[phenixbb] Sa_Omit_map_DNA_low_resolution

Mikalai Lapkouski gort105 at gmail.com
Sat Sep 15 08:10:35 PDT 2012


I want to generate a simulated annealing omit map around DNA molecule in my
protein-DNA complex for publication. My resolution is very low - 5A.

1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part)
from pdb and ran phenix.refine with simulated_annealing=True. But resulted
Fo-Fc in the omitted region is very weak. Is it because of the low
resolution and because big part of the model was omitted?

2. Next, I wanted to generate a composit_sa_omit map as in this case DNA
would be deleted in small portions and the resulted map would give me a map
I can use for publication:

phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True
(to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb
(contains only DNA coordinates). But the job runs too long and still it
seems like it is doing rebuilding. Is this a correct command and correct
action to create a sa_omit map for the DNA in my complex?

Thank you a lot for the help,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120915/e9a91e64/attachment.htm>

More information about the phenixbb mailing list