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. -- ******************************************************* Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [email protected] WWW: www.genzentrum.lmu.de *******************************************************
