- ChimeraX-users - RBVI Mailing Lists

Transparency of cartoon and surface
by Enrico Martinez 09 Apr '24

09 Apr '24

Dear ChimeraX users, I am trying to add transparency on the cartoon representation of the protein that have additionally transparent surface in the same session. hide protein target a surface protein rainbow protein target c palette paired-12 rainbow protein target s palette paired-12 transparency 90 transparency protein 10 target c The last command hides all cartoons. I've also tried adding the transparency option directly to the rainbow command: rainbow protein target c palette paired-12 transparency 20 But it had the same effect as the total disappearance of the cartoons. Is it possible to have two different levels of the transparency on both cartoon and surface representation ? Thank you in advance ! Enrico

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About surface representation
by Enrico Martinez 08 Apr '24

08 Apr '24

Dear ChimeraX users! I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation. 1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ? 2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using # first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80 This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ? Thank you very much in advance Best regards Enrico

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Suggestions for optimizing movie quality when working with file size limits?
by Vorländer,Matthias Kopano 08 Apr '24

08 Apr '24

Dear ChimeraX team, Making movies in ChimeraX is my favorite way of communicating my research, but unfortunately many journals have strict file size limits for supplementary movie files (30 MB in my case). I am wondering if there are suggestions for settings that give relatively small files with good visual appearance, i.e a specific format that works better then others. I am currently encoding in .mp4. Is it preferable to set qscale rather than quality/bitrate? I assume both bitrate and the windowsize scale linear with data size? Or are there recommendations for external software that efficiently compresses high-quality ChimeraX movies? Many thanks, Matthias

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How to download prepared molecule as pdb file in chimera X
by Mokshith Dg 07 Apr '24

07 Apr '24

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Visually filtering out unstructured regions
by David S. Fay 06 Apr '24

06 Apr '24

Hi, I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it. Thanks in advance! David

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ChimeraX becomes the default HTML viewer on Linux
by Guillaume Gaullier 05 Apr '24

05 Apr '24

Hello, I encountered an annoying behavior of ChimeraX on Rocky Linux 9.3, installed with the RPM package: ChimeraX seems to have declared itself the default application to open local html files. When I need to open an html file in ChimeraX's browser, I do it from within ChimeraX. But when I double-click on an html file, I want it to open in my default web browser (which is already running most of the time, and if not it still starts faster than ChimeraX). I could revert this behavior. I also checked that this doesn't happen on a Mac. If it is intended, in my experience it's been mostly getting in the way when doing tasks unrelated to ChimeraX, so maybe it is worth reconsidering. Cheers, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Two-sided surface coloring in ChimeraX?
by Elaine Meng 03 Apr '24

03 Apr '24

> On Mar 31, 2024, at 7:59 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: > > https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht… > Hi Elaine, > How can I mimic this image with chimerax? > Thanks > Krish > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals Hi Krish, That Chimera example includes a Chimera command script that uses a "measure contactArea" command with a "slab" option to draw a surface. <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht…> However, I can't think of a way to do it in ChimeraX, since as far as I know there is no analogous command in ChimeraX currently. ChimeraX has "measure buriedArea" but it does not have an option to create a surface model of just the contact region. Maybe others have ideas? Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: ChimeraX question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, Google Colab can predict sequences of about 2000 amino acids with a free google account -- the limit is set by the GPU memory which tends to be 12-16 Gbytes on the old Nvidia GPUs free Google Colab gives you (K8, T4, V100). You can also pay Google Colab to get GPUs with more memory that can handle up to about 5000 amino acids, but such a prediction can take 24 hours and cost about $50. I don't know anything about cosmic2 alphafold. Tom > On Apr 3, 2024, at 11:03 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Is there a limit on amino acid used for prediction? > > Also does cosmic2 alpha fold is different from google Colab alpha fold prediction? > > Best, > > Amita > > > Sent from my iPhone > >> On Apr 3, 2024, at 1:52 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. >> >> Tom >> >> >>> On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: >>> >>> Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. >>> >>> I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. >>> >>> >>> Best, >>> >>> Amita >>> >>>> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>>> >>>> Hi Amita, >>>> >>>> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >>>> >>>> Tom >>>> >>>> >>>>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> Hello, >>>>> >>>>> I would appreciate if you please answer the following questions: >>>>> >>>>> 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? >>>>> >>>>> 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. >>>>> >>>>> I hope to hear from you. >>>>> >>>>> Best, >>>>> >>>>> Amita >>>>> Department of Biology >>>>> University of Pennsylvania >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >>

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Re: ChimeraX question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. Tom > On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. > > I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. > > > Best, > > Amita > >> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >> >> Tom >> >> >>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hello, >>> >>> I would appreciate if you please answer the following questions: >>> >>> 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? >>> >>> 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. >>> >>> I hope to hear from you. >>> >>> Best, >>> >>> Amita >>> Department of Biology >>> University of Pennsylvania >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >

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Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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