Many thanks for all the replies - I haven't yet tried all of them, but they all
look worth following up on, much food for thought here:
* Several people suggested SITUS COLORES, which I shall certainly try and had
not heard of until now.
* The program ESSENS, from the Uppsala software factory,
When we have needed to do something like this, the following procedure has
worked pretty well for us:
1. Define the volume containing the density into which a model should be docked
(most easily as atoms in a PDB file specifying the centres of spheres), then
get structure factors corresponding
Hi Oliver,
Use CHIMERA- http://www.cgl.ucsf.edu/chimera/
There are video tutorials for docking-
http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html
This is a very good package.
While I have used Situs colores, I find this package more versatile and useful.
You can also use Pymol (but I
Hi Anindito Sen
2013/9/20 Anindito Sen andysen.to...@gmail.com
skip
. You can also use Pymol (but I think thats not free any more??).
/skip
I do not know what your definition of free is, but PyMOL is an
open-source project. You can download the code from
Hi Folmer,
As I said- I think its not free any more is indicative that I am not sure of
its status. In addition to that I do not use Pymol much.
Thanks for the correction.
Best
Dr. Anindito Sen (Ph.D)
Department of Cell Biology Anatomy
Graduate School of Medicine
University of Tokyo
Hi Oliver
a few years ago I used the ccp4 FFFEAR program from Kevin Cowtan for
this sort of domain search. It was very good but also quite
labour-intensive. I have not followed up since to see if it was updated
or the functionality was included in Buccaneer.
cheers
Martyn
Perhaps Situs colores would be useful. We use it to dock models into SAXS maps.
http://situs.biomachina.org/fguide.html
Sent from Jack's iPad
On Sep 18, 2013, at 5:48 PM, Oliver Clarke olibcla...@gmail.com wrote:
Hi all,
Can anyone recommend software to dock previously solved domains
Another vote for Situs colores - we've had very good luck with using it
to dock domain structures into low resolution multi-crystal SAD maps.
Pete
Oliver Clarke wrote:
Hi all,
Can anyone recommend software to dock previously solved domains into a (very)
low-resolution experimentally phased
Hi all,
Can anyone recommend software to dock previously solved domains into a (very)
low-resolution experimentally phased map?
I am working on a rather marginal case where this would be useful - very large
assembly (500kDA per ASU), native goes to 6.9A, and the best derivative goes to
8A
