[Chimera-users] Trouble with display options

Tom Goddard goddard at sonic.net
Tue Jul 17 10:04:20 PDT 2012

Hi Vamsee,

   As Elaine says, the "sym" command allows you to make the symmetric 
copies of the molecule.  You can avoid changing the VIPERdb file suffix 
(.vdb) by specifying PDB format in the Chimera open command, for example,

     open pdb:1bbt.vdb
     sym #0 group i,222

Since 1bbt has ~5000 atoms and this makes 60 copies, the total is 
300,000 atoms and on my 64-bit Mac Chimera that is taking 1.4 Gbytes of 
memory.  That is a small virus model.  So you will need memory.

   Another important point is that Chimera cannot save images in "nogui" 
mode.  It needs to save images to make a movie.  To save images it needs 
access to the graphics card and that is not available unless the 
application has a window.  The one exception is if you use the 
"headless" Linux Chimera daily build.  It only works in nogui mode and 
can save images because it includes Mesa, a software renderer that 
substitutes for the graphics card.


> Hi Vamsee,
> The multimer is made with Multiscale Models: it makes low-resolution surfaces instead of copying all of the atomic coordinates (which would require more memory).  Normally in the GUI mode, you would use the Multiscale Models dialog to change the display of the copies, including loading the atomic coordinates for selected copies and showing them as ribbons, etc.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
> However, in the noGUI mode, that dialog approach is not possible.  Also, splitting is not relevant to this situation.
> Here's my suggestion:
> I believe if you name the file from ViperDB with filename extension ".pdb" you can then open it as a regular PDB file in Chimera.  In that case, it will not use Multiscale Models automatically.  Then you can use the "sym" command to create the multimer with full atomic copies.  Just be aware that that will take a lot of memory to have so many atoms.
> For example, if you open the PDB from viperDB as #0, I believe the command would be something like:
> sym #0 group i,222 surfaces false
> (where "surfaces true" would make the surfaces instead of atomic copies, like Multiscale Models). I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jul 16, 2012, at 10:36 PM, vamsee wrote:
>> Hi,
>> I am Vamseedhar Rayaprolu (Vamsee). I work with viruses and I am trying to generate a movie using only a script and NO GUI. I use a viral protein from the VIPERdb and hence it automatically generates a multimer (capsid) for me. The underlying question is 2-fold. The model generated from a vdb file is a pseudo-model and doesn't carry any co-ordinates for each of the subunits. Therefore the whole model is numbered #modelnumber (#1 in this case). The capsid has 60 subunits and when I mouse-over onto each of the subunits, it shows me the model number and the sub-model number but when I try to access the sub models through the command line, it selects #1 as a whole and not the sub-model. I need to be able to select each sub-model through the command line. Any ideas on this?
>> Next, I need to be able to show each sub-model in a ribbon form. Trying to show the whole model (#1) in the ribbon form using a command doesn't work. It works when done from the GUI though. I know if I can split the above multimer into sub-models I should be able to use the ribbon command and get what I need. But the split command doesn't work on the model as there are not atomic co-ordinates (pseudo-model). Any suggestions on this?
>> Thank you
>> -Vamsee
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