[BiO BB] Generate Quaternary structure of protein from monomer

James Stroud jstroud at mbi.ucla.edu
Thu Mar 3 23:16:29 EST 2005

Hi Subhash,

You will need to get the transformation matrices from the template. This can 
be done in the program O < http://www.bioxray.dk/~mok/o-files.html >.

The commands you will need are:

pdb_read        (to read your pdb-file)
lsq_explicit    (to determine the transformation matrix and store it)

The o manual is at < http://www.bioxray.dk/~mok/o/o_man/manual.html >

Once you have the transformation stored in the o database (".lsq_rt_?????", 
where "?????" is the name you provide to the lsq-expl command), you can load 
your protomer with


Then you can read in the second copy, again with "pdb_read".

Apply the transformation matrix from the template to the second copy with


You can read in further monomers and apply the transformation matrix N times 
until you fill your polymer.

You should then write out every monomer with


and join the files with a text editor, taking care to remove headers and "END" 
statements between files.

Things to think about:

(1) Molecule names in O are the first 5 characters only (this can cause 
serious confusion to first-timers.)
(2) If you have a cyclic N-mer where (N > 2) and (N mod 2 = 0) [i.e. even and 
greater than 2], then you should take care to choose the right two monomers 
from the template polymer to generate the transformation matrix or you will 
skip monomers in your model (think about starting at one vertex of a hexagon 
and transforming 120 degrees versus 60 degrees, etc.--both relate equivalent 
vertices but the former skips three under all transformations).


On Thursday 03 March 2005 07:25 pm, Subhash Agarwal wrote:
> Hi all
> Reply to Dan Bosler answer
> I knew of these sites and visited them again after u
> referred. These sites are useful if u have a pdb code
> avaliable. In my case i have built a homology model
> for which i need to generate quaternary structure.
> Reply to James Strond answer
> Yes, for template structure has a quaternary structure
> and therefore are known.
> My Query:
> How can i use these transformations for generating
> Quaternary structure? Moreover from the pdb of the
> template i also need to understand that the
> transformation are in regard to which monomer. How can
> i know that.
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James Stroud, Ph.D.
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

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