[phenixbb] SA omit map for ligand

Tjaard Pijning t.pijning at rug.nl
Fri May 27 00:43:15 PDT 2011


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,
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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