September 2023 - ChimeraX-users - RBVI Mailing Lists

Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

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Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html) opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

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seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

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Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

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Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
by 18802001045＠163.com 14 Sep '23

14 Sep '23

Dear ChimeraX Maintenance Team, I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX. After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX. I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX. Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response. Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166(a)smail.nju.edu.cn

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Monitor distance angle and torsion angles along trajectoty
by CUNIASSE Philippe 14 Sep '23

14 Sep '23

Dear all, I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_575242473][signature_2653780937][signature_3407707164] -----------------------------------------------

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Setting default volume step and rms level
by Samuel Haysom 13 Sep '23

13 Sep '23

Hello, Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)? KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 12 Sep '23

12 Sep '23

Hi, I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? Is there by chance a demo for such scenario? I'd appreciate your advice. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

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ChimeraX "Fly" Command
by Kayla Deuter 12 Sep '23

12 Sep '23

Good afternoon, I am emailing you to try and troubleshoot the ChimeraX software I am currently using. I just recently downloaded ChimeraX 1.1.1 and I am operating on a Macbook Pro with High Sierra 10.13.6 software. I am currently teaching myself the program by watching tutorials and referencing the User Guide. Everything seems to work fine except for the "fly" command. I am trying to record movies for practice and examples but every command works except for the "fly" command. I went into the user guide, I've tried researching the issue, and I've done about all I can do to try resolving this issue on my own. After I create my view points, I attempt to create transitions by typing "fly view 1 view 2" but every time I try typing fly it always says command unknown and gives me error messages. When I try to further investigate the error code, it is useless and I get no answers. If there is anything I can do to fix this, please let me know. The fly command is crucial for creating a smooth animation. Best, Kayla Deuter

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Re: Trouble installing plugin
by Eric Pettersen 11 Sep '23

11 Sep '23

Hi Barry, We continue to work on this issue, but have not yet succeeded in getting installation as a source dependency to work. We hope to get it resolved soon, but it's hard to say exactly how long it will take, so in the interest of allowing you to make progress I suggest using an alternate approach -- include mdtraj as an additional package in your bundle. In your bundle_info.xml you would use an AdditionalPackages tag with a child tag of "Package" which has a "name" attribute of "mdtraj" and a "folder" attribute of wherever mdtraj got installed. Since mdtraj is not pure Python, you would also have to use a "platform" attribute of mac/linux/windows. If you also built mdtraj on other platforms you could copy it over to the machine you're building the bundle on and include additional Package tags with different platform/folder values. You also have to have a DataFiles tag with a "package" attribute of "mdtraj" and an appropriate "platform" attribute, with child DataDir/DataFile tags enumerating what to copy from the installation. One thing to keep in mind is that the installation has to be compatible with the version of Python ChimeraX is using, which is Python 3.9 for ChimeraX 1.6.1 and Python 3.11 for the daily build. So you would want to include the corresponding dependency on ChimeraX-Core. Also, a binary version of mdtraj is available for Mac (Python 3.9) so you could conceivably include that directly as a dependency (i.e. in a Dependency tag rather than a Package tag) with a "mac" platform attribute and a ChimeraX-Core dependency of ==1.6.1. For reference, SEQCROW uses the AdditionalPackages tag in its bundle_info.xml, which you can see here. <https://github.com/QChASM/SEQCROW/blob/master/bundle_info.xml> --Eric Eric Pettersen UCSF Computer Graphics Lab > OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.

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