- Chimera-users - RBVI Mailing Lists

need a script
by Bala subramanian 26 Jan '09

26 Jan '09

Dear Chimerians, Kindly help me If anybody has a script to do the following. Given two pdb files, the script should calculate the vector distance between the atoms, say CA atoms and draw an arrow representing the magnitude and direction of the vector. Do i need to add some plugin to draw arrows through atoms in Chimera. Thanks in advance, Bala

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Chimera on Ubuntu mounted on MAC using VMware Fusion
by Anindito Sen 23 Jan '09

23 Jan '09

Dear All This may be a bit unusual problem- I am using Chimera (from Daily build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages that run only on LINUX and not on a MAC). The problem is - when I try to get the color panel by clicking on the color tab on the volume viewer- it does not appear. I am not sure if any of you have encountered such problem. 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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Movie Recording
by skmolugu＠miners.utep.edu 22 Jan '09

22 Jan '09

Hi, I am having problems with movie recording. I saved the movie as .avi file and when I upload the movie in to a windows power point slide, it crashes or shows a dark cube. Can you please suggest me a possible solution for this.. Thank you very much for your time. Regards, Sudheer.

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Re: [Chimera-users] Movie Recording
by Sacha De Carlo 22 Jan '09

22 Jan '09

Hi, it sounds lime you're having problems with Windows & Powerpoint, not Chimera... can you play the movie correctly with media player or VLC? Do you have all the video codecs installed correctly? Did you check the Chimera temp directory to see whether the frames have been created? hope this helps. Sacha ------------------------------------------ Sacha De Carlo, Asst. Professor Marshak Building Room 1335 The City College of NY (212) 650-6070 E-mail: sdecarlo(a)ccny.cuny.edu http://www.planetesacha.com/Work.htm ------------------------------------------

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Higher order
by hsosa＠aecom.yu.edu 21 Jan '09

21 Jan '09

Is it possible to assign colors by chain to the surfaces created my the multiscale models 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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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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