- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Delete pseudobonds
by Justin Prado 17 Mar '23

17 Mar '23

Good evening, I am emailing on behalf of a message that was responded to in 2018. It involved the deleting of CONECT records from a PDB file. I was wondering if there were instructions on how that was done? I look forward to hearing from you. Thank you Justin Prado

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Chimera Deployment to several MacOS Computers
by Sonny Mei 15 Mar '23

15 Mar '23

Hello, I hope all is well! I am trying to deploy Chimera into several computers and do not want to manually do this. I decided to write a script and was wondering if there is a direct download link? The link I found on your site requires users to accept the license before the dmg file is installed. Thank you, Sonny Mei -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

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Creating discs
by Prathvi Singh 14 Mar '23

14 Mar '23

Hi Elaine, Is it possible in chimera or chimeraX to create such planes for membrane proteins which show the plasma membrane boundaries as shown in: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedD3R.html If yes, then kindly tell me how to do it. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Query colors?
by Esser, Lothar (NIH/NCI) [E] 13 Mar '23

13 Mar '23

Hi, in my current project I am reading about 50 pdb files. Chimera does a good job at assigning pleasant colors automatically and I would like to get access to the chosen colors to write 2dlabels with the same color. How do I get access to the molecular (ribbon color) ? It's probably trivial but well, I somehow could not figure this out. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

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Selecting planes using command line
by Prathvi Singh 13 Mar '23

13 Mar '23

Hi Elaine, I see that after defining a plane, it gets listed in the "Axes/Planes/Ellipsoids" section with each plane having a unique ID. However, I am unable to use these IDs to select planes individually via command line. Moreover, when I hover my mouse over a plane, it displays: #0:? How to select the planes using the command line? And, can I move these planes independent of the protein model? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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export stl file
by Yifan Wang 07 Mar '23

07 Mar '23

Hi Chimer team, I have a question about exporting stl files. Because I load one pdb file in chimera and export as a stl file then I load in a CAD based software to compare with another stl file I generated through another software. So the input to generate the stl file are the same, but the results are different. The results show that two different stl files in the same 3D quadrant but it got rotated at different angles. What may cause this issue? Thank you so much! Yifan

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Issue with MD movie
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users ! I am working on visualization of MD trajectory dealing with the multi-model pdb composed of 3000 snapshots. First of all, there are no problems with this file in other software like vmd or even Chimera-X. But when I load it into the Chimera (I use context menu tools ... / MD movie), I get three times more frames (9000 !) and the overall dynamics looks very unnatural when I try to play it as a movie. Any possibilities how could I fix it ? Many thanks in advance Best regards Enrico

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Questions about cartoon visualisation
by Enrico Martinez 14 Feb '23

14 Feb '23

Dear Chimera Users! I have several basic commands related to the visualization of cartoon models: 1) Is it possible to color secondary structure elements (normally integrated in the context menu by means of tools -> depiction) via some command called from command line / script ? 2) how could I change the representation style of the cartoon diagrams e.g. radius of loops or introducing some artistic elements in alpha-helixes / B-sheets ? Is it possible to modify it via commands ? Many thanks in advance Best wishes Enrico

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Hydrogen issue with minimization
by Guillaume Grataloup 08 Feb '23

08 Feb '23

Dear support, I currently trying to perform a minimization on a hERG canal pdb file but I run into an issue I didn't manage to solve: "Residue #0:23.A (GLU/glutamic_acid) should have either atom HB1 or HB3, but not both" Maybe the problem comes from the pdb file, I put it in attachment just in case it can help understand the issue. Also my Chimera version is 1.16 and I'm on Windows Thank you in advance Guillaume Grataloup 5th year bioengineering studient at Polytech Nice Sophia, France

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A question abount "define axis"
by squirrel 07 Feb '23

07 Feb '23

Dear Chimera list, I'm Interested in finding and showing the distance of N-terminal and C-terminal between two proteins. As I can't download GUI so I use "chimera --nogui" to compute them. That's my command: open protein.pdb sel:1.Ln; measure center sel mark True radius 0.3 color cyan modelId 1; sel:1.S2; measure center sel mark True radius 0.3 color cyan modelId 2; sel:390.Lz; measure center sel mark True radius 0.3 color cyan modelId 3; sel:44.LH; measure center sel mark True radius 0.3 color cyan modelId 4; distance #1 #3; define axis name Ln_N_Lz_C #1 #3; distance #1 #4; define axis name Ln_N_LH_C #1 #4; distance #2 #3; define axis name S2_N_Lz_C #2 #3; distance #2 #4; define axis name S2_N_LH_C #2 #4; stop But I found that when I input "distance" and "define axis" the terminal shows that "Must specifiy at least two atoms/centroids to define an axis". I am puzzle because I can see the #1,#2,#3，#4 in the list. Can you give me some guidance? Thanks in advance

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