January 2009 - Chimera-users - RBVI Mailing Lists

Volume information
by vamsee 26 Jan '09

26 Jan '09

Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715

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suggested feature/model panel
by Matthew Dougherty 26 Jan '09

26 Jan '09

1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder

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How to display automatically the atoms in Gaussian cube file format
by Hyung Jun Lee 26 Jan '09

26 Jan '09

Gaussian cube file formats include the information about each atom's positions as well as the volumetric data. But, Chimera only displays the volumetric data when importing the cube file format. I want to know how to display automatically the atoms whose positions is included in the cube file, together with the volumetric data.

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Mac 64-bit Chimera version
by Thomas Goddard 26 Jan '09

26 Jan '09

Hi Denis, Conrad Huang in our lab tried building a 64-bit Mac Chimera several months ago. Many of the third-party packages we rely on failed to compile. We decided to pursue this only after Mac OS 10.6 is released. I believe the rationale of that was that Mac OS 10.5 is the oldest Mac OS that supports 64-bit graphical apps. We still support Mac OS 10.4 and our current automated build system targets 10.4. When 10.6 comes out we may target our builds to 10.5. Currently we only provide 64-bit Chimera on Linux. Tom Denis Chrétien wrote: > Dear Thomas, > > We were discussing some time ago about a 64 bit Mac version of Chimera. > Did you progress in this project ? (I'm still very limited for > visualization of large volumes with my mac, although its not a hardware > problem : 16 Gb Ram installed). > > Best regards, > > Denis > > Le 15 mai 08 à 18:41, Thomas Goddard a écrit : > >> Hi Denis, >> >> The Chimera error you reported means there was insufficient memory to >> compute the Fourier transform you wanted. I see from the report that >> your Mac has 18 Gbytes (wow). But our Mac Chimera version is a 32-bit >> program so its memory address space is only 4 Gbytes. In that 4 >> Gbytes has to fit not only data, but all shared libraries, program >> stack and (I think) operating system code. So really you might have >> just 3 Gbytes to work with. Also my Fourier transform code does a >> full complex value FT where it could do a real value FT taking half >> the memory. And the Python library that actually does the FT can only >> use double precision, so 16 bytes per complex value. More memory is >> used when Chimera takes just the magnitude of the FT coefficients. In >> short it is using 20 bytes per grid point. So a 512^3 FT will use 2.5 >> Gb, about the maximum that will fit in the 32-bit address space >> (assuming it isn't already fragmented by other data/libraries since >> you need a 2.5 Gb free block). >> >> We plan on fixing this. We plan on distributing a 64-bit Mac >> Chimera, and have tried compiling it. But some of the ~30 third-party >> libraries Chimera depends on did not compile. So we still need to >> work on that -- maybe within 3 months. Also I plan on making the FT >> code not such a hog, do a real FT and investigate 32-bit float FT >> values for a factor of 4 memory savings. For now your only option >> would be to use one of our 64-bit Chimera versions on Linux or Tru64 >> operating systems. >> >> Tom > > ___________________________ > Université de Rennes 1 > UMR 6026, équipe TIPs > Campus de Beaulieu, Bât. 13 > 35042 Rennes Cedex > France > > Tel. +33 (0)2 23 23 67 64 > http://www.umr6026.univ-rennes1.fr/ > ___________________________ >

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Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion
by Anindito Sen 26 Jan '09

26 Jan '09

Hi Tom You are correct! The color dialog does appear as you mentioned! In addition - While using Chimera- the display window keeps flickering when I move the density map/pdb files. What can be a possible remedy to solve the problem? Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Fri, 23/1/09, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: From: Tom Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion To: emailanindito(a)yahoo.co.in Cc: chimera-users(a)cgl.ucsf.edu Date: Friday, 23 January, 2009, 11:35 PM Hi Andy, Sounds like a windowing system problem, not a Chimera problem. If you show the Surface Color dialog (Tools / Volume / Surface Color) and click on one of its color buttons, does the color dialog appear? Tom Anindito Sen wrote: > 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 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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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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Chimera-users January 2009