On Jan 11, 2013, at 03:47 , Teri Arman <teriar...@gmail.com> wrote:
> Dear Dr. Frolow
> Thank you for your mail. I stated again, and hope it is clear now.
> TA.
>
> On Fri, Jan 11, 2013 at 4:11 AM, Felix Frolow <mbfro...@post.tau.ac.il> wrote:
>
> On Jan 10, 2013, at 18:27 , Teri Arman <teriar...@gmail.com> wrote:
> > Hi, I appreciate If anybody help me couple of things as follows.
> >
> > (a1) how multiple PDBs (of same or different space groups) can be brought
> > into one frame of coordinates, when dealing with many PDBs?
>
> TA: Suppose we have a segment of structure (PDB). That segment carries
> different co-ordinates in different PDBs. How can that segment from hundreds
> of PDBs be converted so that we can see all converted segments in one
> frame/window
> I like to avoid superimposition of hundreds of times
Most probably superposition or any other transformation could not be avoided.
Properly written script will do it for you
>
> You mean that axes of inertia of the same molecule in the different
> structures(PDB's) - L,M,N are superimposed? You superimpose… :-)
>
> >
> > (a2) how does one get scatter plot?
> Scatter of what? :-0
>
> TA: Suppose a surrounding neighbours of a segment as said above.
>
> > (b) how easily can symmetry related units of original PDB (with description
> > of which symmetry element has been used) be made when dealing with many
> > PDBs .
>
Knowing mathematical manipulation of a crystalline space (symmetry operations)
one can write a script that will do it easy.
> You have to explain better what are you meaning. :-\
>
> TA: Each PDB (X-ray structures) has its own space group. I like to generate
> symmetry related whole PDB or a segment of it in hundreds of PDBs of
> different space groups
Again you will need to write or to get a script that will do it for you. Script
(little or larger piece of software written using one of the shell syntaxes or
by modern popular languages such as Python or JavaScript)
may be written to expand each structure by symmetry producing set of
coordinates of interacting molecules (you decide to what distance or to what
neighbouring unit cells you wish to expand your structure,
after that you teach your script to make multiple superposition of all to all
(maybe difficult task) or one to one taking one of the structure as a master
structure to which you superimpose others. After that you probably will which
to clean this set of coordinates from expanded molecules that you do not need
for your research. Again you can do it manually or writing script.
> .
>
> >
> > Thank you,
> > Teri
> >
>
> Dr Felix Frolow
> Professor of Structural Biology and Biotechnology, Department of Molecular
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica F, co-editor
>
> e-mail: mbfro...@post.tau.ac.il
> Tel: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
