June 2023 - ChimeraX-users - RBVI Mailing Lists

No chains in AtomicStructure
by Dominik Sordyl 13 Jun '23

13 Jun '23

Hi, I have created a python plugin that uses AtomicStructure() class to create a model based on the pdb file and custom trajectory file. The problem is that after creating the structure (adding residues and atoms) it has no chains. Due to this issue, I cannot use some of the ChimeraX features (e.g. rainbow coloring) - at least I think this is the reason. While adding new residues one has to specify the chain_id, but even if I do it those chains are not created automatically. Do I have to create chains separately or there is something that I am missing here. Would be grateful for your help. Best, Dominik

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How to play volume series in chimeraX?
by Rayees Mattoo 12 Jun '23

12 Jun '23

Hi, I want to play a volume series in chimeraX. There is an option "volume series" in chimera but could not find the equivalent option in chimeraX. Also, is it possible to 'movie record' the volume series while it is playing? Any suggestion would be helpful. Best

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Triangle attention for alphaFold2
by Cheng Fei Phung 10 Jun '23

10 Jun '23

Hi, This might not be directly related to use of ChimeraX gui software that this mailing list is targeted for. Might I ask if anyone have any suggestions for the use of triangle attention module in https://twitter.com/salmon_shitake/status/1663176260632346624 ? Regards, Phung Cheng Fei feiphung(a)hotmail.com

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sym command
by postmaster＠cgl.ucsf.edu 09 Jun '23

09 Jun '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: sym command Date: June 9, 2023 at 11:55:38 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to generate symmetric copies of the atomic structure in a filament map and I get the following error sym #1 group c6*h,39.1,19.3,7,-1 coord #2 (atomic structure is #1 and the map is #2) error - Expected a keyword What is incorrect in the command. 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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ChimeraX not able to install for ubuntu22
by himanshi singh 07 Jun '23

07 Jun '23

Greetings! Kindly find the attached screenshot for installing in ubuntu22, it says dependencies unmet. Kindly guide me. Thankyou Regards Himanshi PhD candidate IIT Kanpur India

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ChimeraX .cxs session file
by Moustafa, Ibrahim M. 06 Jun '23

06 Jun '23

Dear ChimeraX, I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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clashes & contacts
by Dmitry Semchonok 06 Jun '23

06 Jun '23

Dear colleagues, Probably very simple question, non the less - how to calculate&show the contacts/clashes in the model? We have heptamer and we would like to find out what are the contacts & clashes with 6 surrounding units. I know that chimera can do that. Also, I heard that there is also software called DIMPLOT. Does ChimeraX do the same? Thank you in advance. Sincerely, Dmitry

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Daily builds
by BARRY E DEZONIA 05 Jun '23

05 Jun '23

Hello, I am looking for the daily build for Ubuntu. I go to this page: https://www.rbvi.ucsf.edu/chimerax/download.html No daily build releases are shown for Ubuntu. Are you having trouble with the website?

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The AlphaFold predicted model is always saved as best_model.pdb. It would be nice if you could specify a different name when you start the prediction run but that is not available. I made a ChimeraX feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9128 You can request new features directly with ChimeraX menu entry Help / Report a Bug.... This can be used for both bugs and new feature suggestions. Tom > On Jun 5, 2023, at 11:51 AM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thank you. I am slowly learning how to use ChimeraX. > One other question that I haven't solved yet: when I paste a sequence into the box for structure prediction, is there a way to name it right at the beginning? > All my previous jobs are given the same name "best_model".I know I can rename them later, but it would be easier if I could name them at the start. > Jim > > > On Mon, Jun 5, 2023 at 11:30 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. >> >> Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command >> >> ui dockable false "AlphaFold Run" >> >> Tom >> >> >>> On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu <mailto:james.raymond@unlv.edu>> wrote: >>> >>> Thanks, Tom, >>> I sent another email to say that I think I solved the problem but you didn't see that one. >>> >> >>> >>> >>> Here's a cool protein structure I made today with ChimeraX. >>> I used Yasara to view it. >>> This is so great! >>> Jim >>> >>> >>> >>> On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Jim, >>>> >>>> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >>>> >>>> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >>>> >>>> Tom >>>> >>>> >>>> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> > >>>> > Dear ChimeraX, >>>> > I keep losing this window, whenever I click on it or move it. >>>> > How do I get it back again? >>>> > thank you >>>> > Jim >>>> > >>>> > >>>> > <image.png> >>>> > _______________________________________________ >>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>> > Manage subscription: >>>> >> >>

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ChimeraX - windows 10 installation/running issue
by Dmitry A. Semchonok 05 Jun '23

05 Jun '23

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ChimeraX-users June 2023