Hi Tom,

don't we need to add "maps_only=True" as well (as Manual suggests in

http://www.phenix-online.org/documentation/autobuild.htm) ?

I'm asking because the original question was specific about it: compute map and "nothing extra".

Thanks, Pavel.

On 10/13/2008 2:17 PM, Thomas C. Terwilliger wrote:

...

Hi Vladimir, You can do this with:

phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=sa_omit nproc=4

All the best, Tom T

...

After phenix.refine stage I would like to get just the sa_omit map for

Hi again Pavel and Vladimir, The omit maps are fine. I'm sorry for the false alarm; I had run a tiny test structure with too few omit boxes so that the omitted regions were way too much of the structure and it looked really bad. Using more omit regions fixed the problem. A regular structure (nsf-d2 from the PHENIX structure library) gets a fine sa-omit map with the defaults. A further-improved map can be obtained with a higher-than-default value of "n_box_target=32" (default=12, note that you don't necessarily get exactly the number you ask for as it has to be something that the asymmetric unit can be divided into.) All the best, Tom T Hi Pavel and Vladimir, After all this discussion...I think there is something wrong with the composite omit maps in the current version. They do not finish correctly...I will check this out. If you instead just omit around the atoms in a pdb file with "omit_box_pdb=target.pdb" that seems fine however. I'm sorry for the problem. All the best, Tom T section "Just make maps; don't do any building."; the

...

...

whole assymetric unit (nothing extra). How can I do it? Regards. Vladimir

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb