[phenixbb] phenix.phaser multiple pdbs

[Dr G. Bunkoczi]

Dear G,

could you send me (not the mailing list) the logfiles, so that I can have a 
look?

Thanks, Gabor

On Aug 16 2011, G Y wrote:

>Dear Gabor,
>
>Thanks a lot for your detailed explanation and kind help. I tried your
>comment. The two ways of defining search procedure gave me the same
>solution.
>
>For
>
>search {
> ensembles = a1
> copies = 1
>}
>search {
> ensembles = a2
> copies = 1
>}
>
>I got also only one result contains one best molecule pdb. Would you have
>some idea for this? How could I really get several output for each of the
>input model?
>
>Thanks and regards,
>G
>
>
>
>On Mon, Aug 8, 2011 at 3:13 PM, Dr G. Bunkoczi <gb360 at cam.ac.uk> wrote:
>
>> Dear G,
>>
>> after carefully re-reading your email, I think I have only given half 
>> of the answer. By repeating the 'coordinates' scope, you are defining 
>> one ensemble using multiple PDB files. If you want to define multiple 
>> ensembles, you need to repeat the whole ensemble scope, i.e.
>>
>>
>> ensemble {
>>  model_id = a1
>>  coordinates {
>>    pdb = model1.pdb
>>    identity = 0.9
>>  }
>> }
>> ensemble {
>>  model_id = a2             <= note the change in model_id
>>
>>  coordinates {
>>    pdb = model2.pdb
>>    identity = 0.9
>>  }
>> }
>>
>> If you want Phaser to actually search for all these ensembles, you need 
>> to add a search keyword as well:
>>
>> 1. Conduct a separate search for each ensemble listed. The search order 
>> is decided automatically. The solution contains one molecule of a1 + one 
>> molecule of a2.
>>
>> search {
>>  ensembles = a1
>>  copies = 1
>> }
>> search {
>>  ensembles = a2
>>  copies = 1
>> }
>>
>>
>> 2. Phaser will search for each alternative ensembles in turn and pick the
>> best one (the solution will contain one molecule of a1 or one molecule of
>> a2, but not both):
>>
>> search {
>>  ensembles = a1,a2
>>  copies = 1
>> }
>>
>> HTH, Gabor
>>
>>
>>
>> On Aug 8 2011, Dr G. Bunkoczi wrote:
>>
>>  Dear G,
>>>
>>> I think 'coordinates' is a multiple scope, so you have to define your
>>> ensemble as follows:
>>>
>>> ensemble {
>>>  model_id = a1
>>>  coordinates {
>>>    pdb = model1.pdb
>>>    identity = 0.9
>>>  }
>>>  coordinates {
>>>    pdb = model2.pdb
>>>    identity = 0.9
>>>  }
>>>  coordinates {
>>>    pdb = model3.pdb
>>>    identity = 0.9
>>>  }
>>>  coordinates {
>>>    pdb = model4.pdb
>>>    identity = 0.9
>>>  }
>>> }
>>>
>>> BW, Gabor
>>>
>>> On Aug 8 2011, G Y wrote:
>>>
>>>  Dear all,
>>>>
>>>> I am writing a bash script for running phenix.phaser automatically on 
>>>> an ensemble of multiple pdbs. These pdbs have been superimposed by 
>>>> other tools before running phaser.
>>>>
>>>> The following is what I wrote for the ensemble part in params.eff file:
>>>>
>>>> ensemble {
>>>>  model_id = a1
>>>>  coordinates {
>>>>    pdb = model1.pdb
>>>>    pdb = model2.pdb
>>>>    pdb = model3.pdb
>>>>    pdb = model4.pdb
>>>>    rmsd = None
>>>>    identity = 0.9
>>>>  }
>>>>
>>>> It runs well. When it finished, I want to confirm that it really run 
>>>> MR on all four models or on a ensemble of these models. However in 
>>>> .log file, I found at the refinement part it shown me:
>>>>
>>>> ----------
>>>> REFINEMENT
>>>> ----------
>>>>
>>>>  There is 1 solution to refine
>>>>  Refining solutions
>>>>  0% 100%
>>>>  |==| DONE
>>>>
>>>>
>>>>  Configuring ensembles
>>>>  ---------------------
>>>>  PDB file # 1: model1.pdb
>>>>     This pdb file contains 1 models
>>>>     The (input) RmsD of this model with respect to the real structure 
>>>> is 0.8
>>>>
>>>> **************************** Does this mean that phenix.phaser only 
>>>> run MR with the first model? Does it due to the way I wrote in my 
>>>> params.eff file? What would be the correct way?
>>>>
>>>> Many thanks!
>>>>
>>>> best,
>>>> G
>>>>
>>>>
>>>
>>>
>> --
>> ##############################**####################
>>
>>    Dr Gabor Bunkoczi
>>
>>    Cambridge Institute for Medical Research
>>    Wellcome Trust/MRC Building
>>    Addenbrooke's Hospital
>>    Hills Road
>>    Cambridge CB2 0XY
>> ##############################**####################
>>
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>>
>

-- 
##################################################

     Dr Gabor Bunkoczi

     Cambridge Institute for Medical Research
     Wellcome Trust/MRC Building
     Addenbrooke's Hospital
     Hills Road
     Cambridge CB2 0XY
##################################################