September 2022 - ChimeraX-users - RBVI Mailing Lists

define contour level range when molmap
by Yanhe Zhao 25 Sep '22

25 Sep '22

Dear developer, I have docked several pdb to my reference map, there are still large area of density have not assigned any models. Right now I am doing molmap onGrid of reference map, the contour range of new generated became pretty narrow and start from 0. I was wondering which option I can use to define the contour range? Thanks and best regards, Yanhe

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Orientate models
by Yanhe Zhao 23 Sep '22

23 Sep '22

Dear Developer, I have aligned all my models to one reference model, What is the right way to orient all models based on reference model's xyz axis? (They have different coordinate system) Thanks and best, Yanhe

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(no subject)
by Tianming Qu 23 Sep '22

23 Sep '22

Dear ChimeraX group, My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: [cid:image001.png@01D8CD9D.17E4A690] I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want. Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help. Best, Tianming

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Website downtime starting Tuesday, Sep 27
by Elaine Meng 23 Sep '22

23 Sep '22

The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fixing the PDB
by Dmitry Semchonok 23 Sep '22

23 Sep '22

Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog. I suppose that the pdb file is corrupted somehow. Is there a way to fix it? Kind regards, Dmitry

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Only retrieving the first predicted model in AlphaFold?
by Yao-Chi Chen 22 Sep '22

22 Sep '22

Hi: By ChimeraX, I am using AlphaFold to predict several protein-protein complexes. These complexes totally comprised about 600-800 amino acids. To have the predicted results as soon as possible, I would like to ask: 1: Is there a way to predict only one model(the best one)? 2: what's the advantage of using the Energy-minimized structures? Could I just not use it? Thanks for your help. backy

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AlphaFold July 2022 update to PAE json file - cannot open PAE file with ChimeraX.
by Brandon Payliss 21 Sep '22

21 Sep '22

Hi there, I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows: JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance" It appears that AlphaFold reduced their JSON file size by 4X on July 28th 2022 (https://alphafold.ebi.ac.uk/faq) and it no longer uses “distances”, “residue 1” and “residue 2” keys. Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold? Thanks for your time! Best, Brandon

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fitmap command in chimerax
by Yanhe Zhao 21 Sep '22

21 Sep '22

Greeting there developer, I am using fitmap command of chimerax to fit pdb to map, the command as below: fitmap #2,3 inMap #1 seq 2 res 3.7 #2 and #3 are copy of each other and I manually placed them in different positions in map, #2 and #3 come to same position after the command running, I had shift option false, but come to same result. I remember it works in chimera. Could you please point me out? Thanks and have a nice day, Yanhe

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tips for large 180kda protein for morph
by Krishnan Raman 20 Sep '22

20 Sep '22

I morphed a 180kda protein. Trying to view it in stereo with surface. Works good but slow. Any tips/ideas to make the morph faster? Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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comparison of 2 similar models
by Dmitry A. Semchonok 18 Sep '22

18 Sep '22

2 1

ChimeraX-users September 2022