- ChimeraX-users - RBVI Mailing Lists

Cannot load Chimera X session
by Donghyun Park 29 Jan '18

29 Jan '18

Dear Chimera X users, I have trouble opening saved session in Chimera X. It loads my session for few seconds that shows following error messages: KeyError: 12 File "/private/var/folders/z_/sd6vflps0hs03gjrv5gt73yw0000gr/T/AppTranslocation/A86A6FCF-9B92-4C93-98CE-D4ADBB890140/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/tools.py", line 333, in remove del self._tool_instances[tid] See log for Python traceback. Can anyone please help me? Thanks, Raphael Park

2 1

Question regarding making movies & changing voxel size
by Donghyun Park 18 Jan '18

18 Jan '18

Dear Chimera X community, Currently, I am in a transition from the old Chimera to Chimera X. So far, I am very much enjoying Chimera X. 1) I was wondering if there's Chimera X equivalent of 'savepos' and 'movie recorder' . 2) Also, how can I change the voxel size in Chimera X? I tried to find answers in the User Guide but I couldn't find the right answer. I hope I can get some advice here. Thank you! Best, Raphael Park

2 3

making color zone transparenct
by Yashar Sadian 05 Jan '18

05 Jan '18

Dear all Is there a command or a way to make a zone colored EM map transparent? -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

3 3

invert selection in ChimeraX
by Yashar Sadian 26 Dec '17

26 Dec '17

Hi is there a command to invert selection like in chimera? or simply hide whatever that is not selected -- Best, Yashar Sadian Christoph Mueller's group Structural and computational Biology Unit European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg, Germany Phone: 0049-6221-387-8496 Email: sadian(a)embl.de

2 1

windows compatibility
by Sandrine Le Goff 19 Dec '17

19 Dec '17

Hi I would like to know if ChimeraX can be downloaded on a computer using windows 7 operating system Thanks a lot Best regards Sandrine Le Goff -- ___________________________________________ Sandrine VADON - LE GOFF Equipe Moali - Métalloprotéases et remodelage tissulaire Institut de Biologie et Chimie des Protéines UMR 5305 - Biologie Tissulaire et Ingénierie Thérapeutique - CNRS/Université de Lyon 7, passage du Vercors 69 367 LYON Cedex 07 FRANCE tel : 33(0)437652928

2 1

Export formats
by Mike Goodstadt 11 Dec '17

11 Dec '17

Hi Tom, What formats are you planning to support for exporting scenes? Many thanks, Mike Goodstadt mikegoodstadt(a)gmail.com skype: mikegoodstadt +34 653 756 614

3 2

Mapping local correlation between two maps
by Reza Khayat 06 Dec '17

06 Dec '17

Hi, Chimera allows one to map the CC between two maps onto a map and color the surface using the following commands: vop localCorrelation #0 #1 scolor #0 volume #2 cmap 0.6,red:0.7,white:1,blue I'm having difficulty executing the second command -mapping the values onto the first volume and assigning colors. Any help would be appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

2 2

activate model selectively
by Gabor PAPAI 29 Nov '17

29 Nov '17

Dear ChimeraX developers, I have a very naive question: how can I activate models selectively, like in Chimera? I would like to superimpose a density map with a pdb, but I don’t find how I can only activate and move the pdb. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 3

VR and optional functions
by Matthias Wolf 26 Oct '17

26 Oct '17

Hi Tom et al, Great job on chimeraX! The rendering engine is incredible. I have tried to view our cryo-EM volumes in VR with a new HTC Vive – it’s amazing and it works really well! ChimeraX supporting VR was one of the reasons for me to buy the Vive. Thank you! Now I haven’t used chimeraX before (I have used chimera since many years). I understand that the program is still work in progress. However, I am really missing some of the nice functions of chimera that make it so useful with a “clicky” interface - e.g. color surface by radius or by pdb properties, segmented isocontoured maps, clipping planes, subvolumes, combined shaded and wireframe surfaces, biological assembly, etc – I find these functions very useful and there don’t seem to exist any command line options for this, or I just haven’t studied them enough yet. Many of the existing menus in chimeraX have a fraction of the functionality of their sister program chimera. E.g. volume viewer, model panel, side view – I still have not figured out how to activate only one of several objects for rotation, when in chimera a click on the activate check box in the model panel does that (there is no active checkbox in the model panel of chimeraX and I couldn’t find a command to activate an object). It would be nice if one could simply grab an object in VR and rotate by itself it instead of the entire scene. Do you have a plan to add or port some of these beloved GUI functions from chimera into chimeraX? Could they be added by copying python modules from chimera? It would be great, if one could press a button in VR on the hand controller to display the menu and select functions “by virtual laser pointer”. This could preserve the development effort that went into the GUI design of chimera by reusing it in chimeraX as an identical projected 2D menu in VR and it would prevent having to take the goggles off for simple model adjustments. Best regards, Matthias

3 2

Re: [chimerax-users] error when save sessions of chimeraX in Ubuntu
by Elaine Meng 19 Oct '17

19 Oct '17

> On Oct 18, 2017, at 2:07 AM, Yahui Yan <yahuiuk(a)gmail.com> wrote: > > Hi Elaine, > > I am a new user of chimeraX. I run it (the daily builds on 17th Oct 2017) in my Ubuntu system. All went well until I tried to save the session. An error message '[Errno 25] Inappropriate ioctl for device' popped out. Could you please give me some advice to fix it? Many thanks. > > Kind regards, > Yahui > Hi Yahui, I don’t know the answer, but I’m sharing it to the mailing list: chimerax-users(a)cgl.ucsf.edu … that is the recommended address for ChimeraX questions. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1