- Chimera-users - RBVI Mailing Lists

Memory allocation
by brmorgan＠clarku.edu 13 Sep '06

13 Sep '06

Does Chimera have a fixed amount of memory allocated to it, and if so, is it possible to increase this amount? I am working with very large system sizes and am trying to reduce the amount of time it takes to perform certain operations.

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Re: [Chimera-users] Memory allocation
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom > From: "Brittany Morgan" <brmorgan(a)clarku.edu> > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] Memory allocation > Date: Tue, 12 Sep 2006 20:52:39 -0400 > > I am working with molecules, and it has problems redrawing them in > ball-and-stick representation, although I expect that at larger system sizes > other functions will start slowing down as well. If I look at the memory > usage while it is redrawing them, Chimera seems to be using only about 1/4 > of the available memory, but creating a paging file nonetheless. It will > work, it just takes about 15 minutes to redraw about 64,000 atoms, and I > need to go to system sizes much larger. If I need more memory, that is > possible, I just wasn't sure if that was the issue because it didn't appear > that Chimera was using all of the available memory. I am using Chimera in a > non-standard way (I'm not displaying proteins, but rather many small > (unrealistic) molecule-type objects). > > Thank you for your help! > Brittany

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Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML file?
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Masako, Chimera does not read IMOD files but perhaps I can add a file reader for you. Have you already defined a path in IMOD along the structure you want to measure? Or have you just segmented out the structures. If you have segmentations but no explicitly defined 1 dimensional path then it is not clear how to define the length. Is the IMOD format you are using the following? http://bio3d.colorado.edu/imod/doc/binspec.html Could you send me an example file? Tom > Date: Mon, 11 Sep 2006 17:41:20 -0700 > From: Masako Terada <mterada(a)ncmir.ucsd.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML > file? > > Hi. Thank you for your e-mail. I have tried using volume path tracer > as you instructed. Even though it looks very promising, it is > time-consuming since we have 90 different objects to measure. So I > would like to try your another suggestion, importing trace file into > Chimera and measure lengths. Are you familiar with IMOD segmentation > file format? I tried to import this IMOD file into Chimera, but > unsuccessful, so I am guessing that I have to convert it to something > else... Any more suggestion? > > Masako >

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Can I use "Chimera" to measure length of a VRML file?
by Masako Terada 11 Sep '06

11 Sep '06

Hi. I have a VRML file, which was created with different softwares. Is there anyway I can use Chimera to measure length of this tube-like structure? Thanks, in advance! ---------------------------------------------------- Masako Terada National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego (858)534-7968 mterada(a)ncmir.ucsd.edu ----------------------------------------------------

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display multiple bonds
by Dave Roe 05 Sep '06

05 Sep '06

Is there a way to display multiple bonds so bond types (single, double, triple) can be distinguished? -- Dave Roe roex0050(a)umn.edu

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color a residue
by Xuehong Liu 05 Sep '06

05 Sep '06

Hi, I chose the target as "selected residues", then selected the residue I want to put certain color on, but only a bond color was changed when I did that. However, if I did not select a residue, then the color option will change the color for the whole helix selected. thank Xuehong Xuehong Liu, Ph.D Research Assistant Professor Department of Physiology/Pharmacology Oregon Health & Science University 3181 SW Sam Jackson Park Rd. L334 Portland, OR 97239 phone: (503) 494-3230 fax: (503) 494-4352

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PDB Coordinates
by Albion Baucom 01 Sep '06

01 Sep '06

I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from. Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation? I am using beta version 1 build 2199 01/24/2006 on a linux platform. Thanks Albion

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how to save a copy of the reply log via command line
by Cathy Lawson 01 Sep '06

01 Sep '06

Hi, I'd like to issue a command-line command within a python script read into chimera to save a copy of the reply log. I tried googling the chimera site but didn't find the answer--what would be the command to do this? thanks, Cathy

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question about annealing residues in pdb file
by Shah, Sanket S 31 Aug '06

31 Aug '06

Hello, I have been using chimera extensively for pdb rendering and manipulation. I needed some information that i couldn't find in the archives. I am aware that chimera displays the pdb file according to the co-ordinates mentioned in the pdb file. However in my situation I have changed co-ordinates of some of the secondary structure elements like helices to do a better fit. and I have saved the new coordinates in the same pdb file. So now when i render this pdb file it shows me the structure with the modified orientation, however chimera displays a continuous model. In the sense, the breaks that I had introduced by changing the angles of some of the helices and thus making the linkage discontinuous are somehow annealed by chimera. So my question is what sort of algorithm chimera employs to seal breaks in the pdb structure. The same pdb strucutre when viewed in swiss model deepview software contains gaps/breaks at the junctions where the coordinates of the helices have been modified from the original ones. however no such breaks are seen when displayed through chimera. First I thought chimera does energy minimization to find out the best way to arrange the loops between the helices so as to create the best continuous structure. However it seems that chimera doesn't do energy minimization, yet it's able to display a complete structure. Could you please inform me about how this is accomplished. Thanks Sanket

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change chain id
by Yunierkis Perez Castillo 28 Aug '06

28 Aug '06

Hi all, I need to change the chain ID for a protein, that is, change the chain A to chain B. Can I do that with chimera? Thanks in advance Yunierkis

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