January 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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2dimage?
by Emmott, Ed 31 Jan '18

31 Jan '18

Hi, Is there (or likely to be in future) a 2d image feature, allowing you to overlay 2d graphics (.tif, .png) in the same way as the 2dlabel command (e.g. Xpos Ypos )? My use case is wanting to add additional 2d graphics (e.g. color bar or graphs) over a pdb structure prior to rendering images/generating movies. Whilst I can get ChimeraX to open the images easily e.g. (open "...test.tif"), they are acquiring edges (white background image on white background scene -> grey borders) I assume as a result of being interpreted as a 3d object. Otherwise loving the software! Thanks a lot, Ed Using ChimeraX build v0.5 (2018-01-12) Dr Edward Emmott Research Associate Slavov Lab Northeastern University 332 Mugar, 360 Huntington Ave. Boston, MA.

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Ignored bad PDB record found
by Maurício Menegatti Rigo 31 Jan '18

31 Jan '18

I don't understand, my .pdb file seems perfectly fine, but I keep getting this error: *Ignored bad PDB record found on line 1ATOM 1 N ASN A 1 61.433 13.168 52.787 1.00 69.56 N Ignored bad PDB record found on line 2ATOM 2 CA ASN A 1 62.543 13.695 51.962 1.00 69.56 C Ignored bad PDB record found on line 3ATOM 3 C ASN A 1 61.990 14.337 50.735 1.00 69.56 C Ignored bad PDB record found on line 4ATOM 4 O ASN A 1 60.999 13.878 50.167 1.00 69.56 O Ignored bad PDB record found on line 5ATOM 5 CB ASN A 1 63.479 12.547 51.555 1.00 69.56 C2610 messages similar to the above omitted* I can open it in Chimera, PyMol, VMD, among others. But in ChimeraX is always the same error. I'm working on Linux (Ubuntu 14.04) with ChimeraX version 0.5 (2018-01-24). Any help? Thanks in advance, Mauricio M Rigo, Ph.D

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Consultation about software use
by dejesusm＠sloankettering.edu 30 Jan '18

30 Jan '18

Good day. I am Miguel de Jesus, a graduate student in the lab of Morgan Huse at the Sloan-Kettering Institute, NY. We are embarking on a new project that may require some sophisticated analysis of morphology from time-series imaging data. I have encountered a recent paper (Fritz-Laylin et al., eLife 2017) that used UCSF ChimeraX to analyze lattice light sheet data on neutrophils. I suspect my project may benefit from the same tools, but I have no experience with computational or image analysis as of yet. Would it be possible for me to consult with someone from the dev team, perhaps over Skype or e-mail, to ask rather rudimentary questions about how I might be able to conduct analysis for the planned work? Thanks so much. Miguel DJ Miguel Francisco M. de Jesus Graduate Student (Huse Lab) Memorial Sloan Kettering Cancer Center Zuckerman Research Center, 417 E 68th Street, New York City, NY 10065, USA

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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

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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

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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

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ChimeraX-users January 2018