- ChimeraX-users - RBVI Mailing Lists

Alter method of distance calculated for "closest" command
by Alexander Lee 09 Jul '24

09 Jul '24

Currently, I have these commands to calculate the closest 5 :SIA out of 45 to a binding site each frame parm ../2_md/CPLX_Neut_Sol.parm7 trajin ../2_md/10.1.produ.nc rms :1-1469 first # align receptor closest 5 :132-134 solventmask :SIA closestout SIA2ChainA_Binding_sites.dat name SIA run exit The output file contains Frame Molecule Distance FirstAtom# which to my understanding, the distance is from the :SIA atom closest to the center of mass of the residues :132-134. 1. Is there some way to do the distance from center of mass :SIA to center of mass residues instead? * ex: [distance of closest :SIA atom to residues] > [distance of :SIA center of mass to residues] 2. Is there a way to do RMSD calculation of those selected closest ligands to a pdb reference? I was thinking along the lines of "for FRAME in" maybe? Thank you, Alex

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Label “check_interface” residues in ChimeraX
by Gupta, Arun 09 Jul '24

09 Jul '24

Hello ChimeraX team, I came to know this fabulous ChimeraX custom “check_interface” command to instantly identify interface residues between chains A and B of protein complex model #1. It works nicely with any number of protein complex models for e.g. #1, 2, 3, 4 with chains A and B However, when I am trying to “label” the identified interface residues using the below mentioned ChimeraX command for the various protein complex models #1, 2, 3, 4. It doesn’t seem to work. I am interested to identify and label the interface residues for the related set of various protein complex models #1, 2, 3,4. label sel text "{0.label_one_letter_code}{0.number}" Can somebody suggest what I am doing wrong with the ChimeraX “label” command ?? Thanks a lot ! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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ChimeraX for mobile platforms
by Schäfer, Christian 05 Jul '24

05 Jul '24

Hello I was wondering if you are planning to release a ChimeraX version for mobile platforms such as iOS for iPad? Best, Christian

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markers radius
by Yanhe Zhao 05 Jul '24

05 Jul '24

Dear ChimeraX community, I thought the radius of marker is in angostrom, right? And is that possible to set the transparency of the marker? Thanks and cheers, Yanhe

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Announcing chimerax-emacs
by Zach Pearson 05 Jul '24

05 Jul '24

Hi ChimeraX Users, Over the holiday, I wrote a package that will let you use the command line from Emacs, leveraging ChimeraX’s rest server. https://github.com/zjp/chimerax-emacs This should be helpful if you use Emacs as your main editor and you want to debug your bundles without leaving your editors. Contributions from other emacs users welcome. — Zach

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Doubt about sequence visualization after real.space.refinement in phenix
by Leyre Marin Arraiza 04 Jul '24

04 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding model sequence visualization after real.space.refinement in phenix. After I worked on my model in ISOLDE and Coot, I deleted some residues that were out of the map density. Then, a dashed line appeared in my model, connecting the gap between the remaining residues (example, ALA97------GLN110). When I visualize the model sequence in ChimeraX, the deleted residues appear boxed with a rectangle, to indicate they are missing in the structure. Once I get the results back from the phenix real.space.refinement, and I visualize the model sequence in ChimeraX again, the deleted residues do not appear boxed anymore, but they are gone instead from the visualized sequence, keeping their corresponding numbers but not showing a boxed gap (in the example I mentioned they jump from 97 to 110 directly). I would like to keep the deleted residues boxed in the sequence when I visualize it. Is that possible? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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show 5% or 10% Z-axis of a fibril density
by Binh Nguyen 03 Jul '24

03 Jul '24

Dear all, Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map? [cid:11c579f0-867a-4136-b817-27e4c071e57e] I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. 1. Use volume eraser with a big diameter sphere 2. Build a rough backbone carbon model in 1 layer, and do zone selection. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Doubt about chimera
by DIEGO ANGOSTO BAZARRA 03 Jul '24

03 Jul '24

Hello, My name is Diego. I’m a beginner user of ChimeraX (1.8) and I was wondering if there is an option to check the % of similarity between two structures after making the matchmaker. I mean, I make a matchmaker with two structures, can I see the % of similarity between these two structures? Not between the sequences, but between the structures. Thank you very much for your time and attention. Best regards Dr. Diego Angosto Bazarra Molecular inflammation and experimental surgery group. IMIB. University Hospital Virgen de la Arrixaca

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ChimeraX workshop
by Jisoo Hwang 03 Jul '24

03 Jul '24

To whom it may concern, Good afternoon! I hope this email finds you well. I'm a student doing research at Johns Hopkins and was wondering if it'll be possible for us to set up a zoom meeting to ask some questions about the software. It's my first time using the software and it would be incredibly helpful if we can have a short workshop going over the features of ChimeraX. We're trying to include a 3D structure in a paper that we're planning on publishing soon. Please let me know if there's any other resource that you can point us to if we can't do a zoom meeting. Thank you so much for your help! Best, Suzie Hwang

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Request for Assistance: Selecting and Visualizing Interacting Residues in UCSF ChimeraX
by Rashmi Aggarwal 30 Jun '24

30 Jun '24

Dear UCSF ChimeraX Support Team, My name is Rashmi, and I am currently working on molecular docking studies as part of my research. I have been using UCSF ChimeraX version 1.8 for visualizing and analyzing protein structures. I am facing difficulties in performing the following tasks related to identifying interacting residues between chains A and B within 4 angstroms, similar to what I have previously done in PyMOL: 1. Select residues in chain A that are within 4 angstroms of chain B: select interactA, byres ((chain A) within 4 of (chain B)) 2. Select residues in chain B that are within 4 angstroms of chain A: select interactB, byres ((chain B) within 4 of (chain A)) 3. Combine the selections for interacting residues: select interaction_residues, interactA or interactB 4. Show interacting residues in stick representation and color them yellow: show sticks, interaction_residuescolor yellow, interaction_residues Despite attempting various commands and exploring the graphical user interface, I have been unable to achieve the desired results using UCSF ChimeraX. Could you please provide guidance on the correct commands or steps to accomplish this task in ChimeraX? Any assistance or advice would be greatly appreciated, as I have a pending deadline for my project. Thank you very much for your attention to this matter. I look forward to your prompt response. Best regards, Rashmi

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