[phenixbb] Missing map for model

Folmer Fredslund folmerf at gmail.com
Mon Mar 30 02:00:21 PDT 2009

Dear Pavel

2009/3/30 Pavel Afonine <PAfonine at lbl.gov>:
> Hi Folmer,
> I think I dealt with something similar a while ago. Unfortunately I don't
> remember the details but your description of the problem definitely rings
> the bells.... If I remember, the problem was some miscommunication between
> Autobuild and phenix.refine in terms of using incorrect data columns from
> input mtz file.... Using the right data was a solution.
> I don't know the answer, but I would try the following which shouldn't take
> more than 5 minutes or even less.
> Run phenix.refine to just compute the maps:
> phenix.refine model.pdb data.hkl strategy=none main.number_of_macro_cycles=1
> where data.hkl is your original file with Fobs.

This gives maps looking like what I would suspect them to. Nice.
Thank you for the advice.

Best regards,

Folmer Fredslund

> On 3/28/09 4:29 AM, Folmer Fredslund wrote:
>> Dear all,
>> In phenix.refine (1.4-3) my electron density maps look weird. I get
>> beautiful density for a helix that is missing from the current model,
>> but absolutely horrible density for the rest of the molecule. Any
>> ideas what is going on? Maps from automr look fine and the density
>> modified map from autobuild also look fine, whereas the autobuild map
>> from refinement has the same features.
>> Any ideas what is going on? I am running all programs with default
>> parameters.
>> Best regards,
>> Folmer Fredslund
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