Apologies for not seen the original post, but
$warpbin/arp_warp EOF
MODE MIRBUILD
FILES CCP4 MAPFIND 2fofc.map XYZOUT1 dummy.pdb
SYMM your_sym
CELL your_cell
RESOLUTION resol
MIRBUILD ATOMS atoms_in_protein MODELS 1 RESN DUM
END
EOF
will do it.
I recommend getting a map in a 0.3 A grid.
A.
Hi Dirk,
may be too late... but (may be) better later than never -:)
Here is the working example of how you can do it. Note, the procedure just
builds the dummy atoms in spheres with user-defined centers and radia. You
can specify as many spheres as you wish. Dummy atoms clashing with model
Dear colleagues,
many thanks for all of your kind support, following my request about
placing dummy atoms into en EM-map! Here is a short summary:
Frederic Vellieux kindly offered me to use his programs with clever
positioning of atoms in a density.
Paul Emsley pointed to a program
Dear CCP4ers,
is there a program around that allows to fill an input map or mask with
dummy atoms?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't
work. I would need a program that fills this map with dummy atoms for a
few things that I want to try with this atomic representation.
Best regards,
Doesnt arp/warp start with doing something like this? If you gave a 0/1
mask I wonder what the first build would look like..
You would have to invent a reflection file for the map ...
E
On 10/13/2010 12:49 PM, Dirk Kostrewa wrote:
... maybe, to clarifiy my question a little bit: I want to
Dear Dirk,
For filling an input map you can try ARP/wARP in an 'old-fashion' way.
The script below should place DUM atoms (1.1 times the requested number)
into the highest density. Prepare your map in the CCP4 format, for
example in P1, extended to cover the asymmetric unit in full (0 1 0 1 0
Flood fills a map with water molecules.
http://xray.bmc.uu.se/usf/flood_man.html
On 10/13/10 6:49 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:
... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't
Dear Dirk
You might find one of the programs mentioned by Andreas below useful
for your purpose.
Cheers
Alex
Am 28.07.2010 um 18:26 schrieb Andreas Förster docandr...@gmail.com:
Here's a preliminary summary of the suggestions I got from the ccp4
community regarding the problem stated
