- ChimeraX-users - RBVI Mailing Lists

User defined color values for each residue/position
by Niccolò Arecco 30 Nov '20

30 Nov '20

Hi, I’m using ChimeraX to visualise the structure of a complex of 4 proteins. I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. The input “colouring” file could be something like this tab delimited file: #POS AA SCORE 1 M 0.2 2 V 0.5 …. n N 0.8 But I can reshape it in a better format if necessary. If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this? In the end I’d like to be able to do something like ConSurf (https://consurf.tau.ac.il <https://consurf.tau.ac.il/>) does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least. Thanks a lot! Best wishes Nicco

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Coloring pdb surface by different colors
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow? I tried the surface command option but it seems to color the entire surface in a uniform color. Any suggestions would be very helpful. Thanks Yaikhomba

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Measuring Angles in ChimeraX
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I am trying to measure angles between three atoms using ChimeraX by typing >>> angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C However, the log reports: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C Unknown command: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C I have also tried to check if 'angle' is a valid command in the ChimeraX window I have opened. >>>usage angle In Log ---> "angle" is not a command name However, angle does seem to be a valid command in ChimeraX. In the documentation here -- http://www.cgl.ucsf.edu/chimerax/docs/user/commands/angle.html. I am using ChimeraX-1.0 ( version: 1.0 (2020-06-04)) I might have missed things out - Could you please give an idea of how i could measure angles using the command line in ChimeraX? Thanks Yaikhomba

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Build DNA structure in Chimera X
by Andreas Göransson 27 Nov '20

27 Nov '20

Dear Chimera X users, I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera? THanks in advance, Andreas Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping

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Use of EnumOption
by Daniel Esteban Palma Igor 26 Nov '20

26 Nov '20

Hi, when using the chimerax.ui.options.EnumOption, are you supposed to create a subclass that specifies the attributes "labels" and "values"? the documentation doesn't say anything about it. Regards, Daniel Palma Igor

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access to private chimeraX github
by Johannes Maier 25 Nov '20

25 Nov '20

Hi there, I really like chimeraX and I would like to have access to the github to play around more. Thanks so much in advance, Cheers, Johannes

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Specify GPU id for ChimeraX
by Shasha Feng 25 Nov '20

25 Nov '20

Hi, Is there any way to specify which GPU device for ChimeraX to run on? Currently, it uses the default GPU 0, which can disturb the existing jobs. Thanks. Best, Shasha

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Re: [chimerax-users] Set up to take pictures of structure with a specific angle
by Elaine Meng 24 Nov '20

24 Nov '20

Hi Emilie, How to use the command is shown in the "view matrix" help: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> There is no colon, you would want a command something like the following, all on one line (the Mail app may show it as broken into multiple lines but it should all be one line): view matrix camera -0.97114,-0.2031,0.12509,57.651,-0.030537,0.62598,0.77924,221.24,-0.23657,0.75293,-0.61412,-21.353 I hope this helps, Elaine > > On Nov 24, 2020, at 10:31 AM, EMILIE MONTELLIER <emilie.montellier(a)univ-grenoble-alpes.fr> wrote: > > Dear Elaine, > > Thanks for your answers, it really helps me to understand how to use ChimeraX. > > For the question 2 > I manage to get the camera matrix by using view matrix in the command. Then I moved my structure and tried to apply the camera matrix I had, but I did not suceed. > I did view matrix :the number obtained in camera position > Here is a picture of the log : > Please do you know what I did wrong? > > Thanks by advance for your help, > Best regards, > > Emilie > > > De: "Elaine Meng" <meng(a)cgl.ucsf.edu> > À: "EMILIE MONTELLIER" <emilie.montellier(a)univ-grenoble-alpes.fr> > Cc: "chimerax-users" <chimerax-users(a)cgl.ucsf.edu> > Envoyé: Mardi 24 Novembre 2020 17:09:33 > Objet: Re: [chimerax-users] Set up to take pictures of structure with a specific angle > > Hi Emilie, > (1) Cartoon thickness. You would use the "cartoon style" command to change the ribbon dimensions and shape. It can be done separately for helix, strand, and coil. For example: > > cartoon style coil thickness 1.0 > > There are many options, see: > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> > > (2) Multiple images from different sessions with same orientation. > > (A) If all your different sessions were made with either the same starting structure (same PDB file) or structures that were already fit on each other when they were opened, you could get matrix from the view that you want and apply the matrix to all the others. You would use "view matrix" without arguments in the session that already has the view you want, to report the camera matrix in the Log. Then you would use "view matrix" specifying that camera matrix in your other sessions to put them into the same view. > > (B) If all your different sessions were made with different PDBs that weren't already fit on each other, then I believe the only way is to include a reference structure in each one, make sure the reference structure is in the position you want as in (A) above, and match the structure for the image onto the reference structure (e.g. with matchmaker or align), and then hide the reference structure. > > 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 24, 2020, at 12:45 AM, EMILIE MONTELLIER <emilie.montellier(a)univ-grenoble-alpes.fr> wrote: > > > > Dear ChimeraX users, > > > > I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure? > > > > Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)? > > > > Thanks by advance for your help, > > Regards, > > Emilie

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Set up to take pictures of structure with a specific angle
by EMILIE MONTELLIER 24 Nov '20

24 Nov '20

Dear ChimeraX users, I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure? Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)? Thanks by advance for your help, Regards, Emilie ------------------------------- Emilie Montellier, PhD MSCA Post-doctoral Researcher Institute for Advanced Biosciences - Grenoble, France Prof. Pierre Hainaut's laboratory Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Problems to save my file
by EMILIE MONTELLIER 22 Nov '20

22 Nov '20

Dear ChimeraX Users, I am a new user of ChimeraX and I struggled with saving my files. I have a very naive question. I have downloaded a PDB file for p53 protein structure, then I did some modifications of the structural representation using ChimeraX. Then, I would like to save my file, with this new representation to work on it later. The problem is when I save and open again, it shows the representation from the PDB I originally downloaded, but without the work I have been doing on it. In other words: which settings should I use to save my file to keep all the visual modifications I have been doing? I would like to open the file on Chimera later, and continue my work on this file. Thanks by advance for your help, Regards, Emilie ------------------------------- Emilie Montellier, PhD MSCA Post-doctoral Researcher Institute for Advanced Biosciences - Grenoble, France Prof. Pierre Hainaut's laboratory Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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