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
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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Tom Thank you. Vladimir ===================
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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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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Hi Pavel and Vladimir, Yes, Pavel is right...we need maps_only=True as well: phenix.autobuild data=data.mtz model=coords.pdb \ composite_omit_type=sa_omit nproc=4 \ maps_only=True 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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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Hi Pavel and Vladimir, After all this discussion...I think there is something wrong with the composite omit maps in the current version...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
_______________________________________________ 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
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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
-
Pavel Afonine -
pletnev＠hwi.buffalo.edu -
Thomas C. Terwilliger