VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Tue Apr 04 2006 - 16:04:00 CDT

Thank you for your explanation!
Sincerely,
Margaret

On Fri, 31 Mar 2006, John Stone wrote:

>
> I'm not much of an expert on the crystallographic symmetry stuff, but
> my quick reading of the PDB spec on that makes it sound like the SMTRY
> records may not even be enough. Look at your file and see what combination
> of these records you have:
> SMTRY
> MTRIX
> BIOMT
> CRYST1
>
> You may have to use some or all of those to reproduce the biological unit.
> If this thing is a virus then it's probably available from the VIPER database,
> if it's something else, then worst case you can apply transformations
> yourself.
>
> John
>
> On Fri, Mar 31, 2006 at 05:30:49PM -0500, Margaret Shun Cheung wrote:
>> Dear John,
>>
>> Thank you for the code. Instead of BIOMT, I had SMTRY in the pdb file
>> (the pdb file was downloaded from RCSB).
>> After I edited the pattern matching in the tcl script, the script worked.
>> But it kinda looked weird though. Do I make a mistake by replacing BIOMT
>> with SMTRY? Should I do something more than that?
>> 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
>> ------------------------------------------------------------
>
> --
> 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
------------------------------------------------------------