[phenixbb] SA omit map for ligand

Thomas C. Terwilliger terwilliger at lanl.gov
Fri May 27 06:36:51 PDT 2011


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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>>



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