VMD-L Mailing List

From: Margaret S. Cheung (mscheung_at_uh.edu)
Date: Sun Sep 17 2006 - 09:22:53 CDT

Hello John,
Thank you for the reply. I haven't got emails or scripts regarding this
problem, but I am willing to try working it out. Thank you for pointing
out the PDB website so I can have something to start with.
Thank you again.
Sincerely,
Margaret

John Stone wrote:
> Margaret,
> For transformations not handled automatically by scripts, you can
> use the atom selection "$sel move" subcommand to apply any transformation
> you want. You can create your own matrices from the MTRIXn records you're
> interested in, apply them to the PDB coordinates, save out new files
> and combine them all together if you like. There's more detail about
> the intended use and format of the PDB MTRIXn records here:
> http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_58.html
>
> As I didn't write the script and I'm currently swamped with other activities,
> I'm not the best one to adapt it to reading these MTRIXn records, perhaps
> someone else has already written a script to process those symmetry records?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Sep 16, 2006 at 12:06:13PM -0400, Margaret Shun Cheung wrote:
>
>> Hello John,
>> Thank you for the script. I have another pdb entry whose syntax doesn't
>> follow the format of this script (mono2poly.tcl) which I downloaded from
>> the VMD website again. It started with MTRIX
>> instead of REMARK as below. Somehow the script will not recognize it.
>> Please help.
>>
>> MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1
>> MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1
>> MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1
>>
>>
>> The script gave me error message as,
>>
>>> Main 78 % mono2poly -chain {} -o 2 $sel $matrix
>>>
>> 0
>> Unable to load structure file 2.pdb
>>
>> Please help.
>> Sincerely,
>> Margaret
>>
>>
>> On Fri, 31 Mar 2006, 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
>>>
>>>
>> Margaret S. Cheung,
>> ============================================================
>> Assistant Professor
>> 629C Science and Research I
>> Department of Physics
>> University of Houston http://thoth.phys.uh.edu/~mscheung
>> Houston, TX 77204 email: mscheung_at_uh.edu
>> ------------------------------------------------------------
>> contact info until January 2007
>> Room 2112 Tel: (301) 405-9307
>> 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
>> ============================================================
>>
>
> 

-- 
Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
email:   mscheung_at_uh.edu
website: http://thoth.phys.uh.edu/~mscheung/