- ChimeraX-users - RBVI Mailing Lists

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]

2 2

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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