March 2018 - ChimeraX-users - RBVI Mailing Lists

mutitouch mac
by Edoardo Gianni 01 May '18

01 May '18

Hello, I was wondering if multitouch was available on chimerax for mac, or if you had plans to implement it in the future. Thanks and best wishes, Edoardo

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I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by JEAN-YVES SGRO 29 Mar '18

29 Mar '18

Greetings, thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html which are useful and one can reconstruct the initial display. As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. Simply pressing the "Show atoms" button will display all water molecules as small spheres. But now if I click "Hide atoms" only the ribbon is left. Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html> but that was not the best solution. Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: show ions show ligand select ligand:<3.8 & protein show selAtoms For novices this is a bit complicated to understand. Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. I firmly believe that this would avoid lots of frustration for many new users! P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? Sincerely, Jean-Yves Sgro

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Export as .obj
by Boris Chaumette 28 Mar '18

28 Mar '18

Dear colleagues, I am currently using ChimeraX and would like to save my file as a .obj I tried the following command line: save "ATPtest.obj" obj But model is expected. I don't understand how I can specify it to incorporate the whole figure. Thank you, Best, Boris Chaumette MD/PhD - postdoctoral researcher Laboratory of Guy A. Rouleau Montreal Neurological Institute McGill University Irving Ludmer Building 1033, Pine av. Room: 327 Montréal, Québec, H3A 1A1 Phone: +1 514-398-6821

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Matrixset equivalent
by Reza Khayat 15 Mar '18

15 Mar '18

Hi, Is there a matrixset (from Chimera) equivalent for ChimeraX? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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VR mode not working
by Sebastian Poelsterl 13 Mar '18

13 Mar '18

Hi, I'm trying to view a PDB structure (2fha) in vr mode, but get the following error after executing 'vr on': An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 61, in draw_new_frame view.draw(check_for_changes = False) File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\view.py", line 178, in draw r.draw_background() File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\opengl.py", line 677, in draw_background GL.glClear(flags) File "zr\accelerate\src\errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError (src\errorchecker.c:1270) OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glClear, cArguments = (16640,) ) I'm using ChimeraX 0.5 with an Oculus Rift (1.24.0.545657), NVIDIA GeForce GTX 1060 (driver version 391.01) and SteamVR Version 2018-02-10 (1518226924) under Windows 10 (10.0.0.14393). Any suggestions would be appreciated. Thank you. Sebastian The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Some core modules moving
by Eric Pettersen 07 Mar '18

07 Mar '18

Hi all, In the interest of making ChimeraX’s core smaller and less likely to need frequent updating (since it can’t be updated incrementally via the ToolShed), we will be moving some modules out of the core and into bundles, so those at least will be individually updatable via the ToolShed. Those core modules are atomic, map, surface, and ui. As of tomorrow’s daily build, you can and should use the the new import paths for these modules (e.g. from chimera.atomic import Atom rather than from chimerax.core.atomic import Atom). Old-style imports will continue to work for several months at least, at which time a warning will be raised if the import is still in use (but the import will work). Probably several months after that we will disable the old-style imports. One further note is that the MainToolWindow class can now be imported directly from the ui module, rather than from its gui submodule, so: from chimerax.ui import MainToolWindow is preferred over: from chimerax.ui.gui import MainToolWindow —Eric Eric Pettersen UCSF Computer Graphics Lab

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Surfaces & color by attribute
by Hernando J Sosa 06 Mar '18

06 Mar '18

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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ChimeraX-users March 2018