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.
and fill up the keywords
On Oct 25, 2010, at 21:16, Pavel Afonine wrote:
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 atoms or other dummy atoms will not
be added. The procedure doesn't care about map or data (Fobs or
whatever): it just geometrically adds dummy atoms where requested.
Also note, it uses a PHENIX command line tool that is not
specifically designed for this task but simply can do it with
appropriate set of parameters.
Ok, that was a preambula -:) Now "let's do it":
here is where all the example-files:
/net/cci/afonine/public_html/for_Dirk
The command
phenix.grow_density params
will creates this file with dummy atoms: dummies_DA.pdb
which in PyMol looks like this:
http://cci.lbl.gov/~afonine/for_Dirk/da_only.png
or superposed with the model:
http://cci.lbl.gov/~afonine/for_Dirk/da_plus_model.png
Note, the above command requires the data file (remember, this
command is meant for something else), but if you have just a PDB
file (it can be empty I guess), and don't have any data file, you
can fake it just to run this command. To get fake Fobs:
phenix.fmodel model.pdb high_res=3 type=real r_free=0.1 label='F-obs'
mv model.pdb.mtz data.mtz
I guess this is it. Let me know if I can be of any help with this.
Pavel.
On 10/13/10 4:00 AM, Dirk Kostrewa wrote:
Dear CCP4ers,
is there a program around that allows to fill an input map or mask
with dummy atoms?
Best regards,
Dirk.
--
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