[Chimera-users] Save pdb files only have 5 subunits at 5-fold at virus?

[Elaine Meng]

Hi Jason,
The symmetry or number of subunits does not matter.  You should be  
able to save any extra copies of the protein as PDB.

However, it is important to show all the subunits' atoms before you  
try to save.  Multiscale Models only shows the extra copies with  
surfaces and does not make copies of the atomic coordinates until  
necessary (such as when you show all of the atoms).  This is for  
computational expediency. When you show all the atoms and there are  
large numbers of atoms, operations may be quite slow.

Probably what happened is that you saved when only some of the  
subunits had coordinates loaded, even though surfaces were shown for  
all of them.

To show all atoms:  in Multiscale Models, after you showed the  
multimer you want, click "All" in Select chains.  Then for these  
"Selected chains", change the "Style" to something that requires the  
atomic coordinates, "Show... [anything except Surface]" (because  
Surface does not require the atomic
coordinates).  Then you can clear the selection (Clear in the Select  
chains section) and use File... Save PDB in the main Chimera menu.

A different approach would be to use the Unit Cell tool instead of  
Multiscale Models.  Unit Cell is in the Higher-Order Structure  
section of Tools in more recent versions, in the Utilities section of  
Tools in older versions.  Unit Cell generates copies of the  
coordinates directly.   It can use SMTRY, CRYST1, and/or MTRIX  
records from the input PDB file.

Unit Cell man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/ 
unitcell.html

In general, these approaches are successful for generating copies of  
the coordinates that can be saved.  I don't know which structure you  
are working with, however, so I don't know if there is anything  
strange about it that might interfere with the process.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Sep 1, 2005, at 1:01 AM, Jason wrote:

> Hi all
>
> Is it possible to save pdb files that only have 5 subunits at 5- 
> fold  after using mulitscale tools buliding virus paritle.
> And this pdb file can open at other programs too, ex: DeepView, PyMOL.
>
> When I use File/Save PDB chimera can save pdb file, but this file 
> (model) only can show correctly at chinera.
> If I opened this file at PyMOL or DeepViewit only show the  
> origional 3(A, B, C)chain model
>
> thanks
>
> Jason
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>