- ChimeraX-users - RBVI Mailing Lists

Default Save Location
by William Wang 02 Feb '22

02 Feb '22

Hi ChimeraX Team. Is there anyway to set the default location for the save command as somewhere other than desktop? Thank you William Wang Undergraduate Student Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Building ChimeraX Bundle
by Zeng, Katie 01 Feb '22

01 Feb '22

Dear ChimeraX Users, I'm currently working on a bundle for building lipid membranes and I have a few questions: 1. A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle? 2. Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them. 3. Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them. Thank you so much for your help! Best Regards, Katie

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hbonds and the number of detected interactions
by Enrico Martinez 31 Jan '22

31 Jan '22

Dear ChimeraX users! I have a question regarding calculations of the hydrogen bonds and its visualisation using hbonds. Here is my command: hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color turquoise distSlop 0.4 angleSlop 20 intraRes false So I ignore intraRes (since the ligand is also present in the #1) and calculate hydrogen bonds using default parameters. 1) How can I modify geometric criteria for the calculations (is this distSlop / angleSlop) to increase the distance for the consideration of potential h-bonds ? In particular as you may see on the attached image the bond between the side-chain of the Glu166 and NH of the ligand is absent (I've just checked the same structure using py*ol and it could detect this contact). 2) In the case of another ligand, I could visualize two h-bonds provided by two hydrogens of the side chain of the Gln189 (same residue) with two different oxygens of the ligand. Is this correct? Many thanks for the tips! Yours sincerely Enrico

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ChimeraX 1.4 Download?
by Nayla Abney 27 Jan '22

27 Jan '22

Good evening, Hope you are doing well! I am trying to use your ChimeraX 1.4 download after watching this AlphaFold Protein Complex via ChimeraX Youtube video (https://www.youtube.com/watch?v=6lXeCPuTePs) However, I am having issues finding the download for the 1.4 version because your website only shows the 1.3 download (https://www.rbvi.ucsf.edu/chimerax/download.html) When I try using this version, I am having issues with inputting the sequence in the correct format because I keep getting a sequence argument error. I have tried looking up documentation for this version and this error, however, I am only seeing 1.4 documentation. Could you guide me in the right direction of where I should go ideally for the 1.4 download? I guess my Googling skills could use some help :) Thank you! ------------------------------------------------------ Nayla

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Help viewer is blank after upgrading to Fedora 35
by Nicholas R Silvaggi 26 Jan '22

26 Jan '22

Hello, I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this? Thanks for your help, Nick Silvaggi P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists. Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 372D Phone: 414-229-2647 silvaggi(a)uwm.edu

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Modeller python script
by Mary Liu 26 Jan '22

26 Jan '22

Dear Chimera X team, I'm using Modeller in ChimeraX to build a homology model. Is there a way to look at the python script to know how it works? Thanks Mary

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3Dconnexion
by Wang, Difei (NIH/NCI) [C] 26 Jan '22

26 Jan '22

Hello ChimeraX team, Thanks for developing the ChimeraX! It is easier to use than Chimera. However, I noticed that my 3Dconnexion could not work anymore when I use ChimeraX. Will it be possible to include such a function in the future version of ChimeraX? Thanks, Difei ======================== Difei Wang, Ph.D. Bioinformatician (Contractor) BB/DCEG/NCI/NIH 9609 Shady Grove Rd. Rockville MD 20850 USA Tel: 1-240-276-5092 ========================

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Surface coloring
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the protein-ligand binding visualizations using surface representation for the protein. In this case (please see enclosed example) I used mlp palette moccasin:sienna:sandybrown range -55,55 to make this expression of the protein in the Mountain style :-) Two questions: 1) how can I introduce more "dark" gradients into the cavities (similar to the vulcan) ? 2) is it possible to switch the coloring pattern from such a "realistic" view to the animated "cartoon" style ? 3) Any additional advice for the surface visualisations ? Many thanks in advance! Enrico

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artistic cartoon visualisations
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the improvement of the cartoon visualizations. Here are some options that I have found very cool: preset 'overall look' publication cartoon style coil thickness 0.22 set silhouettes t; set silhouetteColor firebrick; set silhouetteDepthJump 0.02 could you please suggest me something, which may further develop these ideas? In particularly I would like to improve representations of the beta-sheets making the arrow-ends more elongated and cylindrical Many thanks in advance Enrico

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Debian 10 Installation
by Martin Urban 25 Jan '22

25 Jan '22

Dear ChimeraX users, I have a problem with the installation of ChimeraX under Debian 10 buster. I downloaded the ucsf-chimerax_1.3ubuntu18.04_amd64.deb from the official website. I installed it one time with: /sudo dpkg -i //ucsf-chimerax_1.3ubuntu18.04_amd64.deb /and also with /sudo apt-get install .///ucsf-chimerax_1.3ubuntu18.04_amd64.deb./ Both times I get the same error message: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in " " even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. The full error message is as attachment in this mail. I searched the web for an answer and came up with three entries of this mailing list. I followed the described way in these mails, but nothing worked for me (1st mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002797.html; 2nd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002770.html; 3rd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html) Do you have an answer or a solution to my problem? Greetings from Germany -- Martin

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Ribbon Thicken
by Cameron Larson 25 Jan '22

25 Jan '22

Hello, Is there a way to thicken ribbons so I can 3d print a structure? What do you recommend for 3d printing a structure? -Cameron Larson

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Re: [chimerax-users] rename a ligand from UNK 999
by Rangarajan, Amith 25 Jan '22

25 Jan '22

Dear ChimeraX users, When i add a pdb file to chimera , the resulting model displays the ligand as UNK 999 and when i am having multiple models , it will help to be able to edit the UNK to name the ligand. is there a way to do it ? thanks , amith

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Displaying secondary structure elements
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! Could you suggest to me the command which will 1) hide all loops from the selected object? 2) hide all loop regions which contain more than 10 residues (=hide long loops)? Thank you in advance! Enrico

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Surface representation of protein-ligand interactions
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! I am working on the surface representation of the protein-ligand contacts. Here is my script: # load pdb of the complex and keep inly the 1st model open pdb.pdb close #1.2-end #calculate electrostatic surface coulombic protein key true #change view of the ligand size ligand atomRadius +.8 color #1.1 & ligand & C gold style ligand sphere #protein-ligand contacts hbonds #1.1 & ligand reveal true log true contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange ~label ligand hide #1 & protein bonds hide #1 & protein pseudobonds Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand? i've tried: transparency 20 surface, but it change the transparency for whole surface 2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ? 3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange Many thanks in advance! Cheers Enrico

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Color atoms by RMSD
by Nebojsa Bogdanovic 21 Jan '22

21 Jan '22

Hello, I am looking to color the atoms (cartoon representation) by RMSD values obtained from the matching of the two structures. Is there such a function? I would like to show which part of the target domain is moving the most in comparison to the previously x-ray solved structure of a know ligand state without showing the actual structures overlaid. Thank You very much. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Assessment of labeling data using ChimeraX
by Alessio Di Ianni 20 Jan '22

20 Jan '22

Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224

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selecting and translating / rotating 1 of the models/maps
by Dmitry Semchonok 20 Jan '22

20 Jan '22

Dear colleagues, Quick question. In chimeraX, with multiple models, how can I select and rotate/translate only one/ or two of them? In chimera it was possible to make the selection in the model panel. Kind regards, Dmitry

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view and the center of mass of the selection
by Enrico Martinez 20 Jan '22

20 Jan '22

Dear ChimeraX users! I am using view command to center the camera on the ligand an then, to rotate th whole system to the desired position: view #1.1 & ligand orient clip false; turn z 90; turn y 45; turn x -90; turn x 77 may I rather center the camera on the center of mass of the ligand calculated using measure center ligand If so, how may I combine the both commands together? Thank you in advance! Enrico

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Feature requests
by Ishwar Radhakrishnan 19 Jan '22

19 Jan '22

Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: 1. Render by Attribute 2. Ability to read .poc files created by CASTp Thanks, Ishwar

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service unavailable for toolshed
by Bharti Singal 18 Jan '22

18 Jan '22

Hi , I am trying to install isolde and clipper tools on chimerax 1.3 but the toolshed is giving error for last 24 hours "service unavailable". Is it possible to get the download link of these two tools as I need them for some urgent work? Best regards, Bharti Singal Bharti Singal, Ph.D. Postdoctoral Scholar (Al-Bassam's Lab) Department of Molecular and Cellular Biology| College of Biological Sciences| University of California, Davis| 605 Hutchison Dr, Davis, CA 95616, USA

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labeling of protein-ligand interactions
by Enrico Martinez 18 Jan '22

18 Jan '22

Dear ChimeraX users! I am working on the visualization of the protein-ligand interactions. The two below commands are used to visualize and label amino acids involved in the interactions with the ligand contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display How could I increase the font size and change the colour of the displayed amino acid labels (like Tyr-188)? Is it possible to hide the name of the ligand which always appears after the label command? Many thanks in advance! Enrico

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Alphafold multimer
by Rafael Ponce 17 Jan '22

17 Jan '22

Dear Sir or Madam, I want to predict the structure of a complex in ChimeraX using alphafold, but it seems that this feature is going to be in version 1.4 but version 1.3 is the one that is currently available, so I would like to know if you have an estimation of when the version 1.4 will be available to download. Thank you in advance for the information. Best regards, Rafael Ponce

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zoom on the selection after orientation of the selected object
by Enrico Martinez 17 Jan '22

17 Jan '22

Dear Chimera users! I am using ChimeraX for the visualization of protein-ligand interactions comparing two different pdb structures A - ensemble for doclong; B- X-ray pose: open A.pdb open B.pdb' match #2 to #1.1 # close all docking poses with the exemption of the first pose: close #1.2-end view wait # hide the protein from X-ray pose keeping only ligand for visualisation: hide #2 & protein cartoon hide #2 & protein surface hide #2 & protein #orient view on the model 1.1 and zoom closer view #1.1 orient; turn z 90 zoom 1.5 wait The problem is that when I use zoom 1.5 after view #1.1 it hides completely the representation for the molecule on the current GUI. Otherwise, it works fine if I center view on the both A and B: view orient; turn z 90 zoom 1.5 How could I zoom the screen properly after orientation of the view on the first molecule? Many thanks in advance! Enrico

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Cleaning a pdb file
by Martin Urban 16 Jan '22

16 Jan '22

Hey there, I have a specific pdf file (3BMP.pdb) and I would like to "clean" it from the chemical compounds which are in the file. I would like to know if there is anyway in ChimeraX to "clean" the file programmatically? Greetings from Germany - Martin

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Re: [chimerax-users] [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions
by Elaine Meng 16 Jan '22

16 Jan '22

See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. Best, Elaine > On Jan 14, 2022, at 3:03 PM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Thank you very much, Elaine! > I really like ChimeraX and it looks so great for me with all of those > presents :-) I will look for the details regarding the options. Just a > few addtional questions regarding customizing representation of > protein-ligand interactions using ghost preset: > In particular: I would like to color ligand (in orange??) > To add labels (like Try-193) on the displayed side-chains around the ligands > To change background from black to indigo! > :-) > Many thanks in advance! > Cheers > Enrico > > пт, 14 янв. 2022 г. в 23:48, Elaine Meng <meng(a)cgl.ucsf.edu>: >> >> Hello, >> It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa. >> >> As for your other questions, which commands do certain things... >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >> >> >> (1) close submodels except for first one. Maybe something like command: >> >> close #1.2-end >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> >> >> (2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands: >> >> ~ribbon >> surface protein >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> >> >> Or you could try a surface-showing preset, e.g. >> >> preset ghost >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html> >> >> (3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> >> >> You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set" >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html> >> >> ... and the "making images" page with several relevant commands >> <https://rbvi.ucsf.edu/chimerax/docs/user/images.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 Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Chimera's users! >>> First I wish Happy New Year to everyone! >>> I am just switching from Chimera to ChimeraX that I am going to use in >>> no-gui (batch) mode to prepare screen shots of protein-ligand >>> interactions based on the protein-ligand docking poses. Basically I am >>> loading a pdb file of the complex (consisted of protein and ligand in >>> multi-model format) from the terminal of my macOSX. I have a template >>> for a batch file created in the bash script on the fly, that I used 2 >>> years ago with an early version of ChimeraX. >>> >>> # a batch file for chimeraX >>> printf "open ${pdb} >>> view; zoom 1.0; turn x 90; turn z -80; >>> wait >>> # options for appearance >>> preset 'overall look' publication >>> # set bg powder blue >>> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 >>> >>> # make info of the screen >>> 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 >>> ypos .92 size 35 >>> >>> # options for light >>> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 >>> shadows true qualityOfShadows finer >>> >>> save image ${structure}/${pdb_name}.png format png width 800 height >>> 600 supersample 4 transparentBackground false >>> wait >>> exit" > chimeraX.${pdb_name}.cxc" >>> >>> then I use it directly in terminal as >>> chimerax-daily chimeraX.${pdb_name}.cxc" >>> >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >>> >>> Yours with thanks >>> Enrico >> >

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Color Model by Another Model
by Anderson, Jacob 15 Jan '22

15 Jan '22

I have a use case where I would like to color chains of model X by the chains of model Y (they are duplicates). What might be the best way to do this? For example, I thought there may be a way to run something like: "info colors #1 byChain" to get the colors of all chains printed to the log like "#1/A blue, #1/B red . . .". Then one could easily change #1 to #2 with sed in a text editor. Does a tool like that exist in ChimeraX? Or has might anyone have tips for coloring a model's chain by another models chains? jacob

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Saving images in nogui mode
by Tom Goddard 14 Jan '22

14 Jan '22

Hi Erico, Greg is right that only Ubuntu and CentOS Linux ChimeraX versions include rendering images in no gui mode. But I made rendering in no gui mode work on macOS about a year ago, but it is not in the distribution because it is such a rarely used feature it did not seem worth increasing the distribution by 16 Mbytes. But I could provide this to individuals who need it. Tom > On Jan 14, 2022, at 3:05 PM, Greg Couch via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > That is correct. You would need to start ChimeraX with the --offscreen flag to be able to save images in nogui mode (offscreen implies nogui). And that only works with the Ubuntu and CentOS versions of ChimeraX. > > -- Greg > > On 1/14/2022 2:48 PM, Elaine Meng via Chimera-users wrote: >> Hello, >> It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa. >> >> As for your other questions, which commands do certain things... >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >> >> (1) close submodels except for first one. Maybe something like command: >> >> close #1.2-end >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> >> >> (2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands: >> >> ~ribbon >> surface protein >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> >> >> Or you could try a surface-showing preset, e.g. >> >> preset ghost >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html> >> >> (3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> >> >> You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set" >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html> >> >> ... and the "making images" page with several relevant commands >> <https://rbvi.ucsf.edu/chimerax/docs/user/images.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 Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Chimera's users! >>> First I wish Happy New Year to everyone! >>> I am just switching from Chimera to ChimeraX that I am going to use in >>> no-gui (batch) mode to prepare screen shots of protein-ligand >>> interactions based on the protein-ligand docking poses. Basically I am >>> loading a pdb file of the complex (consisted of protein and ligand in >>> multi-model format) from the terminal of my macOSX. I have a template >>> for a batch file created in the bash script on the fly, that I used 2 >>> years ago with an early version of ChimeraX. >>> >>> # a batch file for chimeraX >>> printf "open ${pdb} >>> view; zoom 1.0; turn x 90; turn z -80; >>> wait >>> # options for appearance >>> preset 'overall look' publication >>> # set bg powder blue >>> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 >>> >>> # make info of the screen >>> 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 >>> ypos .92 size 35 >>> >>> # options for light >>> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 >>> shadows true qualityOfShadows finer >>> >>> save image ${structure}/${pdb_name}.png format png width 800 height >>> 600 supersample 4 transparentBackground false >>> wait >>> exit" > chimeraX.${pdb_name}.cxc" >>> >>> then I use it directly in terminal as >>> chimerax-daily chimeraX.${pdb_name}.cxc" >>> >>> may you suggest some commands that I may introduce into my batch file to >>> 1) delete all models from the multi-model pdb file with the exemption >>> of the first model. >>> 2) switch from cartoon to surface representation of the protein >>> 3) visualize protein-ligand non-covalent interactions in the current model >>> >>> Yours with thanks >>> Enrico >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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Re: [chimerax-users] [Chimera-users] Autodock Vina plugin
by Ralph Loring 12 Jan '22

12 Jan '22

Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users(a)cgl.ucsf.edu> wrote: > You can remove hydrogens from the protein part only using Chimera (or > ChimeraX) command: > > delete H & protein > > That would not include the water, however. You could also do this to > remove water hydrogens: > > delete H & solvent > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users < > chimera-users(a)cgl.ucsf.edu> wrote: > > [...] > > one question: > > how I could remove only protein's Hydrogen atoms using Chimera's > > command line (keeping them on the ligand)??? > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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Per-residue correlation coefficient
by Tom Goddard 10 Jan '22

10 Jan '22

Hi Yumeng, It would be useful if ChimeraX could report the per-residue correlation of an atomic model with a map as Phenix can do. I'll made a feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5897 You can make feature requests yourself using ChimeraX menu entry Help / Report a Bug.... Bugs and feature requests go into our ChimeraX issue tracking database. There is a ChimeraX plugin called StrudelScore from the EMDB that gives per-residue fit statistics. You can get the plugin using ChimeraX menu Tools / More Tools.... There is online documentation here https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxstrudelscore> and a tutorial https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introducti… <https://ftp.ebi.ac.uk/pub/databases/emdb_vault/strudel_tutorials/introducti…> Also there is a ChimeraX command resfit that lets you look at the fit of each residue in the density, moving a slider to go to the next residue. It can also make a video, here is an example, https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/images/resfit.mp4 <https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/images/resfit.mp4> https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html <https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html> and here is resfit command documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/resfit.html Tom Example of resfit command display of residue fit to map. > On Jan 10, 2022, at 3:48 PM, Yumeng Yan <yumeng.yan(a)cpr.ku.dk> wrote: > > Hi Tom, > > Many thanks for your reply. It works follow your suggestion. I can not open ChimeraX in the gui mode while the ChimeraX is installed on a remote cluster and I did not configure it correctly, so bad. Another question, could you add the measure correlation with cc output for each residue in the structure like in Phenix? > > Best, > Yumeng > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, January 11, 2022 12:38:42 AM > To: Yumeng Yan > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> > Subject: Re: [chimerax-users] No cc when using fitmap > > You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <http://aka.ms/LearnAboutSenderIdentification> > Hi Yumeng, > > I would not expect any difference in the correlation coefficient between Windows and Linux or with a large map versus a small map. > > First the command you listed does not do any fitting since you use "shift false rotate false" which does not allow the model to move. > > fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false > > So I assume you are doing this just to measure the correlation coefficient. And your output says the correlation coefficient is 0. That most likely means the atomic model is not located in the map. Why don't you just do the same steps in gui mode and see what happens -- it should produce exactly the same result as nogui mode. Also note that the displayed surface level matters because by default fitmap only uses data above the contour level of the displayed surface of the map you are fitting into. That actually may explain why your large map case did not work, because if you open a large map ChimeraX may initially just show a single plane in gray scale instead of a surface, and with no surface it won't have a surface level. So to get a predictable result you should use the volume command to show a surface of the full map and set the threshold level you want to use, for example, > > volume #1 style surface region all level 0.2 > > I see that ChimeraX does not have the "measure correlation" command that is in the older Chimera program. I will try to add that. > > Tom > > > > >> On Jan 10, 2022, at 2:14 PM, Yumeng Yan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> >> When I tried to use fitmap function ChimeraX in Linux with --nogui option, I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me? >> >> Here are the commands: >> open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb >> fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false >> >> Here is the log information: >> INFO: >> UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08) >> INFO: >> © 2016-2021 Regents of the University of California. All rights reserved. >> INFO: >> Executing: open .33092SymAndFit.cxc >> INFO: >> Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80% >> STATUS: >> reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87% >> STATUS: >> Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc >> STATUS: >> Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc >> STATUS: >> Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292 >> STATUS: >> Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles >> INFO: >> Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32 >> INFO: >> Chain information for fit_11.pdb #2 >> --- >> Chain | Description >> [F](cxcmd:select /F:2-219 "Select chain") | [No description >> available](cxcmd:sequence chain #2/F "Show sequence") >> >> >> INFO: >> Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false >> INFO: >> Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32 >> INFO: >> Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points >> correlation = 0, correlation about mean = 0, overlap = 0 >> steps = 24, shift = 0, angle = 0 degrees >> >> INFO: >> Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates: >> Matrix rotation and translation >> 1.00000000 0.00000000 0.00000000 0.00000000 >> 0.00000000 1.00000000 0.00000000 0.00000000 >> 0.00000000 0.00000000 1.00000000 0.00000000 >> Axis 0.00000000 0.00000000 1.00000000 >> Axis point 0.00000000 0.00000000 0.00000000 >> Rotation angle (degrees) 0.00000000 >> Shift along axis 0.00000000 >> >> STATUS: >> 24 steps, shift 0, rotation 0 degrees, correlation 0.0000 >> >> >> Best wishes, >> Yumeng >> >> Yumeng Yan >> Postdoctoral Fellow >> >> Taylor and Rasmussen Group >> University of Copenhagen >> Faculty of Health and Medical Sciences >> Novo Nordisk Foundation Center for Protein Research >> >> Blegdamsvej 3B, building 6 >> 2200 Copenhagen N >> DENMARK >> >> yumeng.yan(a)cpr.ku.dk <mailto:yumeng.yan@cpr.ku.dk> >> >> <OutlookEmoji-1638361915486c0a23484-e68c-4b46-9d5a-75949bd8128d.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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No cc when using fitmap
by Yumeng Yan 10 Jan '22

10 Jan '22

Hi, When I tried to use fitmap function ChimeraX in Linux with --nogui option, I got no CC output when the Cryo-EM map is large(1.6GB) and I think in this situation, the local fit did not work. When the map was cut of a half size, it works. But it works well on Windows. Could you help me? Here are the commands: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb fitmap #2 inMap #1 resolution 4.0 metric correlation shift false rotate false Here is the log information: INFO: UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08) INFO: © 2016-2021 Regents of the University of California. All rights reserved. INFO: Executing: open .33092SymAndFit.cxc INFO: Executing: open ../Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc fit_11.pdb STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 0% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 8% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 16% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 24% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 32% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 40% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 48% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 56% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 64% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 72% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 80% STATUS: reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc 1.6 Gb 87% STATUS: Done reading Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc STATUS: Computing histogram for Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc STATUS: Computing Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292 STATUS: Calculated Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc surface, level 0.292, with 10911480 triangles INFO: Opened Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc as #1, grid size 750,750,750, pixel 1.1, shown at level 0.292, step 1, values float32 INFO: Chain information for fit_11.pdb #2 --- Chain | Description [F](cxcmd:select /F:2-219 "Select chain") | [No description available](cxcmd:sequence chain #2/F "Show sequence") INFO: Executing: fitmap #2 inMap #1 resolution 8.0 metric correlation shift false rotate false INFO: Opened fit_11.pdb map 8 as #3, grid size 40,42,43, pixel 2.67, shown at level 0.0533, step 1, values float32 INFO: Fit map fit_11.pdb map 8 in map Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc using 2211 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 24, shift = 0, angle = 0 degrees INFO: Position of fit_11.pdb map 8 (#3) relative to Basplt_ext_cryosparc_P48_J130_003_volume_map_sharp_local_center.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 STATUS: 24 steps, shift 0, rotation 0 degrees, correlation 0.0000 Best wishes, Yumeng Yumeng Yan Postdoctoral Fellow Taylor and Rasmussen Group University of Copenhagen Faculty of Health and Medical Sciences Novo Nordisk Foundation Center for Protein Research Blegdamsvej 3B, building 6 2200 Copenhagen N DENMARK yumeng.yan(a)cpr.ku.dk<mailto:yumeng.yan@cpr.ku.dk> [1638361915486]

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Blob measurement question?
by Noriega, Heather 10 Jan '22

10 Jan '22

Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago: open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2 For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside: AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6 However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me? AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6 I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements. Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this. Thank you, and I hope to hear from you soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Volume Render settings
by Kelvin Lau 10 Jan '22

10 Jan '22

Hello I was wondering if there is in the future a volume settings function such as that in Chimera in a tool GUI. I am referring to such things such as the Surface and Mesh options which are easily accessible via the GUI in Chimera for things like surface smoothing, subdivision, smoothing etc. I have found a workaround with commands however in this case a GUI implementation is quite useful as one can easily click and see different visualisations. Best regards Kelvin -- Kelvin Lau http://about.me/kelvin.lau kelvin.kclau(a)gmail.com

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Re: [chimerax-users] swapnaa not working in Chimerax
by Elaine Meng 07 Jan '22

07 Jan '22

On Jan 7, 2022, at 9:15 AM, Antón Vila-Sanjurjo <anton.vila(a)udc.es> wrote: > > Hi Elaine, > everytime I try the swapnaa command in ChimeraX I get an error because the command is not recognized. Has swapna being implemented in ChimeraX? > best, > Antón Hi Antón, ChimeraX does not have a "swapna" command currently, although it does have "swapaa". You can see the list of commands using menu: Help... User Guide. There is also a copy of the ChimeraX User Guide at our website, but it may be newer than the version of the program that you have downloaded: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> In the meanwhile, you can use Chimera for "swapna" and save a PDB file, then read it into ChimeraX if you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Nucleotide styles
by Derek Harris 05 Jan '22

05 Jan '22

Hello, I am working on a figure in ChimeraX. None of the nucleotide styles seem to be working for me, whether inputted from the button command on the menu bar or from the command line. The log indicates the command is accepted without error, but there is no visual change to the model. Derek F. Harris Senior Researcher Seefeldt Lab<http://www.seefeldtlab.org/> Department of Chemistry and Biochemistry Utah State University 435.797.7392

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Question on Interactive H-Bond Histogram
by Bing Xu 05 Jan '22

05 Jan '22

Dear ChimeraX staff, I am sorry to bother you. I used ChimeraX to analyze the two protein complexes. I followed the guide for interactive H-Bond Histogram, but I still can not get the interaction amino acid of two proteins like the examples in ChimeraX Web [cid:image001.png@01D80242.867E4970] I am wondering whether you can provide me with more detailed guide for H-Bond histogram function. I do appreciate your help. Best, Bing Xu Research associate Bing(a)mmrl.edu<mailto:Bing@mmrl.edu> Masonic Medical Research Institute Lab: 315-624-7481 / Fax: 315-735-5648 2150 Bleecker Street | Utica, NY 13501 www.mmrl.edu<http://www.mmrl.edu/> [Primary Logo]

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problem on Protein complex prediction
by Bing Xu 31 Dec '21

31 Dec '21

Dear ChimeraX Staff, I tried to used ChimeraX to predict to two proteins complex. After Alfafold Run finished, I can't find the result. Alfafold Run window showed that the prediction was completed. I attached the pictures of Alfafold Run window. Could you please help me to figure out what is wrong with ChimeraX? I do appreciate your help. Thanks and Happy New Year! Bing

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focus and set pivot functions
by Antón Vila-Sanjurjo 30 Dec '21

30 Dec '21

Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón -- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila(a)udc.es

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ChimeraX for complex prediction
by Bing Xu 29 Dec '21

29 Dec '21

Hello Chimerax staff, I used ChimeraX to predict the complex of two proteins. After Alfafold Run finished, the Alfafold Run window is dark, I can not find any result. I tried to run the same two proteins again, it showed the following information. [Graphical user interface, text, application, email Description automatically generated] I am wondering what wrong with these predication. Thanks, Bing

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Question on result
by Bing Xu 29 Dec '21

29 Dec '21

Hello, I used chimerax to predict interaction of two proteins. After load the two protein sequencing and run Alfold prediction, I can not find the result. I check the download fold and there is no Chimerax in the fold. I am wondering how I can find my prediction results I do appreciate your help. Thanks, Bing Xu

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Re: [chimerax-users] [Chimera-users] Move models around independent of each other in Chimera X
by Elaine Meng 24 Dec '21

24 Dec '21

HI Prathvi, Glad you like drag-and-drop! There is a chimerax-users(a)cgl.ucsf.edu address for ChimeraX questions, which I've CC'd here. (1) Yes you can move models selectively with the mouse, but it is different in ChimeraX than in Chimera. In ChimeraX, there are different "mouse modes", meaning what happens when you use some mouse button or touchpad to click and drag. There are mouse modes to move only the model(s) with some part selected, or only the model you just clicked on. You can assign the right mouse button (or its touchpad equivalent) by clicking an icon in the Right Mouse toolbar of icons across the top, or you can use the “mousemode” command to assign the modes to any button or scroll wheel. See Right Mouse toolbar documentation with pictures of the icons and what they mean: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> ... and mousemode command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> For example, for moving things manually (with the mouse or touchpad motions) you would want to use the “translate selected model” and “rotate selected model” mouse modes. Selection in ChimeraX is similar to that in Chimera: <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> (1a) you can also move models selectively with ChimeraX commands like "turn" "move" etc. by using their "models" options. (2) depth-cueing is a option of the ChimeraX lighting command. E.g. command: lighting depthCue false lighting command and its options <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.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 Dec 23, 2021, at 11:42 PM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > First of all, thank a million to the chimera X development team for incorporating the drag & drop feature in chimera X. I really missed it in chimera. > > However, after opening two models in the same window, I am unable to find a way to move/rotate model-1 in such a way that it does not move/rotate model-2. I could do this in chimera by unchecking the box for model-2 but when I do the same in chimera-X, it doesn't seem to work. > > Also, I am unable to find a way to disable depth cueing in chimera X. Please help. > > Thank you > > -- > 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 > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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The problem of ligands disappearing when the file is converted
by Kenji MATSUI 20 Dec '21

20 Dec '21

Dear ChimeraX Thank you very much for your kind words in the past. When I opened the PDB file and mol2 file saved by pymol using the method you gave me, the ligands disappeared. How can I get pymol to display the ligands as well? Here is in detail. As you suggested, I created a new model by combining #1 and #10, and saved the newly single model in a PDB file. However, when I displayed this file in pymol, I could not see the ligand as shown in the figure. [image: image.png] [image: image.png] So we tried to align the ligand OSW-1 to the protein osh4 in this figure, but it was difficult to analyze because OSW-1 was far away from the distance of the protein osh4 as shown in the figure below. [image: image.png] Refernece：Save command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Also, I've looked at tutorials and other sites on the Internet to try to figure out what's causing this, but no luck! I'm sorry for the many questions. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 18 Dec '21

18 Dec '21

Hi Byrne, Thanks for the info about exporting models for iOS. Glad you found a way to export a virus model from ChimeraX suitable for use in iOS apps made with Xcode. The STL format is just a list of triangles, each with 3 vertex (x,y,z) coordinates, used mostly for 3D printing. It does not have vertex normal vectors which are used to give smoother lighting. In the future maybe ChimeraX will directly export Collada (*.dae) files and you will be able to export a usable model without running it through Blender. As I mentioned before we support GLTF but not Collada currently. Our ChimeraX efforts are mostly to help researchers analyze molecular structures so adding this does not have highest priority. Unfortunately there are hundreds of feature requests we do not have time to implement with our limited funding. Tom > On Dec 18, 2021, at 9:34 AM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello again Tom, > > A follow-up follow-up. After extensive testing I have found a useable workflow from ChimeraX to iOS. Of course iOS apps may utilize PDB viewers, this is for folks who may want to incorporate models, in customized ways, into SceneKit for manipulation. > > ChimeraX ––> STL ––(graphics editor)––> DAE ––Xcode––> SCN > > • In Chimera > – reduce polys as much as possible* > – export individual elements, e.g. chains, if you want individual control (materials, etc) > • In a graphics editor: > – eliminate polygonal faceting of STL files > - Blender, check Auto Smooth in addition to toggling on Smooth Shading > - Cinema 4D, add a phong tag > – recenter if desired, add additional elements > > *You might want to add surfaces to your reducing file-size tutorial. In the model below, the spike's resolution was set to 7, gridSpacing 3. You also need to click Hide for Atoms and Cartoons; otherwise they will severely bloat the file even though not seen. The entire file size of this SARS-CoV-2 model, as used by iOS, is 1.2 Mb (all but one of the spikes are all clones). > > Thanks again for the help, > > Byrne > > > > > > >> On Dec 3, 2021, at 11:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> Thanks! So Blender can convert GLTF to Collada. The ChimeraX GLTF is binary and Collada is all text, so no surprise that the file size is much larger. If we add Collada support it would be produced directly from the ChimeraX scene, not converting from GLTF. But we have hundreds of new feature requests so I don't think Collada output is likely to be added soon, unless a funded project needs it. >> >> Tom >> >>> On Dec 3, 2021, at 9:48 AM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>> >>> Hi Tom, >>> >>> A follow-up for future reference. Blender, the one recommendation I found on StackOverflow, is indeed capable of converting GLTF to DAE. But the conversion bloats the files by as much as 10x! In addition, the hierarchy is only partially preserved. I tried an on-line converter with even less satisfactory results. So I think this pathway is a bust. This might serve as a fair warning for ChimeraX developers to avoid an internal conversion from GLTF if introducing a DAE export option. >>> >>> >>> Byrne >>> >>> >>> >>> >>>> On Dec 2, 2021, at 2:22 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> >>>> Hi Byrne, >>>> >>>> I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. >>>> >>>> There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. >>>> >>>> A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). >>>> >>>> Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. >>>> >>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>> >>>> Tom >>>> >>>> Model from gltf export from linked ChimeraX example >>>> >>>> <spike.png> >>>> >>>> >>>>> On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>>>> >>>>> Hello Tom, >>>>> >>>>> Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. >>>>> >>>>> But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. >>>>> >>>>> The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! >>>>> >>>>> Thanks again, >>>>> >>>>> Byrne >>>>> >>>>> >>>>>> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>>> >>>>>> Hi Byrne, >>>>>> >>>>>> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >>>>>> >>>>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >>>>>> >>>>>> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >>>>>> >>>>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>>>> >>>>>> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >>>>>> >>>>>> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >>>>>> >>>>>> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >>>>>> >>>>>> Tom >>>>>> >>>>>>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>>>>>> >>>>>>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>>>>>> _______________________________________________ >>>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>>>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

1 0

Fwd: Question: PDB file creation
by Elaine Meng 17 Dec '21

17 Dec '21

> Begin forwarded message: > > From: Kenji MATSUI <s214903z(a)st.go.tuat.ac.jp> > Subject: Question: PDB file creation > Date: December 16, 2021 at 7:20:41 PM PST > Cc: Kaori Sakurai <sakuraik(a)cc.tuat.ac.jp> > > Dear UCSF ChimeraX > > Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you two questions. > > First, I would like to know how to convert a cxs file saved in Chimera X to a PDB file. > > Aim > To display the interaction between a protein (osh4) and a ligand (OSW-1) in pymol > > Methods I have tried > I found a way to convert mmCIF to PDB file, but I could not find a site to convert cxs file to PDB file. > > Second, How to deal with the following error that appears when the structure of the osh4-OSW-1 complex is shown. > > APBS electron > Error: The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electron density. > Thank you for your cooperation. > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > Mail: s214903z(a)st.go.tuat.ac.jp <mailto:s214903z@st.go.tuat.ac.jp> Hi Kenji, I omitted your cxs file from this message since I thought maybe you wanted to keep it private (messages on this chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list can be seen by the public). I didn't see that APBS error when I opened the cxs file in ChimeraX. It appears to be a message from another program (not ChimeraX): the APBS program, which calculates electrostatic potential. The error is exactly what it says: some residues in the structure are missing some atoms, which would affect the calculation of electrostatic potential values. Short answer #1 is why not look at the interactions in ChimeraX instead of Pymol? You can calculate H-bonds, find contacts, etc. See this tutorial, for example <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>> Short answer #2 is that you can open the session (cxs) file in ChimeraX and then save a PDB file with the "save" command or the menu: File... Save... (choose Files of type: PDB). HOWEVER, a longer answer may be required here because I can see from opening your cxs file that it contains many models, I guess a receptor (model #1) and ligands from docking (models #2-258) with only some ligands displayed (models #10-17). I'm guessing you want to save only the ones that are displayed. You could save models #1,10-17 into one multi-model PDB, file but probably for analysis in Pymol or other programs, you would instead need to combine each ligand with receptor and save it separately. In other words, you may need to make a new model by combining #1 with #10, and then save the new single model to a PDB file. For example: combine #1,10 modelId #300 save /Users/meng/Desktop/result10.pdb models #300 relModel #1 Then repeat for other ligands, combining #1 with #11 to make a new model and saving that new model, combining #1 with #12, etc. See the help links below for the options of each command. Save command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>> Combine command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Color docking resulls by rank
by Visvaldas K. 17 Dec '21

17 Dec '21

Dear Users and Developers, I have a ViewdockX question (but I guess it's a more generic one, about coloring models/submodels): is there a trick to color docking results by rank, like rank was some sort of B-factor? Or even by docking energy (score), but that's maybe too much. I could color each "submodel" by hand, but I don't know how to obtain color gradients, say distributed at even distances between blue and red. Years ago I was able to do similar trick in Chimera, but I completely forgot how I did that :( Thank you, Vis On Friday, December 17, 2021, 05:24:30 PM GMT, chimerax-users-request(a)cgl.ucsf.edu <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 the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, 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. independent centers of rotation (Elaine Meng) 2. Change the directory for data fetched from databases (Guillaume Gaullier) 3. Re: Change the directory for data fetched from databases (Tom Goddard) 4. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 5. Re: Change the directory for data fetched from databases (Tristan Croll) 6. Re: Change the directory for data fetched from databases (Guillaume Gaullier) 7. PDB: 7OVR (Veler, Hana (NIH/NCI) [F]) 8. Re: PDB: 7OVR (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 12:51:58 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Abigail Jackson <ajackson(a)scripps.edu> Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] independent centers of rotation Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Abigail, Ah, you're referring to the "independent centers of rotation" mode in Chimera. By default, the "tile" command in Chimera automatically turns it on. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html> I agree that this mode is very useful, but unfortunately it does not yet exist in ChimeraX. It is listed in the missing features section of the ChimeraX download page. <https://www.rbvi.ucsf.edu/chimerax/download.html> Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 15, 2021, at 12:28 PM, Abigail Jackson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi there, > I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? > > Hopefully that description makes sense. Thank you in advance for your help! > Best, > Abigail Jackson > The Scripps Research Institute ------------------------------ Message: 2 Date: Thu, 16 Dec 2021 10:08:26 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Change the directory for data fetched from databases Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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 ------------------------------ Message: 3 Date: Thu, 16 Dec 2021 14:50:25 -0800 From: Tom Goddard <goddard(a)sonic.net> To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0(a)sonic.net> Content-Type: text/plain; charset=utf-8 Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom > On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hello, > > The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). > > The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). > > Thank you, > > Guillaume > > > > > > > > > > N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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 > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > ------------------------------ Message: 4 Date: Fri, 17 Dec 2021 08:40:06 +0000 From: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se> To: Tom Goddard <goddard(a)sonic.net> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3(a)icm.uu.se> Content-Type: text/plain; charset="utf-8" Hi Tom, This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default. Thank you for your answer. Cheers, Guillaume On 16 Dec 2021, at 23:50, Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> wrote: Hi Guillaume, There is no setting to change the location where ChimeraX caches fetched files. It is always ~/Downloads/ChimeraX On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX. You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux) chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py making _cache_dirs = ['/usr/local/chimerax_fetch'] near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX. Tom On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, Guillaume N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: 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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

2 1

PDB: 7OVR
by Veler, Hana (NIH/NCI) [F] 17 Dec '21

17 Dec '21

To whom it may concern, The command “show sel atoms’ does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine. Would you know what could be the cause? Thanks, Hana

2 6

Change the directory for data fetched from databases
by Guillaume Gaullier 17 Dec '21

17 Dec '21

Hello, The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn’t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands). The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX). Thank you, 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

3 4

ChimeraX Question
by Abigail Jackson 15 Dec '21

15 Dec '21

Hi there, I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera? Hopefully that description makes sense. Thank you in advance for your help! Best, Abigail Jackson The Scripps Research Institute

2 1

Fwd: ChimeraX VR question or suggestions
by Elaine Meng 14 Dec '21

14 Dec '21

> > From: Alejandro Villalta Cásares <alejandrovillaltac(a)gmail.com> > Subject: ChimeraX VR question or suggestions > Date: December 13, 2021 at 4:36:03 AM PST > To: chimerax(a)cgl.ucsf.edu > > Dear ChimeraX staff, > > I tested the ChimeraX VR mode today. I was very happy on how it looks and how easy it was to move and see some parts of the structure compared to the flat screen version. Nevertheless, the function that I think it will very useful the VR is to segment and select different segments to save them later. That I couldn't manage to do it after some time I managed to be able to select one region but no more than one at time. It should be nice to add the ability to select multiple regions or at least as in the flat screen that it tells you the name of the models that you are pointing, like that we could pass through command lines. Also it should be nice that a keyboard appears on the headset in order to type on the command lines, but it is true that is a minor point, if it can be written directly on the PC. > > Thank you very much for this amazing function, > > I hope that this constructive mail could help you to improve it more. > > Sincerely yours, > > Alejandro Villalta >

3 3

Analog command to reinit & create?
by Eric Pettersen 13 Dec '21

13 Dec '21

> Begin forwarded message: > > From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > Subject: Analog command to reinit & create? > Date: December 13, 2021 at 7:11:40 AM PST > To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> > > > Hi everyone, > > I am currently teaching a crystallographic course and this year I am introducing ChimeraX for the first time (previous years we have used PyMol). > I still am in the middle of my personal transiston from PyMol to ChimeraX and potentially I am still stuck too much in the "PyMol"-way to do it, but I still miss a couple of commands. Could anyone help with that? > > 1) Analog to Reinit > I generate all my publication figures with scripts (now cxc). The Reinit command in Pymol, always gave me a fresh enviroment, however the closest analog I found "Close" only closes the current model. All other settings (Lightning etc.) are kept and only reset after closing ChimeraX. Therefore, I do not get the same results from my script, if I run it multiple times... > > 2) Create object > Is there a way to copy a selection of atoms into a new molecule - for complicated visualisations? > > Thanks so far to the developers - I love more things on ChimeraX than I miss 👍 > Best, > Jan > > -- > Dr. Jan Gebauer > AG Baumann / Biochemistry Cologne > Zülpicher Str. 47 / 50764 Köln > +49 - 221 - 470 - 3212

3 2

ViewDockX for Autodock Vina error
by Visvaldas K. 13 Dec '21

13 Dec '21

Dear colleagues, for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported. Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)? If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features... Thank you in advance, Vis

3 2