  
Fetching compressed mmCIF 5mui from http://files.rcsb.org/download/5mui.cif  
Fetching CCD 8OQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/8OQ/8OQ.cif  
Fetching CCD 8PK from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/8PK/8PK.cif  
Fetching CCD ARA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/ARA/ARA.cif  
Fetching CCD FUB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/FUB/FUB.cif  
Fetching compressed mmCIF 3p2n from http://files.rcsb.org/download/3p2n.cif  
Fetching compressed mmCIF 5ta7 from http://files.rcsb.org/download/5ta7.cif  
Fetching compressed mmCIF 6xn0 from http://files.rcsb.org/download/6xn0.cif  
Fetching compressed mmCIF 8g30 from http://files.rcsb.org/download/8g30.cif  
Fetching compressed mmCIF 5gqt from http://files.rcsb.org/download/5gqt.cif  
Fetching compressed mmCIF 2vbk from http://files.rcsb.org/download/2vbk.cif  
Fetching CCD CO2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/CO2/CO2.cif  
Fetching CCD PGR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/PGR/PGR.cif  
Fetching compressed mmCIF 5glp from http://files.rcsb.org/download/5glp.cif  
Fetching compressed mmCIF 5a7v from http://files.rcsb.org/download/5a7v.cif  
Fetching compressed mmCIF 8g3o from http://files.rcsb.org/download/8g3o.cif  
Fetching compressed mmCIF 1yrz from http://files.rcsb.org/download/1yrz.cif  
Fetching compressed mmCIF 2exk from http://files.rcsb.org/download/2exk.cif  
Fetching CCD XYS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/XYS/XYS.cif  
Fetching compressed mmCIF 6xn2 from http://files.rcsb.org/download/6xn2.cif  
Fetching compressed mmCIF 5b0r from http://files.rcsb.org/download/5b0r.cif  
Fetching compressed mmCIF 6n6b from http://files.rcsb.org/download/6n6b.cif  
Fetching compressed mmCIF 3k1u from http://files.rcsb.org/download/3k1u.cif  
Fetching compressed mmCIF 5tik from http://files.rcsb.org/download/5tik.cif  
Fetching compressed mmCIF 7esl from http://files.rcsb.org/download/7esl.cif  
Fetching compressed mmCIF 7bwb from http://files.rcsb.org/download/7bwb.cif  
Fetching compressed mmCIF 4ak6 from http://files.rcsb.org/download/4ak6.cif  
Fetching compressed mmCIF 4ak5 from http://files.rcsb.org/download/4ak5.cif  
Fetching compressed mmCIF 7bj4 from http://files.rcsb.org/download/7bj4.cif  
Fetching compressed mmCIF 1yi7 from http://files.rcsb.org/download/1yi7.cif  
Fetching compressed mmCIF 3qef from http://files.rcsb.org/download/3qef.cif  
Fetching CCD AHR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/AHR/AHR.cif  
Fetching compressed mmCIF 5b6t from http://files.rcsb.org/download/5b6t.cif  
Fetching CCD PB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/PB/PB.cif  
Fetching compressed mmCIF 4mlg from http://files.rcsb.org/download/4mlg.cif  
Fetching compressed mmCIF 7u2q from http://files.rcsb.org/download/7u2q.cif  
Fetching compressed mmCIF 3taw from http://files.rcsb.org/download/3taw.cif  
Fetching compressed mmCIF 3qc2 from http://files.rcsb.org/download/3qc2.cif  
Fetching compressed mmCIF 7k1r from http://files.rcsb.org/download/7k1r.cif  
Fetching compressed mmCIF 4kcb from http://files.rcsb.org/download/4kcb.cif  
Fetching compressed mmCIF 6euj from http://files.rcsb.org/download/6euj.cif  
Fetching compressed mmCIF 6b7k from http://files.rcsb.org/download/6b7k.cif  
Fetching compressed mmCIF 6byt from http://files.rcsb.org/download/6byt.cif  
Fetching CCD 83Y from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/83Y/83Y.cif  
Fetching CCD GCD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/GCD/GCD.cif  
Fetching compressed mmCIF 4ak7 from http://files.rcsb.org/download/4ak7.cif  
Fetching CCD 47N from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/47N/47N.cif  
Fetching compressed mmCIF 4uf7 from http://files.rcsb.org/download/4uf7.cif  
Fetching compressed mmCIF 6byx from http://files.rcsb.org/download/6byx.cif  
Fetching compressed mmCIF 5huk from http://files.rcsb.org/download/5huk.cif  
Fetching compressed mmCIF 3a72 from http://files.rcsb.org/download/3a72.cif  
Fetching compressed mmCIF 4hzy from http://files.rcsb.org/download/4hzy.cif  
Fetching compressed mmCIF 2exh from http://files.rcsb.org/download/2exh.cif  
Fetching compressed mmCIF 5m8e from http://files.rcsb.org/download/5m8e.cif  
Fetching CCD IMD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IMD/IMD.cif  
Fetching compressed mmCIF 8g3r from http://files.rcsb.org/download/8g3r.cif  
Fetching compressed mmCIF 2woz from http://files.rcsb.org/download/2woz.cif  
Fetching compressed mmCIF 7bwc from http://files.rcsb.org/download/7bwc.cif  
Fetching compressed mmCIF 6byp from http://files.rcsb.org/download/6byp.cif  
Fetching compressed mmCIF 8bet from http://files.rcsb.org/download/8bet.cif  
Fetching compressed mmCIF 7jvh from http://files.rcsb.org/download/7jvh.cif  
Fetching compressed mmCIF 5o3v from http://files.rcsb.org/download/5o3v.cif  
Fetching compressed mmCIF 4n2z from http://files.rcsb.org/download/4n2z.cif  
Fetching CCD 1PE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/1PE/1PE.cif  
Fetching CCD BGC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/BGC/BGC.cif  
Fetching compressed mmCIF 4onz from http://files.rcsb.org/download/4onz.cif  
Fetching compressed mmCIF 2bat from http://files.rcsb.org/download/2bat.cif  
Fetching CCD FUL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FUL/FUL.cif  
Fetching CCD NGK from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/NGK/NGK.cif  
Fetching compressed mmCIF 2vsm from http://files.rcsb.org/download/2vsm.cif  
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif  
Fetching compressed mmCIF 3akh from http://files.rcsb.org/download/3akh.cif  
Fetching compressed mmCIF 5uw5 from http://files.rcsb.org/download/5uw5.cif  
Fetching CCD CAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/CAC/CAC.cif  
Fetching compressed mmCIF 4hbs from http://files.rcsb.org/download/4hbs.cif  
Fetching compressed mmCIF 6vy6 from http://files.rcsb.org/download/6vy6.cif  
Fetching CCD MPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif  
Fetching compressed mmCIF 5o3x from http://files.rcsb.org/download/5o3x.cif  
Fetching compressed mmCIF 6r3r from http://files.rcsb.org/download/6r3r.cif  
Fetching compressed mmCIF 6r3u from http://files.rcsb.org/download/6r3u.cif  
Fetching compressed mmCIF 2vwd from http://files.rcsb.org/download/2vwd.cif  
Fetching CCD GBL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GBL/GBL.cif  
Fetching compressed mmCIF 5uw6 from http://files.rcsb.org/download/5uw6.cif  
Fetching CCD ZPR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/ZPR/ZPR.cif  
Fetching compressed mmCIF 3qee from http://files.rcsb.org/download/3qee.cif  
Fetching compressed mmCIF 6lxi from http://files.rcsb.org/download/6lxi.cif  
Fetching compressed mmCIF 8aa2 from http://files.rcsb.org/download/8aa2.cif  
Fetching compressed mmCIF 1yif from http://files.rcsb.org/download/1yif.cif  
Fetching compressed mmCIF 4o8n from http://files.rcsb.org/download/4o8n.cif  
Fetching CCD BTB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/BTB/BTB.cif  
Fetching CCD P6G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/P6G/P6G.cif  
Fetching compressed mmCIF 5z5d from http://files.rcsb.org/download/5z5d.cif  
Fetching compressed mmCIF 3inb from http://files.rcsb.org/download/3inb.cif  
Fetching compressed mmCIF 5o3w from http://files.rcsb.org/download/5o3w.cif  
Fetching compressed mmCIF 1uv4 from http://files.rcsb.org/download/1uv4.cif  
Fetching compressed mmCIF 7fik from http://files.rcsb.org/download/7fik.cif  
Fetching compressed mmCIF 6cc7 from http://files.rcsb.org/download/6cc7.cif  
Fetching compressed mmCIF 2dg0 from http://files.rcsb.org/download/2dg0.cif  
Fetching compressed mmCIF 4gjt from http://files.rcsb.org/download/4gjt.cif  
Fetching compressed mmCIF 7ty0 from http://files.rcsb.org/download/7ty0.cif  
Fetching compressed mmCIF 1wl7 from http://files.rcsb.org/download/1wl7.cif  
Fetching compressed mmCIF 3d61 from http://files.rcsb.org/download/3d61.cif  
Fetching compressed mmCIF 3nvq from http://files.rcsb.org/download/3nvq.cif  
Fetching CCD NDG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NDG/NDG.cif  
Fetching compressed mmCIF 3kst from http://files.rcsb.org/download/3kst.cif  
Fetching compressed mmCIF 5ubj from http://files.rcsb.org/download/5ubj.cif  
Fetching compressed mmCIF 4mr0 from http://files.rcsb.org/download/4mr0.cif  
Fetching CCD BME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/BME/BME.cif  
Fetching compressed mmCIF 5zqx from http://files.rcsb.org/download/5zqx.cif  
Fetching compressed mmCIF 7vci from http://files.rcsb.org/download/7vci.cif  
Fetching compressed mmCIF 6vy4 from http://files.rcsb.org/download/6vy4.cif  
Fetching compressed mmCIF 5b2d from http://files.rcsb.org/download/5b2d.cif  
Fetching compressed mmCIF 3gq7 from http://files.rcsb.org/download/3gq7.cif  
Fetching compressed mmCIF 2exi from http://files.rcsb.org/download/2exi.cif  
Fetching compressed mmCIF 2exj from http://files.rcsb.org/download/2exj.cif  
Fetching compressed mmCIF 6jym from http://files.rcsb.org/download/6jym.cif  
Fetching compressed mmCIF 4n2r from http://files.rcsb.org/download/4n2r.cif  
Fetching compressed mmCIF 3om7 from http://files.rcsb.org/download/3om7.cif  
Fetching compressed mmCIF 3c2u from http://files.rcsb.org/download/3c2u.cif  
Fetching CCD B3P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/B3P/B3P.cif  
Fetching compressed mmCIF 3d5y from http://files.rcsb.org/download/3d5y.cif  
Fetching compressed mmCIF 1gye from http://files.rcsb.org/download/1gye.cif  
Fetching compressed mmCIF 2gop from http://files.rcsb.org/download/2gop.cif  
Fetching compressed mmCIF 7zm6 from http://files.rcsb.org/download/7zm6.cif  
Fetching compressed mmCIF 6i04 from http://files.rcsb.org/download/6i04.cif  
Fetching compressed mmCIF 7txz from http://files.rcsb.org/download/7txz.cif  
Fetching compressed mmCIF 6wvz from http://files.rcsb.org/download/6wvz.cif  
Fetching CCD FMT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/FMT/FMT.cif  
Fetching compressed mmCIF 5zqs from http://files.rcsb.org/download/5zqs.cif  
Fetching compressed mmCIF 3cu9 from http://files.rcsb.org/download/3cu9.cif  
Fetching compressed mmCIF 3d60 from http://files.rcsb.org/download/3d60.cif  
Fetching compressed mmCIF 6a8h from http://files.rcsb.org/download/6a8h.cif  
Fetching compressed mmCIF 3byj from http://files.rcsb.org/download/3byj.cif  
Fetching compressed mmCIF 3om2 from http://files.rcsb.org/download/3om2.cif  
Fetching CCD CIT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CIT/CIT.cif  
Fetching compressed mmCIF 1yr2 from http://files.rcsb.org/download/1yr2.cif  
Fetching compressed mmCIF 5kja from http://files.rcsb.org/download/5kja.cif  
Fetching CCD FE2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/FE2/FE2.cif  
Fetching compressed mmCIF 3pig from http://files.rcsb.org/download/3pig.cif  
Fetching compressed mmCIF 6pdl from http://files.rcsb.org/download/6pdl.cif  
Fetching compressed mmCIF 6ms3 from http://files.rcsb.org/download/6ms3.cif  
Fetching compressed mmCIF 5nmr from http://files.rcsb.org/download/5nmr.cif  
Fetching compressed mmCIF 5c0p from http://files.rcsb.org/download/5c0p.cif  
Fetching compressed mmCIF 3byk from http://files.rcsb.org/download/3byk.cif  
Fetching compressed mmCIF 5kjd from http://files.rcsb.org/download/5kjd.cif  
Fetching compressed mmCIF 8cuk from http://files.rcsb.org/download/8cuk.cif  
Fetching compressed mmCIF 7zns from http://files.rcsb.org/download/7zns.cif  
Fetching compressed mmCIF 6ife from http://files.rcsb.org/download/6ife.cif  
Fetching compressed mmCIF 4xqf from http://files.rcsb.org/download/4xqf.cif  
Fetching compressed mmCIF 8d81 from http://files.rcsb.org/download/8d81.cif  
Fetching CCD Y70 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/Y70/Y70.cif  
Fetching compressed mmCIF 7wb4 from http://files.rcsb.org/download/7wb4.cif  
Fetching compressed mmCIF 6thb from http://files.rcsb.org/download/6thb.cif  
Fetching compressed mmCIF 3d12 from http://files.rcsb.org/download/3d12.cif  
Fetching CCD GL0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/GL0/GL0.cif  
Fetching CCD GXL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GXL/GXL.cif  
Fetching CCD LXB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/LXB/LXB.cif  
Fetching CCD LXZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/LXZ/LXZ.cif  
Fetching CCD NGA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NGA/NGA.cif  
Fetching CCD NGZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/NGZ/NGZ.cif  
Fetching compressed mmCIF 3om6 from http://files.rcsb.org/download/3om6.cif  
Fetching compressed mmCIF 4g56 from http://files.rcsb.org/download/4g56.cif  
Fetching CCD SAH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/SAH/SAH.cif  
Fetching compressed mmCIF 6cmi from http://files.rcsb.org/download/6cmi.cif  
Fetching compressed mmCIF 5kk0 from http://files.rcsb.org/download/5kk0.cif  
Fetching compressed mmCIF 7zb0 from http://files.rcsb.org/download/7zb0.cif  
Fetching CCD BCT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/BCT/BCT.cif  
Fetching CCD IML from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/IML/IML.cif  
Fetching CCD MVA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/MVA/MVA.cif  
Fetching CCD SAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/SAR/SAR.cif  
Fetching compressed mmCIF 6c7k from http://files.rcsb.org/download/6c7k.cif  
Fetching compressed mmCIF 3suc from http://files.rcsb.org/download/3suc.cif  
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif  
Fetching compressed mmCIF 7seu from http://files.rcsb.org/download/7seu.cif  
Fetching compressed mmCIF 3t1e from http://files.rcsb.org/download/3t1e.cif  
Fetching compressed mmCIF 5zqj from http://files.rcsb.org/download/5zqj.cif  
Fetching compressed mmCIF 4xkw from http://files.rcsb.org/download/4xkw.cif  
Fetching CCD GLA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/GLA/GLA.cif  
Fetching compressed mmCIF 4xla from http://files.rcsb.org/download/4xla.cif  
Fetching compressed mmCIF 4h5j from http://files.rcsb.org/download/4h5j.cif  
Fetching compressed mmCIF 6c7p from http://files.rcsb.org/download/6c7p.cif  
Fetching compressed mmCIF 6gvp from http://files.rcsb.org/download/6gvp.cif  
Fetching compressed mmCIF 2biw from http://files.rcsb.org/download/2biw.cif  
Fetching CCD 3ON from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/3ON/3ON.cif  
Fetching CCD FE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif  
Fetching compressed mmCIF 2uzy from http://files.rcsb.org/download/2uzy.cif  
Fetching compressed mmCIF 6vxk from http://files.rcsb.org/download/6vxk.cif  
Fetching compressed mmCIF 6q4z from http://files.rcsb.org/download/6q4z.cif  
Fetching compressed mmCIF 8cyi from http://files.rcsb.org/download/8cyi.cif  
Fetching CCD MTA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/MTA/MTA.cif  
Fetching CCD P2R from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/P2R/P2R.cif  
Fetching compressed mmCIF 7zm5 from http://files.rcsb.org/download/7zm5.cif  
Fetching compressed mmCIF 7vud from http://files.rcsb.org/download/7vud.cif  
Fetching CCD NI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/NI/NI.cif  
Fetching CCD OXN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/OXN/OXN.cif  
Fetching compressed mmCIF 5n4f from http://files.rcsb.org/download/5n4f.cif  
Fetching compressed mmCIF 4xon from http://files.rcsb.org/download/4xon.cif  
Fetching compressed mmCIF 6g90 from http://files.rcsb.org/download/6g90.cif  
Fetching compressed mmCIF 7q3d from http://files.rcsb.org/download/7q3d.cif  
Fetching compressed mmCIF 2vji from http://files.rcsb.org/download/2vji.cif  
Fetching CCD PG0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/PG0/PG0.cif  
Fetching compressed mmCIF 4xm3 from http://files.rcsb.org/download/4xm3.cif  
Fetching compressed mmCIF 4xnf from http://files.rcsb.org/download/4xnf.cif  
Fetching compressed mmCIF 7e7v from http://files.rcsb.org/download/7e7v.cif  
Fetching CCD R3F from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/R3F/R3F.cif  
Fetching compressed mmCIF 6c0m from http://files.rcsb.org/download/6c0m.cif  
Fetching CCD 8LM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/8LM/8LM.cif  
Fetching compressed mmCIF 6nu7 from http://files.rcsb.org/download/6nu7.cif  
Fetching compressed mmCIF 5joy from http://files.rcsb.org/download/5joy.cif  
Fetching CCD 6LW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/6LW/6LW.cif  
Fetching compressed mmCIF 4xlc from http://files.rcsb.org/download/4xlc.cif  
Fetching compressed mmCIF 6gvr from http://files.rcsb.org/download/6gvr.cif  
Fetching compressed mmCIF 4xlh from http://files.rcsb.org/download/4xlh.cif  
Fetching compressed mmCIF 6q4y from http://files.rcsb.org/download/6q4y.cif  
Fetching compressed mmCIF 1gyh from http://files.rcsb.org/download/1gyh.cif  
Fetching compressed mmCIF 5kv8 from http://files.rcsb.org/download/5kv8.cif  
Fetching CCD 6Y6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/6Y6/6Y6.cif  
Fetching compressed mmCIF 5ods from http://files.rcsb.org/download/5ods.cif  
Fetching compressed mmCIF 4xot from http://files.rcsb.org/download/4xot.cif  
Fetching compressed mmCIF 4jf7 from http://files.rcsb.org/download/4jf7.cif  
Fetching compressed mmCIF 2uzx from http://files.rcsb.org/download/2uzx.cif  
Fetching compressed mmCIF 6pwq from http://files.rcsb.org/download/6pwq.cif  
Fetching CCD PG4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif  
Fetching compressed mmCIF 6ue5 from http://files.rcsb.org/download/6ue5.cif  
Fetching CCD Q5J from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/Q5J/Q5J.cif  
Fetching compressed mmCIF 1bpo from http://files.rcsb.org/download/1bpo.cif  
Fetching compressed mmCIF 4eqv from http://files.rcsb.org/download/4eqv.cif  
Fetching compressed mmCIF 3fsn from http://files.rcsb.org/download/3fsn.cif  
Fetching compressed mmCIF 6h0f from http://files.rcsb.org/download/6h0f.cif  
Fetching compressed mmCIF 6q4x from http://files.rcsb.org/download/6q4x.cif  
Fetching compressed mmCIF 1z4y from http://files.rcsb.org/download/1z4y.cif  
Fetching compressed mmCIF 7ado from http://files.rcsb.org/download/7ado.cif  
Fetching CCD PCW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/PCW/PCW.cif  
Fetching compressed mmCIF 4wef from http://files.rcsb.org/download/4wef.cif  
Fetching CCD DF4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/DF4/DF4.cif  
Fetching CCD FSI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/FSI/FSI.cif  
Fetching CCD SFJ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/SFJ/SFJ.cif  
Fetching compressed mmCIF 7zb2 from http://files.rcsb.org/download/7zb2.cif  
Fetching compressed mmCIF 7l0e from http://files.rcsb.org/download/7l0e.cif  
Fetching CCD PLM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif  
Fetching CCD XQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/XQ7/XQ7.cif  
Fetching compressed mmCIF 6k1s from http://files.rcsb.org/download/6k1s.cif  
Fetching CCD CUX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CUX/CUX.cif  
Fetching compressed mmCIF 7mx7 from http://files.rcsb.org/download/7mx7.cif  
Fetching CCD ZR1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/ZR1/ZR1.cif  
Fetching compressed mmCIF 7mo8 from http://files.rcsb.org/download/7mo8.cif  
Fetching CCD IDS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/IDS/IDS.cif  
Fetching CCD SGN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/SGN/SGN.cif  
Fetching compressed mmCIF 7zaz from http://files.rcsb.org/download/7zaz.cif  
Fetching compressed mmCIF 6f5d from http://files.rcsb.org/download/6f5d.cif  
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif  
Fetching compressed mmCIF 7e7u from http://files.rcsb.org/download/7e7u.cif  
Fetching CCD R2F from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/R2F/R2F.cif  
Fetching compressed mmCIF 1gyd from http://files.rcsb.org/download/1gyd.cif  
Fetching compressed mmCIF 8aph from http://files.rcsb.org/download/8aph.cif  
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif  
Fetching CCD CDL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CDL/CDL.cif  
Fetching CCD LMT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/LMT/LMT.cif  
Fetching CCD PC1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/PC1/PC1.cif  
Fetching CCD PEE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PEE/PEE.cif  
Fetching CCD Q7G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/Q7G/Q7G.cif  
Fetching CCD UTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UTP/UTP.cif  
Fetching compressed mmCIF 5l5c from http://files.rcsb.org/download/5l5c.cif  
Fetching compressed mmCIF 8boz from http://files.rcsb.org/download/8boz.cif  
Fetching compressed mmCIF 3fks from http://files.rcsb.org/download/3fks.cif  
Fetching compressed mmCIF 8ap6 from http://files.rcsb.org/download/8ap6.cif  
Fetching compressed mmCIF 4fhm from http://files.rcsb.org/download/4fhm.cif  
Fetching compressed mmCIF 6tdz from http://files.rcsb.org/download/6tdz.cif  
Fetching CCD TRT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/TRT/TRT.cif  
Fetching compressed mmCIF 3iyv from http://files.rcsb.org/download/3iyv.cif  
Fetching compressed mmCIF 7mxc from http://files.rcsb.org/download/7mxc.cif  
Fetching CCD ADN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ADN/ADN.cif  
Fetching compressed mmCIF 4xjr from http://files.rcsb.org/download/4xjr.cif  
Fetching CCD OEL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/OEL/OEL.cif  
Fetching compressed mmCIF 1v3b from http://files.rcsb.org/download/1v3b.cif  
Fetching compressed mmCIF 4mza from http://files.rcsb.org/download/4mza.cif  
Fetching compressed mmCIF 4mze from http://files.rcsb.org/download/4mze.cif  
Fetching compressed mmCIF 8tid from http://files.rcsb.org/download/8tid.cif  
Fetching compressed mmCIF 7m05 from http://files.rcsb.org/download/7m05.cif  
Fetching CCD YJG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YJG/YJG.cif  
Fetching compressed mmCIF 8ctb from http://files.rcsb.org/download/8ctb.cif  
Fetching CCD PWX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/PWX/PWX.cif  
Fetching compressed mmCIF 7chu from http://files.rcsb.org/download/7chu.cif  
Fetching compressed mmCIF 6e0v from http://files.rcsb.org/download/6e0v.cif  
Fetching CCD SR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/SR/SR.cif  
Fetching compressed mmCIF 4qt8 from http://files.rcsb.org/download/4qt8.cif  
Fetching compressed mmCIF 7s0u from http://files.rcsb.org/download/7s0u.cif  
Fetching CCD 81X from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/81X/81X.cif  
Fetching compressed mmCIF 5kv9 from http://files.rcsb.org/download/5kv9.cif  
Fetching CCD I57 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/I57/I57.cif  
Fetching compressed mmCIF 4oj6 from http://files.rcsb.org/download/4oj6.cif  
Fetching compressed mmCIF 4fhn from http://files.rcsb.org/download/4fhn.cif  
Fetching compressed mmCIF 3al8 from http://files.rcsb.org/download/3al8.cif  
Fetching compressed mmCIF 4d4p from http://files.rcsb.org/download/4d4p.cif  
Fetching compressed mmCIF 7s1q from http://files.rcsb.org/download/7s1q.cif  
Fetching CCD 84W from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/84W/84W.cif  
Fetching compressed mmCIF 4xjq from http://files.rcsb.org/download/4xjq.cif  
Fetching compressed mmCIF 7om8 from http://files.rcsb.org/download/7om8.cif  
Fetching compressed mmCIF 3nvx from http://files.rcsb.org/download/3nvx.cif  
Fetching compressed mmCIF 6v0n from http://files.rcsb.org/download/6v0n.cif  
Fetching CCD SFG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/SFG/SFG.cif  
Fetching compressed mmCIF 2jox from http://files.rcsb.org/download/2jox.cif  
Fetching compressed mmCIF 3k44 from http://files.rcsb.org/download/3k44.cif  
Fetching compressed mmCIF 3qcn from http://files.rcsb.org/download/3qcn.cif  
Fetching compressed mmCIF 3qcl from http://files.rcsb.org/download/3qcl.cif  
Fetching CCD NXV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/NXV/NXV.cif  
Fetching compressed mmCIF 2zvf from http://files.rcsb.org/download/2zvf.cif  
Fetching compressed mmCIF 6atd from http://files.rcsb.org/download/6atd.cif  
Fetching compressed mmCIF 6t9a from http://files.rcsb.org/download/6t9a.cif  
Fetching compressed mmCIF 6mdc from http://files.rcsb.org/download/6mdc.cif  
Fetching CCD JEA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/JEA/JEA.cif  
Fetching compressed mmCIF 7vxg from http://files.rcsb.org/download/7vxg.cif  
Fetching CCD 83Q from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/83Q/83Q.cif  
Fetching compressed mmCIF 6suc from http://files.rcsb.org/download/6suc.cif  
Fetching compressed mmCIF 4i6s from http://files.rcsb.org/download/4i6s.cif  
Fetching compressed mmCIF 4i3d from http://files.rcsb.org/download/4i3d.cif  
Fetching CCD BLR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BLR/BLR.cif  
Found 15758 ligands in 277 hits: 47N, ACE, AHR, BMA, CA, CIT, CL, EDO, EPE,
FMT, FRU, FUC, FUL, GBL, GLC, GOL, HOH, K, MES, MFU, MG, MN, MPD, NA, NAG,
NDG, OPX, PEG, PO4, SIA, SLB, SO4, TAR, XYP, ZN  

> select HOH

Expected an objects specifier or a keyword  

> select ligand

1754 atoms, 1637 bonds, 199 residues, 3 models selected  

> select H

108 atoms, 14 residues, 1 model selected  

> close session

> open "C:\Users\rmatusiak\PROTEON PHARMACEUTICALS S.A\Projekt Booster -
> Dokumenty\04
> Bioinformatics_data\Proteins_models\212Ecol018PP_DKPHSRRH_CDS_0005.pdb"
> format pdb

Chain information for 212Ecol018PP_DKPHSRRH_CDS_0005.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
numba 0.61.0 requires numpy=1.24, but you have numpy 2.2.2 which is
incompatible.  
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.2
which is incompatible.  
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.2.2 which is incompatible.  
\---  

pip standard output:  
\---  
\---  

pyKVFinder module installed from PyPi repository.  

QWindowsWindow::setGeometry: Unable to set geometry 361x380+1100+560 (frame:
377x419+1092+529) on QWidgetWindow/"QDockWidgetClassWindow" on "LQ156M1JW03".
Resulting geometry: 367x397+1097+546 (frame: 383x436+1089+515) margins: 8, 31,
8, 8 minimum size: 338x354 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=354, y=393)))  

No structures chosen  
error dialog finished  

> kvfinder


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 566.14
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: pl_PL.cp1250
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: GIGABYTE
Model: AORUS 15P YD
OS: Microsoft Windows 10 Pro for Workstations (Build 19045)
Memory: 34,089,021,440
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.18.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.2
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202502060317
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.16
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 2.5.1
    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: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.15.4
    fonttools: 4.55.8
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    joblib: 1.4.2
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    llvmlite: 0.44.0
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.0
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.0
    numexpr: 2.10.2
    numpy: 2.2.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.2
    pynmrstar: 3.3.5
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.2
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    threadpoolctl: 3.5.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    umap-learn: 0.5.7
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1