- ChimeraX-users - RBVI Mailing Lists

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> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

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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

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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

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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

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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 >

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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

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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

Save ribbons and surfaces with minimal amount of vertices/faces
by Sarah Piper 13 Dec '21

13 Dec '21

Hi ChimeraX team and others, I got a bit of an unusual question and am interested to see whether it is possible! I am trying to use a short helix in ribbon style from ChimeraX into Blender, and use it to create a 'skeleton' for animations. For this, it would be most useful to have as few vertices as possible for the helix (basically only the 'invisible' coordinates themselves as 'line', instead of having it as a 3D view/thick helix. When I export a helix even with a very thin ribbon style through the command line (e.g. width and thickness to 0.1), this is unfortunately still too thick and creates too many vertices/faces. Setting these values to 0 gives errors. I have looked at the ribbon style editor in Chimera as well, and unfortunately the minimum settings are 0.05. Would it be possible to somehow set any of these parameters to 0 and save this as a file format suitable for 3D softwares (e.g. .glb)? Would it work through a python script potentially? (I'm not familiar with python in chimera yet but happy to learn more about this). And if so, would this be also applicable for surfaces, to reduce the numbers of vertices/faces that are exported? On another note, I was wondering whether it would be possible to set the chimaera scene 'world origin' to a particular coordinate set; I think in Pymol this is possible with resetting the camera view: cmd.set_view([ 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 40.0, 100.0, -20.0]) Sorry for these unusual question but looking forward to hearing back from anyone who might have any suggestions! Cheers, Sarah

3 4

Showing long coiled coil alpha helices as tubes
by Huiskonen, Juha T 13 Dec '21

13 Dec '21

Hi all, I am trying to render two long alpha helices forming a coiled coil as tubes instead of ribbons. The tubes rendered with default settings do not however follow the paths of the helices. Instead, the tubes become almost straight. Any suggestions? Best wishes, Juha

3 2

rotation parameters of the map
by Dmitry Semchonok 13 Dec '21

13 Dec '21

Dear colleagues, When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters. How to find them our when a) using just Fit option b) rotation manually and then using the Fit option? Thank you Sincerely, Dmitry

2 2

Question about chimeraX installization.
by 박시훈 11 Dec '21

11 Dec '21

Dear chimeraX users, I want to change the installation folder of chimeaX in linux (centos7.0). The default folder is user/bin however, I want to install chemeraX in the other folder because of my computer environments (the Master and Slave nodes do not share the usr/bin folder). Can I know how to change the installation folder? Best regards Si Hoon Park

2 1

1.3 release
by Eric Pettersen 10 Dec '21

10 Dec '21

UCSF ChimeraX version 1.3 has been released! Updates since version 1.2 (May 2021) include: - AlphaFold tool and command to get AI-predicted protein structures - Selection Inspector to inspect/change attributes of atoms, bonds, etc. - Scale Bar tool and command - new BLAST Protein GUI with easier controls for showing hit info such as source species, crystallographic resolution, ligands in structure - Altloc Explorer tool and command to switch among alternate locations - model loops and missing segments with Modeller - combine or copy models - change bond lengths - apply command files iteratively to multiple input files - list multiple map-fitting solutions from global search For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Enjoy! --Eric

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re-sampled map (volume resample #X onGrid #Y) difference with general mrc map
by Dmitry Semchonok 10 Dec '21

10 Dec '21

Dear colleagues, I have an issue with the output map re-sampled from the resampling step protocol. Could you please explain how different the re-sampled map is compared to the general mrc map (without rotation manipulations)? Because it seems that some important information is missing or/changed in the re-sampled.mrc Kind regards, Dmitry

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Re: [chimerax-users] alphafold predict multiuser syntax
by Tom Goddard 09 Dec '21

09 Dec '21

Hi Jerry, It is unlikely you will be able to get AlphaFold to predict multimers composed of multiple 1000 amino acid proteins even with the most powerful GPUs available. The EBI AlphaFold database produced by Google predicted structures of up to 2700 amino acids. From the paper that was done by combining the memory of 4 GPUs (which cannot be done on Colab), that might be 64 Gbytes. The GPU memory use of AlphaFold is said to be quadratic in number of residues. When I last tested with Google Colab GPUs with 16 Gbytes a few months ago it failed with 1000 amino acids. But that was AlphaFold 2.0 and now we are using AlphaFold 2.1. It would require testing, but it is very likely that 1500 total amino acids in a complex will run out of memory, and quite possibly 1000 will run out of memory when your GPU has only 16 Gbytes. This is one of the limitations of AlphaFold, and of the old Google Colab GPUs with only 16 Gbytes. The AlphaFold database has predictions for human proteins larger than 2700 amino acids made by breaking into 1400 amino acid chunks and computed at intervals of 200 amino acids. Then you can attempt to piece together those chunks. I give an example of that piecing together in ChimeraX here https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html Tom > On Dec 9, 2021, at 10:12 AM, Jerry Honts <jerry.honts(a)drake.edu> wrote: > > Unfortunately several of the proteins I’m studying are ~1000 amino acids and the evidence is they form multimers. So I was wondering if Colab Pro + would actually succeed, or whether this is currently not a feasible solution. > > I should mention that I have students use Chimera in several of my courses to solve problems (and they like it), and I hope to move students to ChimeraX this year. So thanks for maintaining and refining this wonderful software. > > Jerry

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Re: [chimerax-users] alphafold predict multiuser syntax
by Tom Goddard 09 Dec '21

09 Dec '21

Hi Jerry, I have not tried Colab Pro+ which is $50 per month and claims to give faster GPUs, more memory, longer session times. I use Colab Pro which is $10 per month because the free Colab was sometimes not letting me run jobs more than 2 hours per day. https://colab.research.google.com/signup The main factor for running larger predictions (e.g. > 1000 amino acids) is GPU memory. With Colab Pro Google never gave me a GPU with more than 16 GBytes -- I get old Nvidia T4, P100 and K80 GPUs just like with free Colab. At UCSF I can run AlphaFold (not in ChimeraX) using new Nvidia A40 or A100 GPUs which have 48, 40 or 80 GBytes but I have not tested on large proteins to see how large. The runs on 800 amino acid predictions are about 2 to 3 times faster on these new GPUs. Tom > On Dec 9, 2021, at 9:44 AM, Jerry Honts <jerry.honts(a)drake.edu> wrote: > > Hi Tom: > > Many thanks for your quick reply! I so appreciate AlphaFold access being built into ChimeraX—it has already resulted in several interesting leads. > > As a second question if I may ask: would upgrading the Google Collab Pro + help with AlphaFold predictions? Any experience with this? > > Jerry

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alphafold predict multiuser syntax
by Jerry Honts 09 Dec '21

09 Dec '21

I am trying to use the AlphaFold predict multimer function in ChimeraX 1.3 with this syntax like (comma-separated pasted sequences): alphafold predict MPEHPIQLASSNQVVSQILTTTQGSPTRQSKTFVYRSE,MSESPIRSSQYGKHVVNVSHIEKGQAPIYVSQSTVQNPIYVEKIVKVESSNT But I keep getting an error: Missing or invalid "sequence" argument: Sequences argument "MPEHPIQLASSNQVVSQILTTTQGSPTRQSKTFVYRSE,MSESPIRSSQYGKHVVNVSHIEKGQAPIYVSQSTVQNPIYVEKIVKVESSNT” is not a chain specifier, alignment id, UniProt id, or sequence characters I think I am following the syntax given in the online help file, but can you suggest a reason for this error? Single chain predictions have been working fine with pasted sequences. Thanks, Jerry E. Honts Drake University

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Re: [chimerax-users] Regarding animation Tool bar
by Elaine Meng 06 Dec '21

06 Dec '21

Hi Dilip, Sorry, only Chimera (not ChimeraX) has the Animation graphical interface currently. Of course, you can make movies with ChimeraX, but you would need to use a ChimeraX command script to do it. More information about making movies in ChimeraX, including links to tutorials with examples: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.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 5, 2021, at 1:57 PM, Dilip Badgujar <dilip.badgujar(a)kemi.uu.se> wrote: > > Hi Chimera team, > I am new to the the Chimera and I found it is really nice and user friendly. > I have ChimeraX version 1.2.5 on Ubuntu 16.04 system. > I wanted to make movies using the animation tool in ChimeraX but my utilities tab only have two options Registration and updates. > How can I access the animation pane? > Best > Dilip Badgujar

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 03 Dec '21

03 Dec '21

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> 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> >>>>> >>>> >>> >> >

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

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 Tom Model from gltf export from linked ChimeraX example > On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)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> >>> >> >

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Re: [chimerax-users] [Chimera-users] .dae export for ChimeraX
by Tom Goddard 02 Dec '21

02 Dec '21

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 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 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> 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 > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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coloring clipped surface only separately
by Y. Mutum 02 Dec '21

02 Dec '21

Hi Elaine and Team My question relates on how we can color the 'clipped surface only' using a different color independently. This is without messing up the color of the outer surface of the model. Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. Now, using the 'surface cap' command, I can get a clipping plane which is colored 'bychain'. However, if I try to color the clipped surface using a different color, the entire hydrophobicity surface is no longer there. These are my commands below. Is there a way to color the clipped surface by a different color? If not is there a way around? The commands I have used are: >>> open 6g2j; hide all; >>> color #1 green; color /B-G,I,Q,P,R,W,q yellow; Then using the side view tool, clip the surface of the model to get a slice. I am trying to clip in the plane containing Chain D and B. >>> mlp #1; >>> surface cap true; Then, I can get a clipping plane colored by-chain. If I then type >>>color zone #1 near #1 distance 5 Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface. Thus, 1. Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)? 2. Suppose I want to remember this clipping plane for another ChimeraX session and would like to avoid the manual clipping using the 'Side view'. Using command line, is there a way to get back to the clipping plane? Similar to 'camera matrix' command, but, with the 'sectioned plane' also included. Thanks Yaikhomba

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measuring rotation between two homologous PDB models
by Y. Mutum 28 Nov '21

28 Nov '21

Hi Elaine and ChimeraX Team My query relates to measuring rotation between two subunits from homologous models in ChimeraX. Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, * Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). * Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true; The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832 Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help? Thanks Yaikhomba

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Exporting Measure and Color Blob data
by BINGHAM Dominic 25 Nov '21

25 Nov '21

Hello, I am wanting to get the volumetric data of several blobs in a manner I can easily export and analyse. I am using the Measure and Color Blobs tool and I can see the data I need. However, I have lots of models, with lots of blobs. That means me stopping and writing down the volume data each time I click is not very efficient. So is there anyway I can export all the volume data per each selected blobs per each image into one file? Thanks, Dominic Bingham

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Match the scale of OBJ and volume
by Roden Deng Luo 24 Nov '21

24 Nov '21

Hi, As shown in the screenshot, I have opened one volume and one obj. But they should have the same scale. How can I achieve this? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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ChimeraX import multiple positions of the same .pdb structure
by Frey, Lukas 23 Nov '21

23 Nov '21

Dear Elaine, I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html in the command line of chimeraX I had to type in: open path-to-file/test.positions models #1 childModels true matchNames true my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions: 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0 If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output: view matrix camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8 model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0 Somehow the transformation matrix is only applied to #1 but not to #1.1 and #1.2, do you have an idea what I have to change? If I save the transformation matrix of the distorted .pdb structure via the save command: save path-to-file/test_2.positions models #1 childModels true I have the following output: 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30 metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0 missing structure,1,0,0,0,0,1,0,0,0,0,1,0 The goal in the future is to load several positions (1 … 100) of the same .pdb structures. Best, Lukas Lukas Frey Visiting Postdoctoral Associate UMASS Medical School Worcester Grigorieff Laboratory

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Re: [chimerax-users] meshmol in chimeraX
by Tom Goddard 23 Nov '21

23 Nov '21

Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders > On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv(a)scripps.edu> wrote: > > Hi Tom, > > Greetings! Hope are staying safe and healthy. > > I am finally transitioning to chimeraX. > > Could you please tell me what is the equivalent of > > the chimera command “meshmol #26 6” in chimeraX > > Many thanks, > Vijay >

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Toolshed
by Moustafa, Ibrahim M. 23 Nov '21

23 Nov '21

Dear ChimeraX, Trying to install iSolde but toolshed page seems to be down! Is there another link to https://cxtoolshed.rbvi.ucsf.edu ? ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/> Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. cxtoolshed.rbvi.ucsf.edu Thanks, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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Question about Chimerax
by JANE LEE 22 Nov '21

22 Nov '21

Hi, I was wondering how/if I could open saved session files from Chimera in Chimerax? Also, when I tried to open a protein in Chimera, it opened. But when I tried to open the same protein in Chimerax, it only showed up as atoms and I received the message "start residue of secondary structure not found." I was wondering if you have any suggestions for troubleshooting? Thank you! Regards, Jane

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ChimeraX AlphaFold2
by Ichcharisma 20 Nov '21

20 Nov '21

Hi ChimeraX Dev I wondering if I can run oligomer prediction on ChimeraX AlphaFold features. As we can do it with others colabfold version out there. Thank you

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Feature request: windowsize to be stored with session
by mailman-bounces＠cgl.ucsf.edu 18 Nov '21

18 Nov '21

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Date: November 18, 2021 at 8:47:33 AM PST Dear all, I would like to suggest that the current windowsize is associated with a ChimeraX session. This is particularly useful when making figures in a reproducible manner (if I am not mistaken, when opening a .cxs file it will open it with the same windowsize that has been used for the last chimera session, rather than the one that was used when the session was created). I am aware that the windowsize can be specified in a script file. Thanks a lot for your consideration : ) Best, Matthias

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