- ChimeraX-users - RBVI Mailing Lists

Re: ChimeraX-users Digest, Vol 78, Issue 54
by Fabian Bumbak 30 Jun '23

30 Jun '23

leave On Sat, 1 Jul 2023 at 10:45, <chimerax-users-request(a)cgl.ucsf.edu> wrote: > Send ChimeraX-users mailing list submissions to > chimerax-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > chimerax-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimerax-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ChimeraX-users digest..." > > Today's Topics: > > 1. Re: Volume Series tool missing (Elaine Meng) > 2. Re: Volume Series tool missing (Jarrett Bowman) > 3. ChimeraX Questions (Bani Kaur) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Jun 2023 13:14:56 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [chimerax-users] Re: Volume Series tool missing > To: Jarrett Bowman <jarrettbow(a)gmail.com> > Cc: chimerax-users(a)cgl.ucsf.edu > Message-ID: <D9C12F1F-8A96-428D-B572-4D0E83ACD5EA(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Jerry, > The picture shows that the video tutorial you are viewing is for Chimera, > not ChimeraX. Chimera and ChimeraX are two different programs. > > ChimeraX does not have a GUI tool, as you said, but it does have volume > series capabilities via the "vseries" command, see both of the following > and links therein: > > <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hello, > > I am trying to use the volume series tool on ChimeraX version 1.6.1 for > Windows. It doesn't appear to be in my download of ChimeraX possibly along > with other tools. A tutorial I am following shows this picture: > > > > <image.png> > > > > While this is what I have: > > > > <image.png> > > > > Any help would be greatly appreciated! > > > > Jerry Bowman > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Jun 2023 14:49:14 -0600 > From: Jarrett Bowman <jarrettbow(a)gmail.com> > Subject: [chimerax-users] Re: Volume Series tool missing > To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Message-ID: > <CAFN=EO2pGxSNMRJ=ChH+QTG+WSH-G8oshP41fJtKbTBD= > DF_aw(a)mail.gmail.com> > Content-Type: multipart/alternative; > boundary="000000000000d3119b05ff5ef3b8" > > Elaine, > > Thanks! The links helped a bunch > > On Fri, Jun 30, 2023 at 2:15 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Hi Jerry, > > The picture shows that the video tutorial you are viewing is for Chimera, > > not ChimeraX. Chimera and ChimeraX are two different programs. > > > > ChimeraX does not have a GUI tool, as you said, but it does have volume > > series capabilities via the "vseries" command, see both of the following > > and links therein: > > > > <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> > > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> > > > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Jun 30, 2023, at 12:46 PM, Jarrett Bowman via ChimeraX-users < > > chimerax-users(a)cgl.ucsf.edu> wrote: > > > > > > Hello, > > > I am trying to use the volume series tool on ChimeraX version 1.6.1 for > > Windows. It doesn't appear to be in my download of ChimeraX possibly > along > > with other tools. A tutorial I am following shows this picture: > > > > > > <image.png> > > > > > > While this is what I have: > > > > > > <image.png> > > > > > > Any help would be greatly appreciated! > > > > > > Jerry Bowman > > > > >

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ChimeraX Questions
by Bani Kaur 30 Jun '23

30 Jun '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. I have attached a photo where the left one is the selected residue (Thr) and the right photo is the residue when it is changed to Ile. [image: Screen Shot 2023-06-30 at 5.38.22 PM.png] Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. I have attached a photo of the settings. [image: Screen Shot 2023-06-30 at 5.39.01 PM.png] Thank you so much for your help! Best, Bani Kaur

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Volume Series tool missing
by Jarrett Bowman 30 Jun '23

30 Jun '23

Hello, I am trying to use the volume series tool on ChimeraX version 1.6.1 for Windows. It doesn't appear to be in my download of ChimeraX possibly along with other tools. A tutorial I am following shows this picture: [image: image.png] While this is what I have: [image: image.png] Any help would be greatly appreciated! Jerry Bowman

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toolshed plugin upload - disk quota exeeded
by Lugmayr, Wolfgang 30 Jun '23

30 Jun '23

hi, i tried to upload a new starmap release and run into the following error: OSError at /submit_app/ [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Request Method: POST Request URL: https://cxtoolshed.rbvi.ucsf.edu/submit_app/?expect_app_name=ChimeraX_StarM… Django Version: 4.2.1 Exception Type: OSError Exception Value: [Errno 122] Disk quota exceeded: '/usr/local/projects/chimerax/www/production/cxtoolshed3/media/pending_releases/ChimeraX_StarMap-1.2.15-py3-none-any.whl' Exception Location: /wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages/django/core/files/move.py, line 63, in file_move_safe Raised during: cxtoolshed3.submit_app.views.submit_app Python Executable: /usr/bin/python3 Python Version: 3.8.16 Python Path: ['/usr/lib64/python38.zip', '/usr/lib64/python3.8', '/usr/lib64/python3.8/lib-dynload', '/wynton/home/ferrin/cxtoolshed/production-site/lib64/python3.8/site-packages', '/wynton/home/ferrin/cxtoolshed/production-site/lib/python3.8/site-packages', '/usr/lib64/python3.8/site-packages', '/usr/lib/python3.8/site-packages', '/usr/local/projects/chimerax/www/production'] Server time: Fri, 30 Jun 2023 04:53:50 -0700 can you please have a look at the problem? cheers, wolfgang -- Multi-User Cryo-EM Facility @ Centre for Structral Systems Biology (CSSB) @ Deutsches Elektronen-Synchrotron (DESY) Notkestrasse 85 Gebäude 15 (E.247) 22607 Hamburg, Germany Tel.: +49 40 8998-87706 Email: wolfgang.lugmayr(a)cssb-hamburg.de http://www.cssb-hamburg.de/

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Constrained Movement
by Derek Ng 29 Jun '23

29 Jun '23

Hi, Thanks so much for ChimeraX! The tool is amazing so far. Is it possible to do the Constrained Movement GUI feature from the old Chimera in ChimeraX? I couldn’t find it in the GUI nor documentation. Thanks in advanced! Derek

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alphafold PAE map color (bluered), alphafold contacts palette option and selecting interacting residues under certain PAE values
by ahramkim1128＠gmail.com 29 Jun '23

29 Jun '23

Dear ChimeraX team, I have been working with analyzing AlphaFold-predicted structures in ChimeraX and have a few queries/suggestions. 1. Color palette for PAE Maps: One of the outputs from ColabFold is a PAE map rendered in a blue-white-red color palette. I find this color scheme very useful, and the command "alphafold pae #1 palette bluered" is working well for changing the color gradient into blue-white-red in PAE map. I was wondering if it could be integrated as a clickable option in the PAE map settings in ChimeraX, similar to the existing "Color plot rainbow" or "Color plot from structure" options. 2. Alphafold contacts color palette: I'm also interested in changing the color palette for alphafold contacts to match the bluered color scheme. While I attempted to change the color palette using the command "alphafold contact #1 /A to /B distance 5 palette bluered", it resulted in all contacts being colored red, without the expected color gradient. I'm curious if there's an alternative approach or if this could be an added feature in future updates. 3. Residue selection and visualization based on PAE cut-off: Lastly, I'm looking for a method to selectively visualize the connections between certain residues based on a PAE cut-off. For example, using the command "alphafold contacts /A to /B distance 5", I can visualize all the residue connections between A and B under a distance of 5. However, this also displays connections that are poorly predicted (i.e., yellow or red lines corresponding to PAE >15). I'd appreciate if you could suggest a way to filter these poorly predicted connections or provide an option for this in the software. Thank you in advance! Best regards, Ah-Ram

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Measuring Tilt of Helices
by Das, Abhinaba 29 Jun '23

29 Jun '23

Dear ChimeraX users, I’m trying to measure the tilt of the helices with respect to the helical axis (i.e. the z-axis). As depicted in the image below, I was wondering if it would be possible to draw a line parallel to the z-axis, traversing through the stack of helices, and another perpendicular to the z-axis and finally measure the angle between the axis passing through the helix (generated by define axis command) and the perpendicular drawn to the z-axis. [cid:image001.png@01D9A9E2.A0B8D0F0] Thanks in advance Abhi

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Daily build issues
by BARRY E DEZONIA 29 Jun '23

29 Jun '23

Hello, My colleague and I are trying to install daily build(s) of chimerax. A few weeks ago, on Ubuntu 20.04, I installed the daily build for that OS just fine. Now I am trying to show my work to a colleague. We need a daily build because our work relies on a bug fix that was recently made. Anyhow he is on ubuntu 22.04 and needs to install the version appropriate for his OS. When we do so it complains that "libssl3" is missing. And when we find instructions on how to install it apt says the dependency for "glibc" can't be satisified because the version required is newer than the one installed. Now rather than messing with my colleague's system too much I'd like to know your recommendations for getting the daily build installed. Thanks.

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IMOD Generated Model and Tomogram are Offset
by Guilliams,Bradley 29 Jun '23

29 Jun '23

Hi All, I have been working with a tomogram and corresponding model in IMOD and when I load these files into ChimeraX the model and tomogram are offset (see included image). At the highest plane of the tomogram, it intersects roughly halfway up the model. Any advice on how to fix this would be much appreciated! Cheers, Bradley Bradley Guilliams (he/him/his) PhD Candidate Ackerson Research Group Analytical Resources Core - Imaging & Surface Science (ARC-ISS) Department of Chemistry Colorado State University

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Save only the sequence that is present in the model
by Eric Pettersen 28 Jun '23

28 Jun '23

> Begin forwarded message: > > From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> > Subject: Save only the sequence that is present in the model > Date: June 28, 2023 at 6:53:11 AM PDT > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Dear ChimeraX team, > > I would like to save only the sequence of a chain that is actually modelled. As I would like to do this for many files it would be great if this would work via scripting. Is this possible? > > Many thanks, > Matthias

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Docking scores only as integers??
by thomas.wein＠lmu.de 28 Jun '23

28 Jun '23

Dear all, I'm reading glide Docking results into ChimeraX. In the ViewDockX table or charts the docking score is displayed only as integers. However, typical score valus are "-4.1234" or "-8.9876", I only see the "-4.000" etc. For the correct numbers I have to go into the original files which is somehow time consuming. Is there any possibility to get a "real" score value displayed? Thanks Thomas

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Combining two volumes
by Tom Goddard 28 Jun '23

28 Jun '23

Tatiana writes: Dear ChimeraX developers, I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX. Thank you very much if you have time to help me. Tatiana

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Re: [Chimera-users] Questions regarding reply log
by Elaine Meng 28 Jun '23

28 Jun '23

Hi Prathvi, Normally one would *not* include any residue numbers in a mmaker command. You only need model numbers (not chain IDs either, except if you want to make sure that specific chains match specific other chains when each model has more than one chain). Also it is completely useless to include the @ca in a mmaker command because mmaker always only uses @ca for proteins anyway. See the mmaker help for whichever program you are using (Chimera or ChimeraX). Your description does not make sense for Chimera. You must be using ChimeraX. The specifications are different for Chimera and ChimeraX, only ChimeraX uses "/" for chains. In either program, you would simply omit the chain part of the specification if there is no chain ID. To avoid confusing others, make sure to email chimerax-users if you are asking about ChimeraX usage, and chimera-users for Chimera. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 28, 2023, at 1:47 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thank you so much for the info Elaine! > I just have one more question. > Is it possible to run the "mmaker" command without inputting chain IDs of the residues to be superimposed? > I am asking this because I have a few PDB files whose residues lack chain ID information (I know this because when I hover my mouse over one of these residues, it shows something like: "/? PRO 190") > I tried the command: mmaker #0/?:162-172@CA to #1/?:162-172@CA > But it shows the error: No molecules/chains to match specified > > > > On Tue, Jun 27, 2023 at 9:46 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Prathvi, > Both of these things are much easier/better in ChimeraX, since it has commands to do them. We are recommending everybody use ChimeraX if possible (if it has the features that they need). > > In Chimera, the Reply Log has buttons to Clear and to Save, but there are no commands for those functions. If there were commands, it would be mentioned in the Reply Log help. > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/reply.html> > > For saving only (not clearing), there are instructions of how to do it in python at the bottom of this page: > <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jun 27, 2023, at 4:21 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > Hi Elaine, > > Is there a way to clear the Reply Log using the command line? > > Is there a way to write the contents of the Reply log to a text file? > > > > -- > > Prathvi Singh, > > Research Fellow, > > Department of Biological Sciences & Bioengineering, > > Indian Institute of Technology, Kanpur-208016 > > > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu: To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Manage subscription:

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opening multiple csx files at same time
by stevensb＠ufl.edu 26 Jun '23

26 Jun '23

How can you open 2 or more csx files simultaneously in order to have the all contents of both *.csx files showing and superpositioned. This can be done for opening multiple *.pdb files which then shows all the chains of all the opened files superpositioned on the same page. But when I try to open multiple csx files, the second one completely deletes and replaces the currently open csx file and deletes what was showing from the originally open csx file.

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Re: [Chimera-users] downloading and saving multiple PDB's
by Elaine Meng 26 Jun '23

26 Jun '23

Hi Dmitry, You sent this to the chimera-users list but chimerax-users(a)cgl.ucsf.edu (CC'd here) is the better address for ChimeraX questions. We try not confuse Chimera users with ChimeraX answers and vice versa. Since your text said "Chimerax" I will answer for ChimeraX. Not sure what you mean by "multiple" ... of course you can fetch structures from the PDB using their IDs, e.g. commands: open 1zik open 2gbp 2fw0 1plx 1plz <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> If by "multiple" you mean a huge number that is not practical to put in a single command, that is a different matter. Also, a single "save" command only saves one file and it does not have option to automatically figure out filename from model name. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, ChimeraX does allow writing a single command script (.cxc file) and applying it to multiple input files when the .cxc file is opened with the "open" command and "forEachFile" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> It also allows substituting part of the input file name as the output file name. However, it was intended for the case where all the input files are local files. So as far as I know you would have to first fetch all the files from the PDB so that they are in your local cache (~/Downloads/ChimeraX/PDB/ ) and then in a separate step, use your .cxc file with this forEachFile mechanism. To do so, you would probably also need to segragate these files into their own directory since you don't also want to run the script on all of the other structures you've previously fetched from the PDB using ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 26, 2023, at 9:39 AM, Dmitry Semchonok via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear colleagues, > > Is there a way to > > • download the multiple pdb/mmcif using Chimerax knowing their ID entry? > • save multiple opened pdbs using their corresponding original names in Chimerax? > Thank you in advance. > > Kind regards, > Dmitry

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Electrostatics
by Ryan Gardner 26 Jun '23

26 Jun '23

Hello, I just want to verify that the electrostatic potential is measured in volts (V). Is this correct? Here's an example of my analysis: [image: image.png] Sorry to be a bother! -Ryan

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error opening Swissdock generated output file
by Fussner-Dupas, Eden 26 Jun '23

26 Jun '23

Hello, I am having trouble using ViewDockX with a file generated by Swissdock. When I open the clusters.dock4.pdb file it opens without issues - but when I try to use the ViewDockX tool to view each predicted pose one at a time I get the error “No suitable models found for ViewDockX” Any help warmly appreciated Cheers, Eden

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Save Image Dialog box
by McClean, Phillip 25 Jun '23

25 Jun '23

Hi Everyone, I am using ver 1.6 of Chimerax. I want to save an image for print publication, so I want to save it as 300 dpi. I used the Snapshot icon from the toolbar and it saved a 72 dpi image. In the user guide, there is mention of a Save Image dialog. The guide sounds like I can make use the dialog to select the dpi. But, I cannot find the Save Image menu. Can someone point me to it and add any help/hints on save a 300 dpi image. As always, thanks for your help. Phil McClean

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Aligning two ligands
by Karim Rafie 25 Jun '23

25 Jun '23

Hi all, I was wondering if there's a command that will allow me align two ligands to each other? Couldn't find anything online and when I try the match command I constantly run into an error, even when specifying certain atoms between two ligands. Any help would be greatly appreciated. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:e5366e3a-666f-40ea-9f71-eb5b2b395016]

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Changing spin movie default save location?
by Daniel Gilliam 21 Jun '23

21 Jun '23

Hi, How can I change the default filepath that 'Spin movie' saves to? The default for me saves to location without save permissions, so I have been unable to save images or movies. Apologies if I missed an easy answer to this in the documentation. Thanks, Daniel Gilliam

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Invert selection
by Leonardo Talachia Rosa 20 Jun '23

20 Jun '23

Dear ChimeraX community Apologies for the very naive question. In old chimera, there was a "Select - Invert selected models" command which would invert the selection solely in the selected model, whereas in chimeraX I could not find an equivalent command or option in the menu. The select invert menu will invert the selection for all open models. Is there a way to invert selection only in one model? Thank you for your time Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

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ChimeraX - Without NVIDIA
by Nguyen, Tuan /US 16 Jun '23

16 Jun '23

Hi, I'm trying to install the ChimeraX 1.6.1 on Ubuntu 22 without NVIDIA driver, I can launch the chimerax, but it gives me an error about the graphic driver, and I'm trying to open a pdb file, I don't see the image at all. Please see attached below. Would you please help? Thanks, Tuan [cid:image001.png@01D9A02C.7D05AF30]

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600 DPI Quality Images
by Dillon P Cao 15 Jun '23

15 Jun '23

Hello, How would I save an image on ChimeraX as 600 dpi? Apologies if this has been answered before. Sincerely, Dillon P. Cao

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Selecting segments overlapping atomic model
by kizziah4＠uab.edu 15 Jun '23

15 Jun '23

Is there some degree to which a segment must overlap an atomic model to be selected with "Over Sel. Atoms"? Can it be changed? I frequently use Segment Map to create custom masks for focused refinement and classification and for signal subtraction. I tend to use reference atomic models to expedite this process, but I am having problems selecting segments overlapping atomic models (compared to older versions of Chimera). I am on Windows 10 with ChimeraX version 1.5 (2022-11-24). I have experienced the same on Ubuntu-20.04 with ChimeraX v1.6.1. For example, I have an unsharpened map estimated at 4.8A resolution from RELION and an atomic model of the same structure downloadeded (via ChimeraX) from the PDB. After deleting some unneeded chains and duplicating others, fitting the model into the map using simulated density (4.8A resolution, 0.77 correlation), segmenting the map at a low threshold that covers all (but a couple of loops) of the atomic model, ungrouping the segments once for granularity, selecting the entire atomic model, and clicking "Over Sel. Atoms", no segments are selected. If I try repeating the process with the backbone only (0.80 correlation), no segments are selected. I have succeeded in some cases by ungrouping all segments ~4 times, but in this particular case it only selects a few segments corresponding to parts of some alpha helices.

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Question about MatchMaker with nucleic acids
by Leonardo BETANCURT ANZOLA 14 Jun '23

14 Jun '23

Hello, I’m currently using ChimeraX to compare different DNA binding proteins and would like to align them using match maker and the DNA helix. The problem is that the structures do not have the same DNA sequence and that is the parameter the MM uses to align. Would it be possible to align DNA using only the phosphate-sugar backbone of the molecule? In that case I’d like to tell chimera which phosphates should one aligned to which. Thank you, Leo B.

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