November 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Placing a ligand in a protein structure from PDB
by Elaine Meng 30 Nov '22

30 Nov '22

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler(a)kemi.uu.se> wrote: > > Hej Elaine, > > I found you on the ChimeraX website, and I have a question. > > I have a PDB file of my protein, but not showing a ligand. > > I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX? > > Best regards, > Amit > Hi Amit, We recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) to make it more likely you get a response. Not sure what you mean by add a ligand. Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save. But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program. ChimeraX does not do docking. You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX. Moving models by hand, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Or maybe you don't have a structure of the ligand. If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command open pubchem:12120 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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font size on the task bar
by Krishnan Raman 29 Nov '22

29 Nov '22

Is it possible to change the font size(larger) on the first line of the of the taskbar file…edit select etc… For viewing at from a distance on a big screen? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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tile and 2dlabels
by Krishnan Raman 29 Nov '22

29 Nov '22

Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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chimerax hbonds batch analysis
by Visvaldas K. 28 Nov '22

28 Nov '22

Dear ChimeraX wizards, I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc", where in the script I put the following commands: open /Users/visvaldas/temp0000.pdbselect /B hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true quit However, something is wrong with hbonds line since I am getting this error:Executing: runscript myscript.cxc Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script code = compile(data, stream.name, 'exec') File "myscript.cxc", line 4 hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true ^ SyntaxError: invalid syntax What I am doing wrong? (Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent truefrom the GUI does not work either) Best wishes, Visvaldas

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Cα distance per residue in alignment
by Michael Habeck 28 Nov '22

28 Nov '22

Dear ChimeraX forum, I'm interested in getting the distance between Cα for all residues in an alignment. I've noticed that the Cα RMSD values in the txt file obtained from the header of the sequence alignment created by matchmaker via sequence header rmsd save are different from the distances measured using the rmsd or distance command. The Cα distance measured is approx. 41% higher across the entire alignment than in the saved output. When selecting a pair of aligned residues from the alignment viewer, the distance shown does not match the one in the output file but the distance measurement. I've attached a file with the respective distances for the alignment of chains A in 3c4f and 3gqi as an example. Not sure if this is a misunderstanding from my side or a bug, yet I'd greatly appreciate a clarification of the differences. With thanks in advance and best regards, Michael

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Align with specific atoms (but against all other molecules)
by Kim, Doo Nam 28 Nov '22

28 Nov '22

Hi, I’ve used align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N … to align #2 molecule against #1 molecule with backbone atoms #3 molecule against #1 molecule with backbone atoms #4 molecule against #1 molecule with backbone atoms etc… However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule with backbone atoms at once in chimeraX? I’ve used align all toAtoms #1 matchAtomNames true align all toAtoms #1 matchNumbering true to align all molecules to #1 molecule at once. However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning. I think that there should a 1 line command that aligns all molecules with specific atoms only or there is chimeraX equivalent python script as from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages Best, Doo Nam

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input delay on one computer and only for ChimeraX
by Barbara S Holme 28 Nov '22

28 Nov '22

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Re: [chimerax-users] [Chimera-users] Writesel command in chimeraX
by Elaine Meng 27 Nov '22

27 Nov '22

Hi Prathvi, Please use the chimerax-users(a)cgl.ucsf.edu address to ask ChimeraX questions (instead of chimera-users(a)cgl.ucsf.edu) so that users will not be confused about which program we are discussing. In ChimeraX you can use the "info" command to report the selection to the Log, as detailed in this previous post. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/003963.html> "info" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> It does not have an option to save a file. Instead you have to save the ChimeraX Log in another step. You can use "log clear" before you use "info" and then "log save" to save to HTML file. "log" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 26, 2022, at 5:04 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is the writesel command available in chimeraX because I could not find it in the Actions menu? > If not, then is any equivalent available apart from the command which saves selection as a new PDB file? > > Thanks once again in advance

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how to remove axes?
by Francisco Murphy Pérez 26 Nov '22

26 Nov '22

After loading a mtz file, 3 axes appear in the middle of the screen. How do I remove them? Thanks

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Display sequence alignment from structure alignment
by James H Naismith 25 Nov '22

25 Nov '22

In Chimera I can sort of print out a sequence alignment based on structural superposition. (Match-align) I can make a very nice structural superposition of very unrelated proteins with matchmaker, all I want to do is print out the resulting sequence alignment (where residues are with y A of each other) Any help gratefully received. With best wishes Jim Division of Structural Biology, Roosevelt Drive, Oxford, OX3 7BN james.naismith(a)strubi.ox.ac.uk Pronouns: he, him, his

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