PISA does just this - download pdb to ebi server; let iyt cluster molecules
and read back the assembled fcoordinates - plus lots gf useful info..
Eleanor
On Feb 24 2012, David Shin wrote:
Hi Gloria,
It depends on if you mean hard as in thinking up a slick trick, or hard as
in maybe 20-30 mins of tedious work. I had the same problem with 18 in the
ASM, where the solution had scattered models, but didn't want to think
about it, so just used pymol.
1) open the first model with the original 6 models
2) then make separate files with each of the other subunits (with the CRYST
line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you
can read easily in the gui later for saving)
3) then open m1.pdb
4) on the left, go to the "A" or action menu for m1 .pdb > generate >
symmetry mates > within 100 Angstroms (this can be smaller or larger, just
need to see them)
5) then you'll have the symmates on the screen and the list of each right
listed as m1_100-1-100 etc. So you can just click them on and off to see
which one you like, then save that molecule.
6) Then delete the symmates "delete m1_*" so you can check
7) Open the saved symmate to check
8) go to step 3 for the next model, ie. m2.pdb
not a slick answer, but can be done when tired with minimal error.
On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl
<gborgst...@gmail.com>wrote:
Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each
other.
Then we read this into molrep as the "fixed" model and solved for the
second part.
The solution was found but the 6 for the second model are in different
ASU's and unit cells.
What is the easiest way to get everyone together in one asu?
We can think of hard ways to do it, but any advice?
Thanks, Gloria
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
