- ChimeraX-users - RBVI Mailing Lists

ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

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Chimera-Animation equivalent utility/command
by Ray Y.-R. Wang 01 May '20

01 May '20

Dear all, I have been searching for the equivalent function in ChimeraX for the Animation functionality (under Tools/Utilities) in Chimera, where we can save many checkpoints as "scenes" in one Chimera session. I am wondering whether there's a command-line equivalent thing in ChimeraX I can adapt. Thanks so much! Best, Ray

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Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

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morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

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addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

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How to hide dashed lines?
by Steve Chou 24 Apr '20

24 Apr '20

Dear ChimeraX developers and users, I see a dashed line between an ion and a side chain when I display the side chain. Is there a way to hide the dashed line, either in command line or GUI? How to select all the atoms in residues (e.g., /A:10-100) except n, c, and o atoms? Many thanks, Steve -- Steve Chou

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displaying ribbon and tube simultaneously
by Joel Meyerson 23 Apr '20

23 Apr '20

Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel

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Molecular Docking problem
by Estela Fernandes e Silva 23 Apr '20

23 Apr '20

Dears, Good night! I'm starting to use SwissDock to investigate new drugs. I'm having trouble viewing “the best result” through Chimera for Web (the browser cannot be configured) In the option “Download your predictions file” I can open all the ligands through ChimeraX (my computer's desktop) at the same time. But I would like to see only one ligand at a time. Would it be possible? Best regards Estela

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deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

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Problem with showing 4 Fe-4S in pdb with chimerax
by Meinan Lyu 22 Apr '20

22 Apr '20

Dear chimerax-users(a)cgl.ucsf.edu, There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which 4 Fe-S is in /B,F,J:303. Thanks very much. Be safe and Best, Meinan Postdoc from CWRU

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