[phenixbb] sa_omit-map -- it's fine

[Thomas C. Terwilliger]

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

> Hi Tom,
>
> don't we need to add "maps_only=True" as well (as Manual suggests in
section "Just make maps; don't do any building.";
> 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
the
>>> whole assymetric unit (nothing extra). How can I do it?
>>>  Regards.
>>> Vladimir
>>>
>>>
>>>
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>>
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>