- Chimera-users - RBVI Mailing Lists

Installing colorbrewer for Chimera Python
by Paul Kibet Korir 18 Feb '16

18 Feb '16

Hi, I want to use the chimera API and I've managed to configure a successful import of chimera except that I get that colorbrewer is not installed. >>> import chimera Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 73, in <module> import palettes File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 103, in <module> _initPresets() File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 95, in _initPresets from colorbrewer import ColorBrewer ImportError: cannot import name ColorBrewer What is the right way to go about this? (I could create a symbolic link to my system colorbrewer, but that doesn't seem clean). -- With kind regards, *Paul K Korir, PhD* /Scientific Programmer/ EMBL-EBI Main Building, A2-35, WTGC, Hinxton, Cambridge CB10 1SD P: +44 1223 49 44 22 F: +44 1223 49 44 68

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Query
by manan 17 Feb '16

17 Feb '16

Chimera allows users to add ions to a given structure using Amber tools. This option has a predecided set of ions. Is it possible to add ions other than those mentioned in the add ions option. For example,Ca2+ is not included in the list, so is it possible to add Ca2+ ions? -- Manan Desai Research Student Department of Biochemistry The Institute of Science 15 Madame Cama Road, Mumbai-400 032 India

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Error when starting Chimera
by Jérémie KNOOPS [531802] 16 Feb '16

16 Feb '16

Dear Chimera Users, When I launch chimera, I get directly the "Chimera Launcher Error" box with this message : "chimera exited abnormally; the exit code was: 1" I got this screen when I used the debugging command:

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StructureViz and Chimera Path in Cytoscape
by Pat Daley 12 Feb '16

12 Feb '16

Hi, It doesn't remember the path to Chimera after closing/opening Cytoscape. Any ideas? Can I manually write the path into a config file somewhere? Thanks!

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mapping between MRC and PDB
by rongjian li 12 Feb '16

12 Feb '16

Hi, I am a beginner in using Chimera. I have a simple question for you experts and I really appreciate any guide for me. I am working on a project needs to create a one-to-one mapping between MRC grid and PDB atoms. For example, from the PDB file, I know the physical coordinates of each atom. I want to know whether each atom is out of the 3D volume of MRC or not. If it is inside the volume, I hope to know which voxel grid this atom is in. I have figured out the mapping between the physical origin of PDB system and its grid index in MRC using Chimera Volume Viewer -- > Features ---> Coordinates ----> Origin Index. But I am not sure whether the information of 'Rotation axis' is also very important, which is usually [0,0,1] in Chimera Volume Viewer -- > Features ---> Coordinates ----> Rotation axis. Thank you very much. Best, Rongjian

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Will ChimeraX be built with a universal undo?
by Oliver Clarke 10 Feb '16

10 Feb '16

I realise this is probably impossible to alter in the current version of chimera, but will the next-gen Chimera be built with a universal (or at least much expanded) undo function (or set of functions)? Or if not what are the devs thoughts on this - I know it is a complicated issue, but the capacity to backtrack after making a color change, deleting a selection, etc, would be very very welcome. Cheers, Oli

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Thoughts re enhancements for ChimeraX
by Oliver Clarke 10 Feb '16

10 Feb '16

Hi, just thinking about a couple of possible enhancements relating to things that are probably difficult to fix in the current framework, feel free to take or leave them. * Hover to label residue is useful, but slow. Maybe hold down alt/option and have the residue currently under the cursor instantly bring up a residue label (or put the residue label in the lower status bar, and have it change when the cursor moves over another residue)? * Selecting molecules inside (e.g. mesh) density maps is a little cumbersome in that it requires un-showing the mesh map first, even though model is clearly visible - ctrl-clicking on an atom usually selects the map instead (which is only rarely the desired outcome). perhaps a modifier key to specifically allow selecting atoms, ignoring maps, would be useful in this instance? Cheers, Oli.

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Do attribute names have to be case sensitive?
by Oliver Clarke 10 Feb '16

10 Feb '16

Apologies for spamming the message board... in Chimera at present, attribute names (e.g. stickScale) are case sensitive. I understand that this is the way it was built and there is probably no changing it in the current version of Chimera, but assuming ChimeraX has a similar concept of attributes built in, would it be possible to make these case-insensitive? I can't imagine there are many situations where case would make a difference to the intended attribute (and if there are there probably should not be). I have many cases where I type e.g. "setattr m stickscale 2.0", nothing happens and there is no error message, and I am confused until I realise I should have typed "setattr m stickScale 2.0". Alternatively, raising an error message in the status bar when a user attempts to alter a nonexistent attribute would also be helpful. Cheers, Oli.

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measure distance
by Jingchuan Sun 09 Feb '16

09 Feb '16

Hello, I use "measure center #11 mark true radius 20" to make a ball to represent a model, then use "measure distance #13 #14 show true". I get a number of distance between the two balls. Is it pixel value or angstrom? Is it between the center or surface of the two balls? Best, Jingchuan

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uninscribe
by Barry Lever 08 Feb '16

08 Feb '16

-- A. B. P. Lever, FRSC Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 http://www.chem.yorku.ca/profs/lever

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