September 2022 - ChimeraX-users - RBVI Mailing Lists

protonation of small molecule
by Enrico Martinez 05 Sep '22

05 Sep '22

Dear ChimeraX users! I need to protonate a small molecule from the input pdb file producing another pdb with the protonated ligand. I use the following batch script: open 'ligand_without_H.pdb' addh hbond false save ligand_with_H.pdb displayedOnly true exit Depending on the complexity of the input 3D structure of the ligand some protons could not be added so the final protonation state is not correct. Is there a possible way to fix this issue? Many thanks in advance Enrico

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AlphaFold
by Hernando J Sosa 02 Sep '22

02 Sep '22

Dear Chimera/ChimeraX, I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? Thanks Hernando [cid:fec1a7e2-7922-44b8-b86e-eb2401cd211c]

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What to do if chimerax encounters a problem that cannot be opened？
by 胡玉霞 01 Sep '22

01 Sep '22

Greetings. Thank you for the great work you have done for ChimeraX development to meet the research needs of the majority of researchers. Recently, I have encountered a problem with the ChimeraX, when I open the software I have the following prompt and then the software does not work properly. So I would like to ask if there is an update for ChimeraX (the version I am using is macChimeraX-1.4.dmg, my computer system is macOS Monterey 12.1) or if I need to download the appropriate plugins and where can I download the plugins? Thanks for reading the email and I look forward to hearing from you. Yuxia Hu Fudan University

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ChimeraX-users September 2022