- ChimeraX-users - RBVI Mailing Lists

Alphafold2_multimer on chimeraX
by Margulies, David (NIH/NIAID) [E] 08 Nov '23

08 Nov '23

Beginning yesterday, I have had repeated failure of alphafold2_multimer running through chimerax to generate models of two protein complexes (Ab H cand L chains, for instance). Individual chains work fine. The error from Colab AI says: The error is due to a bug in the ColabFold library. The kabsch function in the colabfold.py file is using the linalg.svd function to calculate the singular value decomposition of a matrix. However, the linalg.svd function is not guaranteed to converge, and in some cases it can fail to converge. This can cause the kabsch function to fail, and in turn cause the plot_protein_backbone function to fail. The bug has been fixed in the latest version of the ColabFold library, which is available on GitHub. To fix the error, you can upgrade to the latest version of the library. You can do this by running the following command in the Colab notebook: content_copy !pip install colabfold --upgrade Use code with caution<https://g.co/legal/generative-code> Once you have upgraded to the latest version of the library, you can run the code again and the error should be fixed. Can you advise? Thanks for your help. D David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: 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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Zone interaction in rRNA
by tim smith 07 Nov '23

07 Nov '23

How do we select a zone in ribosomal RNA (nucleotide residues of rRNA) to visualize all its interaction interfaces with ribosomal proteins/H2O/ions using ChimeraX? Thank you for your support. Thank you. Best Tim

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Dynamic bonds
by Michael Patzschke 07 Nov '23

07 Nov '23

Dear colleagues, I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold. I would appreciate any help in the matter. Kind regards, Michael Patzschke

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Change default colour cycle for EM maps
by James Hooker 06 Nov '23

06 Nov '23

Hello all, I am looking for a way to change the qualitative colour cycle in ChimeraX from the default (grey, yellow, blue, purple, pink, …). I have flicked through the online documentation, but have not yet found a solution. Many people must have desired to do this at some point, right? Any advice is welcome! Best, James

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commandline to hide a map region or set a transparency in chimeraX
by Rayees Mattoo 06 Nov '23

06 Nov '23

Hi, I was wondering if there is a command line in chimeraX to hide a region of the map. To be more specific if I have to hide map around a model #1 chain A, how could I do that? Also, using the same case how do I set a transparency of 50% for the map around the chainA model #1? Actually, I want to make a movie of the vseries where I need to hide/delete/transparent some portion of the map to show the internal details of the map while playing the vseries. Any suggestions are welcome. Best

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problem with color by conservation option
by elzbieta.wator＠doctoral.uj.edu.pl 06 Nov '23

06 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator

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color by conservation problem
by Elżbieta Wątor 05 Nov '23

05 Nov '23

Hi, I am trying to color my protein structure by conservation. I prepared alignement file i fasta format and when I upload it to the ChimeraX and use command: color byattribute seq_conservation palette cyanmaroon not the whole structure of my proteins get coloured. Namely despite no mismatch in the PDB file and sequence which is first in aln file there are several residues which stays in the previously selected colour. I've already made sure that the sequence is correct and I have no further ideas how to solve this problems. I will be very grateful for your tips. Best, Ela Wator [cid:e1499547-d8cf-48a6-89cb-b2ea6e696097]

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Select truncated residues in PDB
by Vorländer,Matthias Kopano 05 Nov '23

05 Nov '23

Dear ChimeraX team, Is it possible to select all residues in a model that have been truncated to backbones rather build as a complete sidechain? Many thanks, Matthias

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installing plugin
by Dmitry Semchonok 04 Nov '23

04 Nov '23

Dear colleagues, Is anything happened with the website https://cxtoolshed.rbvi.ucsf.edu/ It seems to be still down. Kind regards, Dmitry

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mseries oscillate/loop ?
by vincent Chaptal 04 Nov '23

04 Nov '23

Hi again, it is possible to use vseries play #1 loop true, but the same command with mseries doesn't work. Same with oscillate or similar commands. I've also tried mseries #1.1-20-1 or mseries #1.20-1 but these 2 commands don't work. Is there a way to make the movement go back to the origin? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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