- ChimeraX-users - RBVI Mailing Lists

Renaming of "Non-standard residues" upon file opening
by Mikkel Dahl Andreasen 07 Jun '24

07 Jun '24

Hello I have a question regarding ChimeraX renaming residues upon loading pdb files. I am specifically referring to a pdb file containing the following lines: TITLE PLACEHOLDER_TITLE REMARK PLACEHOLDER_REMARK CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 NC3 DOPCA 1 93.725 50.146 69.265 1.00 0.00 ATOM 2 PO4 DOPCA 1 93.471 50.284 66.361 1.00 0.00 ATOM 3 GL1 DOPCA 1 93.591 50.038 63.469 1.00 0.00 ATOM 4 GL2 DOPCA 1 94.818 50.396 63.498 1.00 0.00 ATOM 5 C1A DOPCA 1 93.669 50.374 60.367 1.00 0.00 ATOM 6 D2A DOPCA 1 93.738 49.939 57.365 1.00 0.00 ATOM 7 C3A DOPCA 1 93.390 49.936 54.359 1.00 0.00 ATOM 8 C4A DOPCA 1 93.358 50.194 51.480 1.00 0.00 ATOM 9 C1B DOPCA 1 96.261 50.393 60.395 1.00 0.00 ATOM 10 D2B DOPCA 1 96.060 50.114 57.261 1.00 0.00 ATOM 11 C3B DOPCA 1 96.224 50.032 54.669 1.00 0.00 ATOM 12 C4B DOPCA 1 95.844 50.135 51.528 1.00 0.00 TER END When I load this file into ChimeraX using "open file.pdb" it renames the residue name "DOPC" to "DOP". A table appears in the Log regarding "Non-standard residues in file.pdb" wherein it lists "DOP - (DOP)" without mentioning "DOPC". However, when I open another file which contains many different types of molecules, then it does not rename "DOPC" to "DOP", even though the "Non-standard residues in file.pdb" table also appears, though this time with an entry containing "DOPC - (DOPC)". I have also previously experienced that ChimeraX renames some (not all) of my cholesterol molecules to "CHO" (instead of using the actual residue name which is "CHOL"). I had a look through the documentation for the "open" command, but I couldn't find anything useful about it. I was wondering why this is happening and if there is a way to prevent it. And just so i am clear, by prevent I don't mean revert (e.g. rename them back to "DOPC" after loading), but actually preventing the initial renaming done by ChimeraX. Kind regards, Mikkel Dahl Andreasen

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modeller fails in chimerax RC-1.8
by Roberto Marabini 06 Jun '24

06 Jun '24

Hi, I just installed chimerax RC-1.8 and tried to use "modeller" (tools->sequence->modeller comparative). The resulting error message is attached to this email. If I use chimerax 1.7 with the very same data modeller works. Am I doing something wrong or did I find a bug? cheers Roberto Follows the complete log: === modeller comparative aligned_1.fasta:2 numModels 5 fast false multichain false hetPreserve true hydrogens false waterPreserve falseWebservices job id: GN1G33GHX39IPCAE Modeller job (ID GN1G33GHX39IPCAE) finished Modeller error output Traceback (most recent call last): File "ModellerModelling.py", line 74, in <module> a.make() File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 624, in homcsr self.check_alignment(aln) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 577, in check_alignment aln.check() File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in check self.check_structure_structure(io=io) File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : Modeller run output MODELLER 10.5, 2024/01/19, r12711 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 wilkins.cgl.ucsf.edu 4.18.0-513.24.1.el8_9.x86_64 x86_64 Date and time of compilation : 2024/01/20 00:40:16 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2024/06/06 03:33:20 environ____W> The class 'environ' is deprecated; use 'Environ' instead openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL10v5}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL10v5}/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 ${MODINSTALL10v5}/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 ${MODINSTALL10v5}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL10v5}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL10v5}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL10v5}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL10v5}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL10v5}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL10v5}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806 0.269 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544 0.284 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583 0.298 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661 0.328 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 344285 336.216 0.328 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment XSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSP PDB SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPH Match * * Alignment residue type 24 (X, UNK) does not match pdb residue type 16 (S, SER), for align code 1pbx.cif_2/A (atom file 1pbx.cif_2), pdb residue number " 1", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 1pbx.cif_2/A No output models from Modeller; see log for Modeller text output.

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Converting a carbonyl group to carboxylic acid group
by Prathvi Singh 06 Jun '24

06 Jun '24

Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Molecule_to_sphere
by Noriega, Heather 05 Jun '24

05 Jun '24

Hello, I hope this email finds you well. I have a molecule that I created through the build feature in Chimera, and what I would like to do is just create a sphere of as many copies as it can fit to see the estimated encapsulation volume. However, there is no symmetry assembly to use the matchmaker and I was trying to use the sym command, but it isn't even recognizing the command. sym #1 i,222 sym #1 i, n25 Sym#1 i, 222r I have tried others with the center command, and I also tried to add copies false NewModel true at the end. What am I plugging in wrong? The molecule is saved as a pdb, and uploads no issue on ChimeraX. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Push and pulling model/map towards/away
by Pranav Shah 05 Jun '24

05 Jun '24

Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Selecting the N or C-terminus of every chain in a PDB file
by André Graça 05 Jun '24

05 Jun '24

Hi everyone! I could not figure this one out just yet, but it might be easy (?): I am interested to make a quick selection that targets the first or last atom of all the chains present in a given PDB file. /André Graça

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Fetch many pdbs/maps from the pdb-redo?
by Francisco Murphy Pérez 05 Jun '24

05 Jun '24

Dear all I thought this was going to work, `open "1iee, 2blx, 2bly" fromDatabase redo format mmcif`... but it does not. I have many more ids that I want to open... Can I fetch them all with a single command? Thanks

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Morph command for protein-ligand complexes
by Enrico Martinez 05 Jun '24

05 Jun '24

Dear ChimeraX users! I have a question about recording movie with the transitions between different conformations using morph command. Having five conformations for the same protein, after its supermpostiion using mm #2-5 to #1 I generated a trajectory with the transition using: morph #2,3,4,5,6 core 0.1 frames 100 wrap f rate linear And then recorded movie using: # start recording movie record size 3840,2160 supersample 1 coordset #7 1,400,1 computeSs true wait 400 My question is about morph command. Assuming that all 5 models are very well superimposed and the difference is only the bound ligand (which is different in every model!), would it be possible to include these different ligands in the final morphed trajectory, thus making a smooth transition between different binding poses ? Many thanks in advance ! Enrico

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How to reproduce the output of "info" in python script?
by Artie Kushner 04 Jun '24

04 Jun '24

Hi there, hope you are all doing well I'm wondering if anyone has a good idea of how to reproduce the output of the *info* command in the GUI inside a python script. Precisely the *info* command without any specifiers s.t. that all models and submodels are listed with minimal info. Like the following: *...#1.87, 4v6x Cu, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cu)#1.88, 4v6x Cv, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cv)#1.89, 4v6x Cz, shown1741 atoms, 1769 bonds, 217 residues, 1 chains (Cz)* Perhaps there is a better way to do this, but my use case is splitting a bigger structure into multiple chains (as you can tell from above there are 89 chains in 4V6X). I'd like to be able to correlate chain IDs (ex. *Cz*) with the model identifiers (ex. *#1.89*) programmatically from within python to script against individual chains further. I'm sure there is more than one way to do it, but i haven't been able to find either so far. Most that i found is the model_info command: *from chimerax.list_info.util import spec, model_info...def test_func(session, structure: AtomicStructure): print(model_info(structure))**<<<Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".* *def register_ribrepr_command(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import AtomicStructureArg, Chain, Residue, Atom desc = CmdDesc( required = [("structure", AtomicStructureArg)], required_arguments = ["structure"], synopsis = "representation ", ) register("test_func", desc, test_func, logger=logger)* but it presupposes that I pass the model by spec I pass the "top-level" structure. It throws error saying that it contains 89 instead of 1 structures: *Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".* Any other way of getting at the correspondence dict between chains/"submodels" created with i.e. *`split chains`* and their chain_id's (aka *auth_asym_id* 's) in Python space would work for me. Perhaps there is a way to list all objects in the "Models" section (picture below)? Thanks in advance Artie [image: image.png]

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Question/ GPCR complex
by Ranti Dev Shukla 03 Jun '24

03 Jun '24

Hello, Greetings from NIH, Maryland. I am trying to make FRET for G-proteins. I put CFP protein within G.alfa2 on a loop between two nearby helixes and YFP protein on the N-terminal of G-beta. I made the complex using Alphafold but how to see this complex along with the membrane? Is there some command for it please? I would appreciate your kind help. Thanks Ranti Best wishes, Ranti Dev Shukla Visiting Fellow, NIH, Rockville, MD Email: rantibio2(a)gmail.com *rantibio3(a)gmail.com <rantibio3(a)gmail.com>* Phone: +1 865-910-2985 *Teachers* make a lasting impact in the lives of their students

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