- ChimeraX-users - RBVI Mailing Lists

User/expert community of chimera/chimeraX
by Shivam Gupta 01 Jul '22

01 Jul '22

Hello chimera team, Greetings of the day! I was wondering if we have any official support, user or expert community of chimera and chimeraX where I can get my queries,problems and bugs solved. Looking forward to your reply. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

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Aligning a trajectory to its first frame
by Shubham Devesh Ramgoolam 30 Jun '22

30 Jun '22

Hi all, I hope you are doing well. Is there a way to align all the frames of a trajectory to its first frame for the purpose of visualization? I’m trying to visualize a residue pair in a trajectory and I have done the following: select both residues; view sel; play the movie. The issue here is that the position of the pair changes (the pair rotates across the screen) with the frame. Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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ChimeraX via Remote Desktop
by Dmitry Semchonok 30 Jun '22

30 Jun '22

Dear colleagues, Could you please share the experience on remote desktop work with ChimeraX? The ChimeraX is installed on Centos 7. Probably a certain issue holding ChimeraX from starting (OpenGL)? Kind regards, Dmitry

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Error when joining two pdbs
by Praveen Ranganath Prabhakar 29 Jun '22

29 Jun '22

Hi all, I am Praveen, a graduate student at UC Irvine. Hope you are doing well. I am using Chimera X. In my project, I have to join a protein to a peptide sequence via a peptide bond. I have loaded the PDB files of both the protein and the peptide sequence & I have identified where (between which atoms) the peptide bond has to be. After loading the PDBs, I use the following in the command line "*select #1:12.A@C#2:1.A@N*" (basically identifying the residue/atoms where the peptide bond has to be formed) to join but I get the error "*Expected an objects specifier or a keyword*" . I am sorry if this is a common error and I have missed something, I am new to Chimera. Also it would be great if someone could tell me if there is a way to save the final pdb after joining them? Thank you so much for your time, Best, Praveen

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Marking movies in ChimeraX
by Eric Pettersen 27 Jun '22

27 Jun '22

> Begin forwarded message: > > > Hi, Eric, > > Since you are here answering my question, I would like to make use of this > opportunity to ask you a question about making movie, I want to make a > movie with five different density maps from cryo-EM with different ligands > binding in two different conformation, there is no animation interface in > ChimeraX as the same in Chimera, right? It is easier for me to use > animation in Chimera to make the movie, but I have all my sessions with > colored density map in Chimera, I know I could use commands to make such > kind of movie in ChimeraX, but I found it difficult for me. Can you give > me some suggestions what should I do? I am sorry that if this bothers you. > > Have a nice day! > > Best, > Lu

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Trajectory computation slowing down overtime
by Shubham Devesh Ramgoolam 27 Jun '22

27 Jun '22

Hi all, I hope you are doing well. I have a Python script for analyzing specific residue pairs for every frame in a trajectory. It does so, by using 2 for loops: For frame in list_frames: Set current frame to frame For pair in specific_residue_pairs: Do computation The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles). The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below: [cid:image003.png@01D87E37.C872FDF0] Is there a way to maintain the same computation time for every frame in the trajectory? Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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using variables in command files
by Pranav Shah 26 Jun '22

26 Jun '22

Hi Team, Is it possible for one to declare a variable in a command file that can then be passed to via the chimeraX command line interface. A minimal example of something I would like to do is - command.cxc open $file color radial palette rainbow save $outfile.png height 512 width 512 transparentBackground True In the chimeraX command line window I would then like to run open command.cxc infile.mrc outfile.png 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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Pymol view
by Rechiche, Othman 24 Jun '22

24 Jun '22

Hi everyone, Is there a way to import/open “views” set with PyMol and open them in Chimera or ChimeraX? Best Regards, Othman

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How to gradually crop a volume with perframe command
by Edoardo D Imprima 24 Jun '22

24 Jun '22

Hi all, I would like to make a movie showing a volume gradually cropped along one axis .e.g. volume #1 region 0,0,0,410,375,336 (start) volume #3 region 0,0,0,410,375,31 (end). Could you please tell me how to provide the range in “perframe” command to perform this operation? Ie as trying something like this perframe "volume #1 region $1" 0,0,0,410,375,200 0,0,0,410,375,336 frames 10 without success though. Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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user inputs for python scripts
by Pranav Shah 24 Jun '22

24 Jun '22

Hi Team, Is there a way to provide user input to python script files? I tried using sys.argv but I keep getting an out of list error message when I call the script from the ipython shell (accessed from within the chimeraX window) 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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