- Chimera-users - RBVI Mailing Lists

Selecting Protein portions
by Reiner Villavicencio 20 Nov '05

20 Nov '05

Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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creating cubes and other 3D shapes
by Stephen A. Smith 18 Nov '05

18 Nov '05

Hi I want to create a cube (box; 1Å^3, 2Å^3, etc.) at specific grid points and color them as needed. Is this possible in Chimera? It is easy to do with spheres by specifying an atom at the desired location and then defining its VDW radius. I would like to create cubes and rectangles of various sizes, related to regions of my protein, to denote specific atomic / residue features. Any help would be greatly appreciated. Thanks Steve __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

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Reference Manual
by Reiner Villavicencio 17 Nov '05

17 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? I realized that under the documentation section of the website, that only online references are present. Having an offline user guide would be more convenient because there is no need to go online everytime a problem is encountered. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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Reference Manual
by Reiner Villavicencio 16 Nov '05

16 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? It woulb be more convenient, because its hard to go online whenever you have a problem. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Science and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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export tiff...
by Panizzi, Peter 14 Nov '05

14 Nov '05

To whom it may concern, I have been using the chimera program and I cannot save or export a tiff or jpeg file is there some trick to doing this? Thanks, Pete

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Rotation callback
by Charlie Moad 11 Nov '05

11 Nov '05

Is it possible to register a python callback for when a protein is rotated and get the rotation information? Thanks, Charlie

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v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models?
by Sabuj Pattanayek 11 Nov '05

11 Nov '05

Hi, In v1.2184 is it possible to specify the color of the tube object connecting the sugar to the backbone in a nucleic acid model? Currently clicking apply in the nucleic acid depiction dialog changes its color to whatever the color of the base is set to. Thanks

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chimera question
by cjamesgrant＠earthlink.net 09 Nov '05

09 Nov '05

Does chimera have the capability of automatically connecting the elements of a protein to reveal its overall shape. I am trying to determine the amino acid sequence of the attached protein, but I am having a hard time visualizing how the elements are connected to each other. I am new to this program, so any help would be greatly appreciated. Thank you, C Grant

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Mac OS X 10.4.3 update breaks Chimera
by Eric Pettersen 03 Nov '05

03 Nov '05

Hi, The 10.4.3 update to OS X breaks a significant amount of Chimera functionality. Attempts to use that functionality cause Chimera to exit. In particular, for structures that contain residues other than the standard amino/nucleic acids or water, anything that directly or indirectly makes Chimera determine atom types will cause the failure. Such things include adding hydrogens, finding hydrogen bonds, and going into ball-and-stick or sphere representation (the atom sizes are based on atom types) -- though stick-only mode is okay. We are working on a fix. Until we have one, you will have to weigh the improvements offered by 10.4.3 against the loss of Chimera functionality. I'll send mail to the list as soon as there are developments. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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RGB->CMYK color conversion
by James Puckett 02 Nov '05

02 Nov '05

Dear Chimera users, I am writing to see if there are suggested methods for ensuring good color conversion of rendered Chimera images from RGB to CMYK in Photoshop (or other image editing programs). When printing to a Tektronix Phaser 740 color laser, I am getting poor correlation between screen colorings and the printed ones. I have heard that the CMYK color space is basically a subset of the RGB color space. If this is actually the case, is there a recommended way to pick RGB colors that are relatively "safe" for conversion to a CMYK color space? Thanks, Jim Puckett

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