Hi, I am trying to make an SA-omit Fo-Fc map for a sugar ligand (chain B) bound to protein (structure solved by MR), without doing any rebuilding of protein or ligand – just calculate an Fo-Fc map that I can load into PyMol. So far I used the AutoBuild – Create omit map module with these settings : - input files : model (protein+ligand+waters), data (.mtz), restraints for sugar ligand (.cif) - omit map type : simulated annealing - omit region : omit selection - omit map options : keep input waters, omit chain list : omit_chain_list chainB However, the ligand gets modified even though I use “omit_chain_list chainB”. What are the parameters to set to keep the model (protein, ligand, waters) from being rebuilt ? Furthermore, what is the procedure to load the SA Fo-Fc omit map into pymol ? Phenix version is 1.6.4-486. Thanks in advance, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85
Hi Tjaard, I am guessing that the specification of the chain as "chain B" rather than as "B" might be the problem, but I am not certain of that. In this particular case...it may be a lot easier to simply remove the ligand from your structure and run SA refinement, then look at the resulting map. All the best, Tom T
Hi,
I am trying to make an SA-omit Fo-Fc map for a sugar ligand (chain B) bound to protein (structure solved by MR), without doing any rebuilding of protein or ligand just calculate an Fo-Fc map that I can load into PyMol. So far I used the AutoBuild Create omit map module with these settings :
- input files : model (protein+ligand+waters), data (.mtz), restraints for sugar ligand (.cif) - omit map type : simulated annealing - omit region : omit selection - omit map options : keep input waters, omit chain list : omit_chain_list chainB
However, the ligand gets modified even though I use omit_chain_list chainB. What are the parameters to set to keep the model (protein, ligand, waters) from being rebuilt ?
Furthermore, what is the procedure to load the SA Fo-Fc omit map into pymol ?
Phenix version is 1.6.4-486.
Thanks in advance, Tjaard Ing. Tjaard Pijning Research Assistant
Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85
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On Fri, May 27, 2011 at 6:36 AM, Thomas C. Terwilliger wrote: I am guessing that the specification of the chain as "chain B" rather than
as "B" might be the problem, but I am not certain of that. That's half of the problem - based on viewing the original email with screen
captures (which the list server rejected), the other problem is that the
full parameter input was this:
omit_chain_list chainB
I suspect there's some confusion with the command-line documentation. You
don't need to include the parameter name in the GUI, just the actual value,
i.e.
chain B
(without quotes)
But I agree with Tom, running phenix.refine on a modified PDB file will be
easier. I think Pavel plans to introduce an even easier way to do this in
phenix.maps at some point in the future.
-Nat
participants (4)
-
Nathaniel Echols -
Pavel Afonine -
Thomas C. Terwilliger -
Tjaard Pijning