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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