From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Fri Mar 31 2006 - 16:19:20 CST

Dear John,
Thank you for the second script. The first one didn't work out for me.
but when I use your pdb example 1c8e.pdb, it works.
I'll try this one again.
Thanks.
Margaret

On Fri, 31 Mar 2006, John Stone wrote:

> Hi,
> I've attached another version of the script which will auto-generate
> chain ID codes if you don't provide a list of codes to go with each
> monomer transformation matrix, this should be a bit easier to use than
> the last one. (see attached script)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 31, 2006 at 03:52:08PM -0600, John Stone wrote:
>> Hi,
>> I've got a VMD script that Mashaojienuaa sent to me which
>> reads the BIOMT records from a PDB file, applies the appropriate
>> transformations to them, and writes out a new PDB file with the
>> complete structure. I tested it on the the 1c8e virus structure
>> and was able to get it to work after commenting out the line of code
>> he's got that assigns a new chain ID to each of the transformed
>> monomers (this could be fixed in a few minutes of work so that it
>> auto-generates its own chain list when not specified explicitly..)
>> If you want to assign the chains to the the transformed monomers, you'll
>> want to enable that code again (it's marked with an XXX comment next
>> to it) and you'll need to specify a chain list of the same length as
>> the number of transformed monomers it's going to create.
>>
>> I used it like this:
>> source mono2poly.tcl
>> mol new 1c8e.pdb
>> set sel [atomselect top all]
>> set matrix [parsematrix 1c8e.pdb]
>> mono2poly -o outname $sel $matrix
>>
>>
>> The script is attached to this email.
>>
>> Enjoy,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Fri, Mar 31, 2006 at 03:33:51PM -0500, Margaret Shun Cheung wrote:
>>> Dear VMD wizards,
>>>
>>> I downloaded a structure from PDB, but it only includes the monomeric
>>> structure from its multimeric native structure (it's from X-ray).
>>> Is there a script for VMD to reinstate its symmetry and give back its
>>> multimeric coordinates?
>>> Thanks!
>>> Sincerely,
>>> Margaret S. Cheung,
>>> Ph. D. Postdoctoral Fellow,
>>>
>>> ------------------------------------------------------------
>>> Room 2117 Tel: (301) 405-4892
>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>> University of Maryland http://glue.umd.edu/~mscheung
>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>> ------------------------------------------------------------
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
------------------------------------------------------------