Hi, I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link: http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html however was wondering how you implement this sort of thing in the GUI? Thanks, Simon --------------------------------------------------------------- Dr. Simon Kolstoe Honorary Senior Research Associate Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London, NW3 2PF http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------
Hi Simon, based on how far you can stretch your imagination "exclude some atoms from refinement " may be something broad: - do you want to exclude selected atoms from coordinate? occupancy? B-factor? ...etc. refinement? - do you want these atoms to be excluded from bulk-solvent mask calculation too (or should they still contribute to the solvent mask)? - should they still be included into geometry term calculation (so, for example, the other atoms are aware of their presence). .. list of possibilities is long. So could you please specify more precisely how you want to exclude selected atoms (what they still should and should not contribute to)? Pavel On 4/16/13 9:36 AM, Simon Kolstoe wrote:
Hi,
I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link:
http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html
however was wondering how you implement this sort of thing in the GUI?
Thanks,
Simon
Hi Pavel, I want to make an omit map however whenever I delete my ligand the residues/atoms around the binding site get pulled into the ligand density. So I just want to fix the relevant side-chains/atoms in place whilst doing my simulated annealing step. So exclude from xyz movement is the main thing, occupancy, B-factor, bulk solvent etc. is not as important. Thanks (and also thanks Nat), Simon On 16 Apr 2013, at 18:24, Pavel Afonine wrote:
Hi Simon,
based on how far you can stretch your imagination "exclude some atoms from refinement " may be something broad:
- do you want to exclude selected atoms from coordinate? occupancy? B-factor? ...etc. refinement? - do you want these atoms to be excluded from bulk-solvent mask calculation too (or should they still contribute to the solvent mask)? - should they still be included into geometry term calculation (so, for example, the other atoms are aware of their presence). .. list of possibilities is long.
So could you please specify more precisely how you want to exclude selected atoms (what they still should and should not contribute to)?
Pavel
On 4/16/13 9:36 AM, Simon Kolstoe wrote:
Hi,
I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link:
http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html
however was wondering how you implement this sort of thing in the GUI?
Thanks,
Simon
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Simon, ok, now I got. Here are the steps to do this: - set occupancies of atoms to omit to zero: phenix.pdbtools model.pdb occupancies.set=0 selection="chain A and resseq 1:20" - run phenix.refine with the new PDB file. Make sure you tell the mask calculation to not set the bulk-solvent mask in omit region by using refinement.mask.ignore_zero_occupancy_atoms=False Pavel On 4/16/13 2:17 PM, Simon Kolstoe wrote:
Hi Pavel,
I want to make an omit map however whenever I delete my ligand the residues/atoms around the binding site get pulled into the ligand density. So I just want to fix the relevant side-chains/atoms in place whilst doing my simulated annealing step. So exclude from xyz movement is the main thing, occupancy, B-factor, bulk solvent etc. is not as important.
Thanks (and also thanks Nat),
Simon
On 16 Apr 2013, at 18:24, Pavel Afonine wrote:
Hi Simon,
based on how far you can stretch your imagination "exclude some atoms from refinement " may be something broad:
- do you want to exclude selected atoms from coordinate? occupancy? B-factor? ...etc. refinement? - do you want these atoms to be excluded from bulk-solvent mask calculation too (or should they still contribute to the solvent mask)? - should they still be included into geometry term calculation (so, for example, the other atoms are aware of their presence). .. list of possibilities is long.
So could you please specify more precisely how you want to exclude selected atoms (what they still should and should not contribute to)?
Pavel
On 4/16/13 9:36 AM, Simon Kolstoe wrote:
Hi,
I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link:
http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html
however was wondering how you implement this sort of thing in the GUI?
Thanks,
Simon
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Tue, Apr 16, 2013 at 9:36 AM, Simon Kolstoe
I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link:
http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html
however was wondering how you implement this sort of thing in the GUI?
On the "Refinement settings" tab, below "Refinement strategy", there is a drop-down menu labeled "Modify atom selections for" which gives you access to these settings. -Nat
participants (3)
-
Nathaniel Echols -
Pavel Afonine -
Simon Kolstoe