- ChimeraX-users - RBVI Mailing Lists

capture reply from run(session, command)
by Sean Connell 08 Sep '21

08 Sep '21

Hello I was wondering if it is possible to capture the output that goes to the log when you run the python command run(session, command). For example if I run: run(session, "mmaker #2/A to #1/A”) Can I store in a variable the reply in the log file that has information about the RSMD? Sean

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distance between centers of mass using python API
by Diego Amaya 08 Sep '21

08 Sep '21

Hello, I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways : 1. *rc(session, 'define centroid :43 massWeighting true name AA1')rc(session, 'define centroid :35 massWeighting true name AA2')rc(session, 'distance AA1 AA2') * 2. *rc(session, ' measure center :43 mark true name AA1')rc(session, 'measure center :35 mark true name AA2')rc(session, 'distance AA1 AA2')* But I get this error in the third line in both cases : *chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier * What is wrong ? Thanks in advance. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Question about use of ChimeraX
by Jonathan Choong 07 Sep '21

07 Sep '21

Hi there, Hope you are doing well. I just had a question regarding ChimeraX that I was hoping to get some clarity on. I was wondering whether it was possible to use ChimeraX commands (such as open, run, save) in the system command line without actually opening the application interface? Thanks, hope to hear back from you. Kind regards, Jonathan

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Re: [chimerax-users] [Chimera-users] matchmaker for more than one chain
by Elaine Meng 03 Sep '21

03 Sep '21

Hi Mani, There is a different e-mail address for ChimeraX questions: it is chimerax-users(a)cgl.ucsf.edu CC'd here. Responses below... > On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi ChimeraX-users, > I have used recently the mmaker cmd to align two pdb each have multiple chains as below. > > mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true > > But the sequence view shows only the alignment of chain L and S. > > 1. I would like to have aligned sequences of all chains used in mmaker alignement. Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models. The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit. To use all three pairs of chains, you need to also use the "pairing ss" option: mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true pair ss Then you would get three pairwise sequence-alignment windows: L/S, M/A, and N/B. matchmaker or mmaker command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> pairing options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> > > 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? Yes, but with several steps so it may not be that convenient. Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change. However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> The attribute name is seq_rmsd as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> > > 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? For the first question, 3A: yes, depending on the "pairing" option as explained above. For the second question, 3B, I'm not sure what you want. Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment. By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses. You could tell it to use all positions, but that would change the superposition. If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition. Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition. cutoff option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDis…> rmsd command (calculate RMSD in current positions, no fitting) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> Matchmaker only gives alpha-carbon RMSD. The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures. So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward. > > 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. > > [similar to 'Edit sequence name' in the sequence viewer in chimera] Sorry, there is no way yet to change the displayed sequence name in ChimeraX. > > Please let me know how this can be done. > thank you very much > with kind regards > Mani. 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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bundle dependency not installed
by Lagerwaard, I.M. (Ilse) 02 Sep '21

02 Sep '21

Hello, I'm currently developing a bundle with a dependency on pandas. Even though I included this dependency in my bundle_info.xml file, I get "ModuleNotFoundError: No module named 'pandas'". For now, I have installed pandas on the ChimeraX console via the command prompt. For future distribution, however, it would be nice if it were immediately installed together with the bundle. I would greatly appreciate your help with this issue. Thanks in advance, Ilse

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Re: [chimerax-users] output mmCIF file
by Elaine Meng 02 Sep '21

02 Sep '21

> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it? > Thanks, > Xiangan > ---------- > File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save > mmcif_write.write_mmcif(session, path, **kw) > File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure > KeyError: ('a1', 'RPGMMDSQEFS') > > KeyError: ('a1', 'RPGMMDSQEFS') > > File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure Hi Xiangan, We recommend using the chimerax-users(a)cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time). The address you used is just for commercial licensing. Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail. You may need to attach your session file so that we can reproduce the problem. I don't know the answer, so I'm using this address to share your question with the others. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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ChineraX saves huge session files
by Dror Noy 31 Aug '21

31 Aug '21

Hi Recently, ChimeraX on my Mac (macOS Catalina) started saving very large session file. Regardless of the size of the pdb file I load - the session file is 124 MB even for small 2-3 MB pdb files. I’d appreciate any help. Thanks Dror

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Region-wise specific sub-coloring of SS elements
by Gupta, Arun 30 Aug '21

30 Aug '21

Dear ChimeraX team, Is there an easier way around by which we can do region-wise specific sub-coloring of secondary structural elements within a large protein instead of using the tedious way of identifying the secondary structural elements and then describing the residue wise specific selection of set of residues related to secondary structure elements? I am aware that we can do coloring of specific secondary structure elements in ChimeraX by following commands for e.g “color helix “darkcyan” targ c”. But, I am looking forward to do coloring, let’ say “all the helices within a protein from residues 1-300 as dark cyan and residues 300-500 as blue” Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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Adding labels in chimera X?
by rob.gruninger＠gmail.com 27 Aug '21

27 Aug '21

I am trying to figure out how to add labels to a figure in chimeraX. It was easy in the older Chimera using 2d labels but I can’t find a similar function in chimeraX and the website seems to be down so I can’t access documentation. Any direction for how I can do this? I’m wanting to add residue labels to some specific residue (catalytic and substrate binding site residues) I want to point out in a paper Thanks Sent from my iPhone

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ChimeraX site down?
by Jonathan Sheehan 27 Aug '21

27 Aug '21

It might be pointless to send this query to the list (if it runs on the same server), but are you aware of any problems with your webserver right now? I'm trying to get the files for the latest density-fitting tutorial here: www.cgl.ucsf.edu According to this site, I'm not the only one having trouble reaching it: https://www.isitdownrightnow.com/cgl.ucsf.edu.html It claims it's "Down for everyone" and "for more than a week." Thanks! -Jonathan

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