- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] Cylinder coloring extension
by Elaine Meng 03 Jul '19

03 Jul '19

Hi Thomas, Chimera “pipes” are always a single color each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pi…> However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color. Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs. <http://www.rbvi.ucsf.edu/chimerax/index.html> In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this: ... and then command “color by bfactor palette rainbow” gives this: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom(a)gmail.com> wrote: > > Dear Chimera Team, > > I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? > > Looking forward to an answer, > Thank you for your time reading my suggestion. > > Thomas M

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mclip - surface clipping per-model
by bertrand beckert 03 Jul '19

03 Jul '19

Hi Elaine, I just wonder if the option clipping per-model has also been introduced in ChimeraX like it is in chimera ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod…) ? Apparently the command mclip doesn't seem to exist... Has it been replaced? Best Bertrand

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MacOS two-finger swipe on help window
by Alexis Rohou 02 Jul '19

02 Jul '19

Hi all, Not sure this is a bug, but on my MacOS laptop when I use two finger swipe motion while hovering over the help window (to browse up and down the page), the help page is scrolled as expected, but simultaneously the view in the main window is rotated. Is this expected behavior? It seems a bit counter productive to me. Cheers, Alexis

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color a surface by volume data
by bertrand beckert 02 Jul '19

02 Jul '19

Dear all, I have been searching in the documentation for quite a while and I haven t yet found the solution of how we can in chimeraX color a surface/volume by a volume data like in chimera ... i.e: local resolution map in cryo-em... in chimera: volume viewer/Tools/Surface color/color suface by is it possible to do so in ChimeraX? Any Help would be really appreciated! Thanks also for the amazing software ! Best Bertrand

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An error opening chimerax seesion
by Yehuda Halfon 02 Jul '19

02 Jul '19

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

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Placing markers using the VR wands
by Schmid, Michael F. 01 Jul '19

01 Jul '19

Hi- I don’t seem to be able to activate the Marker Placement functions in the menu that it called up by pushing the menu button (above the trackpad of the wand) to display a floating menu. It doesn’t seem to work with “vr off” either, using the mouse. I’d like to place markers in a tomogram, either in a density, or (preferably) at a specific 3D position with the wand. Thanks, Mike Schmid

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suggestion for ChimeraX on MacOS
by Alexis Rohou 01 Jul '19

01 Jul '19

Hi there, I noticed that when I do "open browse", the native MacOS file browser is started, but when I click on File > Save..., a file browser from some other toolkit is used. I find this inconvenient because that file browser does not know about my recent history, bookmarks, etc. Any chance the File > Save... dialog could use the native OS file browser? Cheers, Alexis

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Restoring views and how to use clip
by Yazan Abbas 01 Jul '19

01 Jul '19

Hi, Instead of using chimera sessions (which can get very big) to save my work when preparing figures for publications, I save all my commands in a .cxc file to be read by chimeraX later. Is there a single command that outputs all the necessary information in an appropriate format needed to restore a view? Currently what I have done is *alias myview view matrix; zoom *to output the information into the log, but the output needs to be re-formatted whenever I want to use that information with the view matrix and zoom commands. Is there a command that outputs that information in a format ready for copying and pasting? I know name view can partially fulfil what I am looking for, but it is only session specific. On a related note, I want to also restore the clipping for each figure/panel I create, but I don't seem to be using the clip command appropriately. For example, if I enter the command clip list, and the output is Using 2 clip planes: far -34.697, near -45.723, executing the command clip far -34.697 near -45.723 does not restore the same view. Am I missing something? Thanks, Yazan

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Orientation and pre-superimposition of the PDB
by James Starlight 28 Jun '19

28 Jun '19

Dear Chimera Users! I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation). The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!) Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX! Thanks in advance!

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Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, Apologies if this has been posted before, still new to chimerax and the mailing list. Was wondering if there are plans to add support for modifying mouse keys with ctrl (similar to what is in chimera). I am also wondering if there are plans to create a recenter + change pivot button/function that is also part of chimera. Thanks, Yazan

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