- Chimera-users - RBVI Mailing Lists

Question regarding chimerax module
by Prathvi Singh 05 Apr '22

05 Apr '22

Hello again Elaine, Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Extracting secondary structure residue info
by Prathvi Singh 03 Apr '22

03 Apr '22

Hi Elaine, I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How to run a script in ChimeraX
by Shanti Pal Gangwar 30 Mar '22

30 Mar '22

Hi I am trying to run a script in chimeraX but it did not work. I even downloaded the example files and that also did not work. I wonder if a script can be run in ChimeraX as we do in PyMol. Any help would be appreciated. Thank you Shanti Pal

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using old cmd files in chimerax
by Hansen, Bryan (NIH/NIAID) [E] 29 Mar '22

29 Mar '22

Hi, How do I used/open old cmd scripts I have or outputs from things like resmap in chimerax? Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Hello could you please help me and my editor
by Kevin Kelly 25 Mar '22

25 Mar '22

I am a visual artist from the university of Manitoba in Canada My name is Kevin Kelly I am a associate professor at the school of art . First I want to say how absolutely amazed I am at the quality and precision of this astonishing software!!!!! I am working on trying to make an animation with the images and am working with a very clever animator editor and digital designer BEN KATZ that works with CINEMA 4D. We are trying for hours to figure out how to export all the variables of visualizations of the 3D molecular models into a useable 3D model. Is there a way to export the whole model with layers? Like the surface, atoms and ribbons? And is there anyway to export the model with colors? Any suggestions would be greatly appreciated . It would be super if you could help us out! And once again WOW! All my best Kevin Kelly Sent from my iPhone

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change the protonation states
by 孙钦超 25 Mar '22

25 Mar '22

I would like to make the Glu and Asp protonated, and the Lys and Arg uncharged. While I was trying to do it by addH function with chosing the protonation sates option -> Asp, or chose His. The resulting protonation states of Glu and Arg were the same, as Glu deprotonated and Arg protonated. How could I reach the right protonatation states as I expected? Thanks Qchao

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tile function
by Hansen, Bryan (NIH/NIAID) [E] 23 Mar '22

23 Mar '22

Hi, Is there an option with the tile command in ChimeraX to get the volumes to rotate in place like it did with Chimera or maybe a different command now that I haven't found yet? Right now when I use Tile the maps rotate together round a single axis, but I liked it a lot in chimera with the tile were the maps rotated on their own axis. Thanks I'm sure it's most likely a command option that I missed in the documentation or a new command I haven't found yet. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Visualizing
by Prathvi Singh 23 Mar '22

23 Mar '22

Hi Elaine, I was wondering whether it is possible to show the axis guides at the bottom left or bottom right side of the screen just like in VMD? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Mac Studio
by Greg Williams 21 Mar '22

21 Mar '22

I just bought a Mac Studio running OS 12.3. I downloaded Chimera 1.16. None of my old .py files will open. The app tells me the files are open, but there’s no content. I can Fetch new files from the pdb, and they work fine. Is this an incompatibility with the new hardware? I know you encourage people to use Chimera X, but I need the vrml export function, so 1.16 is what I have to use. Thank you. Greg Williams

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reading output files (pdbqt) from an external vina dock run back into chimera
by Joern Werner 20 Mar '22

20 Mar '22

Hello is there a way of reading a series of pdbqt files of docked ligands using vina dock externally back into chimera for inspection and analysis? It looks like Viewdock, should do this but I have a directory full of individual ligand files and I don't know how to prepare them so that Listview reads them into an ordered set i.e. ligand1 ligand2 etc. I can read individual ligands fine. Many thanks Joern

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