January 2009 - Chimera-users - RBVI Mailing Lists

transparency change for a whole model
by Neil Ranson 21 Jan '09

21 Jan '09

Dear All, I am revisiting a movie I made in chimera some time ago with a painfully long script. In this script, I used a command syntax like this: transition transparency #0 0 0.1 1 copy file 'filename' To change the global transparency of model #0 (with lots of different elements all coloured and represented differently) This command seems to have disappeared. Is there an equivalent way now? The only way I can find is to use transparency in the colordef command, but that will be extremely cumbersome. What is the preferred way to fade a model in and out now? Thanks in advance, Neil Ranson Neil Ranson PhD Level 2 Biochemistry Tutor University Research Fellow Astbury Centre for Structural Molecular Biology IMCB University of Leeds, Leeds, LS2 9JT, UK. EM Image Processing Suite - Miall 6.02 Tel: 44 (0) 113 343 7065 email: n.a.ranson(a)leeds.ac.uk

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command files
by Matthew Dougherty 20 Jan '09

20 Jan '09

I have a command file that has a number of reset commands. I would like to 1) interrupt a command file during execution, aborting all further commands, stopping the graphics configuration at the abort (e.g. threshold values, active models, etc) 2) be able to place a hold in a command file, say after the a reset command, and be able to continue the command processing after pressing a key on the keyboard. Does this capability exist? thanks, Matt

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Coulombic Surface Coloring
by Martin Kampmann 20 Jan '09

20 Jan '09

Hello, I saw on the Chimera online manual that there is a Coulombic Surface Coloring function, which displays an approximate electrostatic potential without having to calculate a file with delphi etc. This sounds great and I would love to use the function. However, in the Tools > Surface/Binding Analysis menu, I don't find it. Is it something to be implemented in future versions of Chimera? Or is there a way of using it in the current release (I have version 1.3 build 2577 from December 9) Thanks a lot! Martin

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marginal issues on installation (linux)
by Francesco Pietra 20 Jan '09

20 Jan '09

hi: replaced hd, installed chimera-1.3.2577-linux.exe on debian i386 lenny ok, though i have to give the full path /usr/local/chimera/bin/./chimera to launch chimera. notice that the directory /chimera is chown to me as user. with previous versions and debian i386 etch (last installation daily built 17 Sept 2008), execution of chimera from anywhere was provided on installation. never mind, are there available env variables for the executable? thanks francesco pietra

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Matchmaker
by hsosa＠aecom.yu.edu 20 Jan '09

20 Jan '09

Is it possible to retrieve the transformation matrix (or angle of rotation and translation) that the Matchmaker tool used to align two atomic models ?. I know that you can get this information when fitting an atomic model into a density map using the tool Fit in Map and then pressing the Results button. Is there anything similar for the MatchMaker tool ?. 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 hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] Protskin
by Elaine Meng 15 Jan '09

15 Jan '09

On Jan 15, 2009, at 7:07 AM, Patton, John (NIH/NIAID) wrote: > > Hi Elaine, > Do you have any information concerning using Protskin in conjunction > with > Chimera? The only information I have come across applies to PyMol. > Thanks, > John Hi John, I haven't tried Protskin, but my understanding is that its purpose is to map conservation in a multiple sequence alignment to protein display. (Protskin page: <http://www.mcgnmr.ca/ProtSkin/intro/> ) Chimera itself can (A) read your multiple sequence alignment (many formats, just use File... Open) (B) calculate any of several measures of conservation (entropy, variability, etc.) - in the sequence window menu, choose Preferences... Analysis, set "Conservation style" to "AL2CO" to access further options for calculating conservation, which is shown as a histogram above the alignment <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… > (C) show them on your structure(s) with any color mapping you desire, or with "worm" thickness - any open structure(s) will associate automatically with sequence(s) in the alignment - in the sequence window menu, choose Structure... Render by Conservation, change attribute to "mavConservation" and show with color or worms <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html… > Example image, 1bzm colored by conservation in PFAM Carb_anhydrase seed alignment: <http://www.cgl.ucsf.edu/chimera/feature_highlights/1bzm-al2co-highlight.png > This tutorial includes coloring by conservation: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> Back to ProtSkin: ----------------- It sounds like ProtSkin emits some file listing the residues and associated values. Certainly you could reformat that into a Chimera "define attribute" file, read it in, and then show the values as in (C) above. Since Chimera already performs the preceding steps quite well and with many powerful options, there hasn't been much impetus to hooking it up to ProtSkin. However, I don't see any barrier other than your needing to convert the output file into the simple "define attribute" format described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > Getting a sequence alignment: ----------------------------- Perhaps you didn't already have a sequence alignment, and find ProtSkin to be helpful in generating one. There are many alternative approaches. For example, the ConSurf server does a great job of automatically generating an alignment of a diverse set of sequences related to your single uploaded structure. (ConSurf server: <http://consurf.tau.ac.il/> ) There are more ideas in this page I wrote on "sources of sequence alignments" for use in Chimera: <http://www.cgl.ucsf.edu/home/meng/sources.html> I would be happy provide more detailed help on using Chimera to color by conservation as it applies to your system of interest, i.e. feel free to write back. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Rotating about an axis
by Thomas Goddard 14 Jan '09

14 Jan '09

Hi Kevin, The command "turn x 23" will rotate active models about the screen x axis by 23 degrees. The command "turn 1,1,0 180 center 0,2.5,2.5 coord #1 models #1" rotates just model #1 by 180 degrees about axis 1,1,0 defined in the local coordinates of model #1 about center point 0,2.5,2.5 also in model #1 local coordinates. The fancier forms of the turn command are only in Chimera 1.4 daily builds. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html You align multiple structures by aligning them all to one reference structure. You can align specific residues with the "match" command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Do do a sequence based structure alignment look at the MatchMaker tool or command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… Best to send questions to chimera-users(a)cgl.ucsf.edu. Tom Kevin Koehntop wrote: > Hi Tom, > > In Chimera, how do you rotate a structure along an axis by X degrees? > How is the specific axis selected? Finally, is it possible to align > multiple structures (e.g. their tops, bottoms, centers, etc.)? Thank you > > Kevin

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Docking crystal structure in density map
by Anindito Sen 14 Jan '09

14 Jan '09

Dear All I have docked the crystal structure of a protein monomer manually in the density map ( of a filament) and with some movements done with a long alpha helix(part of the crystal structure) to make a decent fit. However when I generated multiple copies of the docked structure- regions where manual adjustments on the alpha helix were made- came out like thin wires instead of being a ribbon. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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chimera on fedora10
by Bala subramanian 14 Jan '09

14 Jan '09

Hello, I installed chimera on fedor10. The installation was done but when I try to open, it gives me the following error. How should i resolve the problem python2.5: can't open file '/usr/local/share/checkOpenGL.py': [Errno 2] No such file or directory Thanks, Bala

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Saving a Morph movie
by R. Andrew Byrd 14 Jan '09

14 Jan '09

Greetings, I have been trying to use the Morph tool in the production release from summer 2008. The tool works very well and allows playing the trajectory in the graphics window. However, when I try to save the file as a movie, it consistently crashes. I am running Win XP SP3, on a Dell M1330 laptop. It has also crashed on a Dell desktop running XP SP3. Are there special tricks to saving the movie for use in a Powerpoint presentation? Thanks for any help/suggestions! Andy -------------------------------------------------

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Chimera-users January 2009