[phenixbb] Missing map for model

Pavel Afonine PAfonine at lbl.gov
Mon Mar 30 08:09:51 PDT 2009

Hi Folmer,

I'm glad that this solved the problem!
But it leaves me uncertain about what exactly happened and why... It 
would be very helpful for us PHENIX developers if we could reproduce 
this problem and fix it so no-one else falls into this same trap in 
future. We can only do this if you send us the data and model, along 
with telling the steps you have done. Is that possible?


On 3/30/09 2:00 AM, Folmer Fredslund wrote:
> 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
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