- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] tile command in chimeraX
by françois SERRA 22 May '19

22 May '19

Hi Elaine, thanks for the quick reply. my usual routine with 3D models involves loading tens of them, match them (now align :P) and then "tile", so yes its a bit tedious. I'll keep doing this in "old" chimera, and look forward for the advances in chimeraX. thanks again for the tool!! francois On Mon, 20 May 2019 at 19:25, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX > currently. If you don’t have too many structures, you could first > superimpose them all in the middle, zoom out somewhat (“zoom” command) and > then translate them individually up/down (y axis) and left/right (x axis) > with the “move” command, but it would be a little tedious and require some > trial and error as to spacing. It may be useful to save/restore positions > with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> > wrote: > > > > Hi, > > sorry for the stupid question, but I spent quite some time searching for > it. > > Is there some alternative to the "tile" command in chimera X? > > thanks! > > great tool :) > > francois > > -- *François Serra* **senior researcher - comparative epigenomics** *Computational Biology Group - *Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona *Tel: +34 934 137 97*

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Fwd: tile command in chimeraX
by Elaine Meng 20 May '19

20 May '19

> > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] tile command in chimeraX > Date: May 20, 2019 at 10:25:27 AM PDT > To: françois SERRA <serra.francois(a)gmail.com> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX currently. If you don’t have too many structures, you could first superimpose them all in the middle, zoom out somewhat (“zoom” command) and then translate them individually up/down (y axis) and left/right (x axis) with the “move” command, but it would be a little tedious and require some trial and error as to spacing. It may be useful to save/restore positions with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On May 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> wrote: >> >> Hi, >> sorry for the stupid question, but I spent quite some time searching for it. >> Is there some alternative to the "tile" command in chimera X? >> thanks! >> great tool :) >> francois >

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tile command in chimeraX
by françois SERRA 20 May '19

20 May '19

Hi, sorry for the stupid question, but I spent quite some time searching for it. Is there some alternative to the "tile" command in chimera X? thanks! great tool :) francois -- François Serra *senior researcher - comparative epigenomics* Computational Biology Group - Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona Tel: +34 934 137 97

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smoothen coils
by Gabor PAPAI 13 May '19

13 May '19

Dear developers, I would like to show helices as tubes (this I know how to do) and coils between them with smooth trajectories, more schematic, as it is drawn in Chimera using Pipes and Planks (or even more). I would appreciate your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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Feature Request: Dust ranges and new object as output
by Scott, Brandon L. 30 Apr '19

30 Apr '19

We can currently remove objects of a given size; it seems like it would be fairly straightforward to allow a range of object sizes to be kept from the middle, i.e. remove objects less than 20 and greater than 1000. Additionally, it would be really helpful if we could output the 'dusted' components as a new model so they could be individually colored and displayed, or be able to access the measured sizes of the objects for further analysis. Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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morph with molecular surface for part of molecule
by Susan Lea 30 Apr '19

30 Apr '19

How can I generate a morph with a molecular surface representation? many thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

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Some preferences will reset
by Eric Pettersen 25 Apr '19

25 Apr '19

Hi all, In order to improve the modularity and maintainability of the ChimeraX code, the way some settings/preferences were handled was changed so that the code for that setting/preference could be kept in the appropriate tool bundle rather than in the ChimeraX core. A consequence of this change is that for settings/preferences that moved, they will revert to their initial default values rather than any values you may have saved for them. This will only happen for builds later than today, and furthermore if you go back to an older build it will still have your old values. For most settings/preferences this is not a big deal — you can easily just change them and save them again. The one setting that may be a little tricky is the “Startup commands” setting since there might be a lot of text saved in that one. Nonetheless, as long as you don’t delete your old build you can just start that and copy the commands from that into the new build. The preference categories that got moved are: Clipping Distances Labels Log Startup Trackpad Window —Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX python crush in no-gui mode
by James Starlight 16 Apr '19

16 Apr '19

Dear ChimeraX users! I am using a cxc script together with the following options to run ChimeraX in no-gui mode. chimerax-daily --offscreen --nogui test.cxc here is my scrript # chimeraX script windowsize 800 600 open ./test.pdb view; zoom 1.0; turn x 90; turn z -80; preset 'overall look' publication color byattribute bfactor palette rainbow range 2,100 # make info 2dlab create title text "B-factors for" color red font gothic xpos .04 ypos .90 size 30 # options for light light depthcuestart .4 depthcueend .8; lighting full save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false This script works fine with GUI producing very good picture but with the --nogui it gave me error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py", line 699, in init commands.run(sess, 'open %s' % arg) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 421, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 203, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/image.py", line 43, in save_image raise LimitationError("Unable to render images to save them") chimerax.core.errors.LimitationError: Unable to render images to save them could you help me how it may be fixed? Thank you in advance! Gleb

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by Elaine Meng 15 Apr '19

15 Apr '19

Hi James, There is a different email address for asking ChimeraX questions (CC’d here). Yes, you can script imaging in ChimeraX with nogui if you are using Linux and start with the “nogui” and “offscreen” options on the system command line (they have dash-dash in front but my Mail keeps editing it to a long hyphen instead). <http://rbvi.ucsf.edu/chimerax/docs/user/options.html> In ChimeraX the command script filenames end in .cxc <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> The commands may be different than in Chimera. Open is with “open” save is with “save” and there is no publication preset but you can change to white background and show silhouettes with the “set” command. See the individual command help pages <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> making images <http://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 Apr 15, 2019, at 2:14 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > Would be possible to use new ChimeraX for execution of some simple > scripts for structure visualisation and imaging via no-gui mode? > > I am using bash script to loop over pdbs and would like to > > 1) open each pdb which contains b-factors info in chimeraX > 2) apply preset publication > 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" > 4) save high quality image at the selected directory using chimera render > > Would it be possible to do these things directly from linux terminal > providing each time pdb and some script file with the list of the > applied commands? > > chimerax-daily ${pdb} ${script} > > Thank you in advance!

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Dome projection camera mode
by Tibor Füzik 10 Apr '19

10 Apr '19

Dear ChimeraX developers, I have not found the "dome" projection camera mode in ChimeraX (as it is in Chimera). Is there any equivalent projection (camera mode) or a workaround to get it? Would it be hard to implement it ChimeraX? Thanks. All the best, Tibor

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