- ChimeraX-users - RBVI Mailing Lists

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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Cororing by B-factor
by Rajiv G Govindaraj 23 Feb '18

23 Feb '18

Hello, I am NOT able find the coloring atoms by bfactor in ChimeraX. I have a b-factor values range from negative to positive, and wants to color them from min to max(blue to red) as normal bfactor colors. Appreciated if you could tell me how it can be done in ribbons and surface using ChimeraX? Thank you. Regards, RJ

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ChimeraX user guide display issue
by Jerry Honts 19 Feb '18

19 Feb '18

Unlinked and linked text is *invisible* in user guide (and elsewhere in interface) because font color is *white* on white background. The apparently invisible text can be selected and displayed after copy and paste to another text field. Hyperlink underlines remain visible. Is this a CSS style sheet problem? Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Olin Hall 324 (office)

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open local pdb files "containing no atoms and bonds"
by Fekete Attila 15 Feb '18

15 Feb '18

Dear Colleagues, I have tried to open several local *.pdb files, but in each case I got the error: "Opened PDB data containing 0 atoms, 0 bonds and 0 coordinate sets", and a series of warnings (for each lines of the files) and ChimeraX doesn't show the structure. I have also tried different versions of ChimeraX (0.1/0.5 and even alpha releases, recently I'm using 0.5 under Ubuntu 16.04). I can open any online files (*pdb,*mmCIF) from the RCSB database, however if I download the same file, I got the above mentioned error message, so I have absolutely no clue to resolve the problem because I suppose this isn't related to pdb format issues but a bug can be somewhere in the softwere. I am really impressed by the visualization capabilities of ChimeraX so please help me if you can. Yours, Attila

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ChimeraX surface coloring
by Nadishka Jayawardena 14 Feb '18

14 Feb '18

Hi there, I recently installed ChimeraX and been trying to figure out a way to colour a cryo-EM map by radius- however, I couldn't find a way to get this done? Is this feature not implemented on ChimeraX as yet? Is there a way to colour the map by using a python script? Many thanks Nadishka P.S. Must say that this new version is a huge improvement!

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spin movie error
by Andrey Feklistov 05 Feb '18

05 Feb '18

Dear chimera X developers, upon trying to record a spin movie with a corresponding button I get an error: dyld: Symbol not found: _clock_gettime,Referenced from: /Volumes/ChimeraXInstaller 2/ChimeraX.app/Contents/bin/ffmpeg,Expected in: /usr/lib/libSystem.B.dylib Typing the command manually results in the same error. I remember that the feature used to work when I first tested ChimeraX last year. Thanks for any advice.. Andrey

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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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