October 2006 - Chimera-users - RBVI Mailing Lists

window size
by Viktor Hornak 06 Oct '06

06 Oct '06

Dear All, I was wondering if there's chimera command that sets the size of chimera window. Basically I just want to have a well defined window size when I save pictures (or movies)... Thanks, -Viktor -- Viktor Hornak SUNY at Stony Brook

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OpenGL error in GfxInfo::initialize 'out of memory'
by Dmitry Osolodkin 05 Oct '06

05 Oct '06

Hello all, I have a very small but annoying problem. I had two versions of libGL.so.1, so I have renamed the version in /usr/X11R6/lib/. Now I can run Chimera, but it works rather slow and says OpenGL error in GfxInfo::initialize 'out of memory'. I use Mandriva Linux 2006 and FireGL drivers by ATI. Could anone help me? Thanks. Dmitry Osolodkin

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Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 2
by Jonathan Hilmer 05 Oct '06

05 Oct '06

Pu Qian, Although resources-intensive, I find it useful to have multiple, identical, overlapping copies of the same density set. It allows complex 'removal' of sections in the final image by the combination of multiple clipping planes. For example, the three planes with definitions of [1,0,0], [0,1,0], and [0,0,1] all with an origin at the center of your data will cut away 1/8 of a spherical region, if you have three copies of the density loaded. This also makes it easy to animate the cutout. The alternative is to use the volume eraser (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase…), which works, but I've found it less useful for movies. When working with large data sets and this method, use cropped density sets to minimize unnecessary resource usage. Jonathan > > To whom it may concern, > > > > I'm a new user of Chimera. It is a very good software! > > > > Here, I would like to ask you a few questions? To show inside of > > protein > > (3d model),I need to cut it into half (sometime, maybe only part, > > for example, > > 1/4 etc.). Just like an apple, if I want to show its core, I need > > to cut the > > apple into two parts from its middle. Does Chimera has such > > function? (I think > > it has.) My 3d data comes from electron microscopy single particle > > analysis > > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > > which type of > > 3d data I should produce for Chimera? It would be a great > > appreciated if you > > could reply me in your convenience. Hope it will not bother you too > > much. > > > > Sincerely yours, > > > > > > Pu Qian > > > > Dr. Pu Qian > > Department of Molecular Biology > > The University of Sheffield > > Firth Court, Western Bank > > Sheffield, S10 2TN > > UK

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Spider to Brix
by Batsal Devkota 05 Oct '06

05 Oct '06

Hi, When I convert spider file to brix and load both of them in Chimera, they do not superimpose on top of each other. I adjusted the origin to be 0,0,0 for both the maps and still the maps seem to be rotated with respect to one another. any insight?? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

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volumetric filling
by jayant_jacques 04 Oct '06

04 Oct '06

hi! I am striving to perform voluertric filling of a crystal structure into an EM reconstruction. I have down loaded and complited the Linux_64 bit version. I first load my crystal structure and then the EM reconstruction on the same screen and set the EM reconstruction as DATa. I am not able to figure out where the FIT buttons is located in the pop up menus!!! I would be very grateful if you could help me sort out this issue! Thanks Jayant NB I am using the online manual to help me in this endeavour http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… 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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Slicing a 3d model
by Thomas Goddard 04 Oct '06

04 Oct '06

Hi Pu Qian, Use clip planes to cut a model in half in Chimera. There are two types of clip planes. The front and back clip planes are always parallel to the screen. The per-model clip planes can be oriented at any angle. Both can clip away the back as well as the front. The following web page describes how to use both for EM density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab Clipping works on all types of data in Chimera including atomic models of proteins. For EM data it helps to have Chimera cover the holes left when a contour surface is clipped. This is described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping Also you can color according to density on the sliced surface. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorc… All of these URLs come from the Chimera guide to volume display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html and you may find other useful features for viewing your EM map there. The following page shows examples of clipping, capping and coloring including a movie of a slab moving through an EM map of a virus particle. http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR, Purdue image format, ...) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume I do not know if IMAGIC5 uses any of these formats or has its own. Chimera does not read any specific IMAGIC5 format. Tom > From: P Qian <P.Qian(a)sheffield.ac.uk> > Date: October 4, 2006 1:43:50 PM PDT > Subject: Sheffield Qian, how to make cut 3d model > > > > To whom it may concern, > > I'm a new user of Chimera. It is a very good software! > > Here, I would like to ask you a few questions? To show inside of > protein > (3d model),I need to cut it into half (sometime, maybe only part, > for example, > 1/4 etc.). Just like an apple, if I want to show its core, I need > to cut the > apple into two parts from its middle. Does Chimera has such > function? (I think > it has.) My 3d data comes from electron microscopy single particle > analysis > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > which type of > 3d data I should produce for Chimera? It would be a great > appreciated if you > could reply me in your convenience. Hope it will not bother you too > much. > > Sincerely yours, > > > Pu Qian > > Dr. Pu Qian > Department of Molecular Biology > The University of Sheffield > Firth Court, Western Bank > Sheffield, S10 2TN > UK >

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Chimera-users October 2006