November 2005 - Chimera-users - RBVI Mailing Lists

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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2D labels not saved ?
by Boaz Shaanan 02 Nov '05

02 Nov '05

Hi, I used the 2D labels utility to make a few labels but when I save the image as tif I don't see them when I re-open the tif file. Is that possible ? Thanks, Boaz

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chimera and STRAP ?
by Dr. Christoph Gille 01 Nov '05

01 Nov '05

Hi, I contact you because users of the program STRAP for protein structures and sequences asked whether Chimera could be used within STRAP for visualization. Currently Jmol and Pymol are used for visualiziation. For example the results of 3D superpositions and the location of mutations can be viewed. But some users apparently prefere Chimera. My question is whether Chimera could be linked to STRAP as well. The most important point is, what mode of interprocess commmunication exists in Chimera. For example Pymol and STRAP are linked via the stdin/stdout streams. STRAP can send commands to Pymol and is notified when atoms are picked. STRAP uses the scripting language of Pymol to load proteins, create selections and rotate proteins. Could all this be done with Chimera in a similar way ? Best regards Christoph

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how to select multiple residues in multiple chains
by Eric Gillitzer 01 Nov '05

01 Nov '05

I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.

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Display of qpack color output
by Eric Dawson 01 Nov '05

01 Nov '05

In the older UCSF MidasPlus incarnation of your software, there was a feature that allowed an interface with Gregort & Cohen's QPACK software for coloring according to molecular packing density using a sphere growth method. Per residue packing scores were applied with a color range after running qpack with the special option, '-m'. http://www.cmpharm.ucsf.edu/cohen/software/pages/qpack.html In the primary literature report of QPACK, it was suggested by the authors that they would work to make this feature available in UCSF MidasPlus and 'its successors'. Since this is a very fast and convenient way to evaluate the quality of models, I would like to recommend/request that this feature be enabled (or added) to Chimera. In MidasPlus, it was a command line option. The user simply entered qpack; there was a .midasrc file that contained the explicit local path to the qpack binary as well as a command line script to launch the package with the '-m' option. Thanks for your consideration of this suggestion. Best regards, Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211 "All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring

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Chimera-users November 2005