October 2023 - ChimeraX-users - RBVI Mailing Lists

ChimeraX fading?
by Elaine Meng 19 Oct '23

19 Oct '23

> On Oct 19, 2023, at 4:21 AM, Carl Johan Hagstromer <carl.johan.hagstromer(a)ki.se> wrote: > > Would love fading options, like in PyMOL > Hi Carl, We aren't Pymol users so we don't know exactly what you are referring to, but it may well be possible in ChimeraX if you could give more detail. We can put this discussion on chimerax-users(a)cgl.ucsf.edu (CC'd here) so that more folks can weigh in. ChimeraX can do: depth cueing (fading front->back), gradual fading in/out of structures and/or 2D labels by increasing or decreasing transparency over a number of image frames, and/or color modification (e.g. increasing whiteness of all current colors). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Isolde usage in Chimera
by Dmitry Semchonok 19 Oct '23

19 Oct '23

Dear colleagues, How to drag the structure, preserving the secondary structure (alpha-helix and beta-sheet) geometry in Isolde? Can I set up certain restraints to keep the correct geometry of the structure while dragging it? Many thanks! Kind regards, Dmitry

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Uncaught bounce notification
by postmaster＠cgl.ucsf.edu 18 Oct '23

18 Oct '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: command for moving atomic models in ChimeraX Date: October 18, 2023 at 5:51:07 PM PDT Dear All, I have a set of 8 proteins forming a mega complex that we are working on. The density map of the mega complex has a resolution of 2.7Ang. The atomic structures of the proteins were determined. Out of the 8, proteins 3 have C5 symmetry. I am trying to generate potential models using the atomic structures where these pentameric proteins can be expanded out (kindly see the schematic diagram S1 to S2). Is there a command (move command ??) to do so? Thanks Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Movie Record/Encode with GPU?
by Alexander Hung Lee 18 Oct '23

18 Oct '23

Hi everyone, I have another question about scripting. I decided to use the morph command over a trajectory with 200 frames (imported as separate pdb's) to make a really smooth movie. Currently, my .cxc has matchmaker #2-200 to #1; morph #1-200 frames 8 same true play false; close #1-200 (< 5 mins) hbonds #201:UNL restrict :UNL :< 5 reveal true interModel false cacheDa true coordsets true (< 5 mins) movie record supersample 4; perframe "~label; label hbondatoms" ; coordset #201 1,1593; wait 1593; ~perframe; movie encode output movie.mp4 bitrate 6000 framerate 25 (> 1 hr) The output is buttery smooth, and the hbond calculation only takes 3-4 mins even with 1600 frames. However, I have a problem with the speed of recording/emcpdomg... it's more than an hour. I found it strange since if I played the trajectory from morph using coordset/slider, it barely takes any time and is very smooth. I was wondering if there was a way to make this recording/encoding faster or to switch from cpu to gpu if that was possible (and if it would help any)? On another note, I'm experimenting with smooth_md.py script but with trajectory files instead of pdb's. I'll see which one looks better/is faster Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Open small molecule cif
by Jaremko, Matt Joseph 18 Oct '23

18 Oct '23

Hello, How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: [cid:image001.png@01DA0026.3D6BC080] Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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memory questions
by Tintos-hernandez, Alonso A 17 Oct '23

17 Oct '23

Hi i was trying to do some modeling using the alfafold colab but it says that i need to buy more memory to run more modeling, hos should i do that ? Jesus Tintos Childrens Hospital of Philadelphia Senior scientist II

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model becomes invisible behind the map when color with hexadecimal color codes
by Kai Cai 17 Oct '23

17 Oct '23

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color. This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0. Here is an example if you would like to test it: open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Opening series of pdb's in incorrect sequential order
by Alexander Hung Lee 13 Oct '23

13 Oct '23

I have a series of pdb's in a folder numbered 1 - 500 (so 1.pdb ... 500.pdb). I'm opening them in ChimeraX using *.pdb. I'm expecting 1.pdb to have ID1 and 2.pdb to to be ID2, but it appears ChimeraX is only looking at the first digit and not the whole number. Is there a way around this? For now, my work around is to use 001, 002 ... 500 instead [cid:d19d2d17-71bb-430f-8a09-65921a0ca962] Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Gaussian surface visualization of a subset of residues
by Stefano Pellegrini 13 Oct '23

13 Oct '23

To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org

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About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 12 Oct '23

12 Oct '23

Hi there! I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are: Why did the program fail to download my results? Is there a possibility to obtain my results without to re-run the process? Thanks in advance Cris Vallejo IBt, UNAM, México <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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