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

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 1 11:04:49 PDT 2005

Hi Jason,
     What I would add to Elaine's answer is that the replicated  
subunits are in separate Chimera models, and when you use Save PDB  
the dialog will give you the option of saving into a single file or  
multiple files.  If you save into multiple files I think those other  
programs will be able to handle that.  If you save into a single  
file, it is basically as if those multiple files were concatenated  
together and the other programs might not allow for that.  In  
particular, in the single file there are multiple END records, one  
per model.  Those other programs may stop once they hit the first END  
     Saving into a single file doesn't renumber anything or reletter  
chain IDs -- it is just the concatenation.  For a large multimeric  
system, renumbering atoms and residues could easily exceed the field  
width allotted to those fields in the PDB ATOM record, and there  
could easily be more than 52 chain IDs (A-Z and a-z).  Therefore, we  
use the concatenation method.


On Sep 1, 2005, at 10:12 AM, Elaine Meng wrote:

> 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
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