October 2006 - Chimera-users - RBVI Mailing Lists

rotating molecules for movies
by wendy ochoa 30 Oct '06

30 Oct '06

Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? Thanks

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generating electrostatic potential map
by bala 27 Oct '06

27 Oct '06

Hello all, I want to generate the electrostatic potential map using Chimera. I tried through Delphi controler, however i am repeatedly getting an error as follows. I have successfully installed Delphi. Can someone suggest me what is wrong. __________DelPhi V. 4 Release 1.1 ______________ | | | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | many dielectric regions, multisalt ionic | | strength, different probe radii, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | | Recompiled on Linux and PC | | January 2002 -------- Walter Rocchia | |__________________ ___________________| DelPhi V. 4 program started on Fri Oct 27 2006 at 14:55:00 opening parameter file /tmp/tmpvpgS8V At least 30 nonlinear iterations atom radii read from file /usr/people/ojha/BALA/chim_amber.siz unknown header format in radius file: O5' A 1 1.7210 First it showed the same for H5 atom [which was the first atom in the siz/charge file], then i just tried by deleting the first line in the radius and charge file. Then the same error is coming for the second atom O5' in the file. Thanks in advance, Bala

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viewing grid density
by bala 26 Oct '06

26 Oct '06

Hello all, 1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same. 2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc. 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it. Bala

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To except box information in MD movie
by Atsutoshi Okabe 25 Oct '06

25 Oct '06

Hello, I viewed Amber format trajectory files ( topology/parameter file and trajectory file ) by MD movie. But I got the figure( attached file) I didn't intend. I think the reason is to read box information in the Amber trajectory file . How can I except the box information in MD movie window ?

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To color atoms
by Atsutoshi Okabe 24 Oct '06

24 Oct '06

Hi, I visualized one ligand molecule (a kind of sugar) written by PDB format within chimera. But all atoms have non color(attached file ) I want to color these atoms (i.e. the oxygen has red .) Could you please teach me how to color atoms?

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1.2304 production
by Eric Pettersen 23 Oct '06

23 Oct '06

We haven't received any major bug reports for the release candidate, so we have promoted it to a production release (1.2304) which includes a few quite minor bug fixes and some documentation improvements relative to the release candidate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Movie - Display Spheres
by Jared Godar 20 Oct '06

20 Oct '06

Hello, I am trying to use the 'represent spheres' command to draw attention to specific residues in a model that is displayed as a ribbon. I would like to first show the ATP binding site of the molecule with magenta spheres, then show the three residuse which get phosphorolated. Currently, I am able to display one of these elements or the other as spheres, but not both at the same time. I've tried to use a single represent sphere command to specify all of the desired atoms, but can't seem to get the context right, represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 & #0::ATP weren't working. Help on the syntax to simultaneously display the two commands listed below which are currently mutually exclusive would be appreciated. #SHOW ATP: color magenta #0::ATP; color magenta #0::mg; represent sphere #0::ATP #SHOW PO4 Residues show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red #0:432; represent sphere #0:426,431,432 Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

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Dock?
by S Joshua Swamidass 19 Oct '06

19 Oct '06

Hello, Are there any plans to develop a gui frontend for DOCK using chimera? Josh

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force fitting a protein into select volume in a EM reconstruction
by jayant_jacques 17 Oct '06

17 Oct '06

hi! Is it possible in chimera to choose a particular part of a EM envelope and a protein and fit them? AS the protein that I am trying to fit into the map finds a better fit else where in the EM envelope, after I painstakingly align it to the place where its supposed to be!!! Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

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release candidate
by Eric Pettersen 17 Oct '06

17 Oct '06

We've made a release candidate (version 1.2303) available for download. It has many new features relative to the previous production release (1.2199). The features/improvements are listed here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2303.html Please let us know if you encounter any problems with the release candidate. If no major problems surface in the next few days, we will promote the candidate to production release status. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera-users October 2006