[phenixbb] unit cell discrepancies

Pavel Afonine pafonine at lbl.gov
Wed Apr 20 21:35:04 PDT 2011


Hi Michael,

I'm still confused.. What is .map file?

Are you running refinement as following:

phenix.refine model.pdb data.mtz

?

OK, I got the CRYST1 from model.pdb, now what is the unit cell 
parameters in data.mtz (you can get it with "phenix.mtz.dump data.mtz")? 
What is CRYST1 record in PDB file with refined model 
(model_refine_001.pdb) ?

May be it's easier if you send the relevant inputs (off list) and tell 
how you arrived to observing different unit cell parameters..

Pavel.


On 4/20/11 9:19 PM, Michael Hothorn wrote:
> Dear Pavel,
>
> find attached the requested output.
>
> CRYST card from refined pdb file
> CRYST1  175.170   67.236  119.246  90.00 121.42  90.00 C 1 2 1
>
>
> phenix.mtz.maps test.map >
>
> Title: None
> Space group symbol from file: C2
> Space group number from file: 5
> Space group from matrices: C 1 2 1 (No. 5)
> Point group symbol from file: 2
> Number of crystals: 2
> Number of Miller indices: 40081
> Resolution range: 101.452 2.52205
> History:
> Crystal 1:
>   Name: HKL_base
>   Project: HKL_base
>   Id: 0
>   Unit cell: (175.093, 67.251, 119.05, 90, 121.55, 90)
>   Number of datasets: 1
>   Dataset 1:
>     Name: HKL_base
>     Id: 0
>     Wavelength: 0
>     Number of columns: 0
> Crystal 2:
>   Name: crystal
>   Project: project
>   Id: 2
>   Unit cell: (175.093, 67.251, 119.05, 90, 121.55, 90)
>   Number of datasets: 1
>   Dataset 1:
>     Name: dataset
>     Id: 1
>     Wavelength: 1
>     Number of columns: 13
>
> I made sure that this file is indeed the one being read by the .def file.
>
> best wishes
> Michael
>
>
> On 04/20/2011 08:36 PM, Pavel Afonine wrote:
>> Hi Michael,
>>
>> phenix.refine should take crystal symmetry from data file if there is 
>> a choice between PDB file and data file.
>>
>> Did you mean phenix.mtz.dump? Can you send the output of
>>
>> phenix.mtz.dump data.mtz
>>
>> command, and CRYST1 record from PDB file as Nat asked?
>>
>> Pavel.
>>
>>
>> On 4/20/11 3:36 PM, Michael Hothorn wrote:
>>> Dear all,
>>>
>>> I am sure there is a simple explanation for this, but I cannot find 
>>> a solution. I am reading in an .mtz file in phenix.refine. mtzdump 
>>> reports the following unit cell constants on the file test.mtz itself:
>>>
>>> 175.0930   67.2510  119.0500   90.0000  121.5500   90.0000
>>>
>>> The refined .pdb file and .maps report however a slightly different 
>>> unit cell, as does the logfile
>>>
>>> >snip
>>> Miller array info: test.mtz:FP,SIGFP
>>> Observation type: xray.amplitude
>>> Type of data: double, size=39702
>>> Type of sigmas: double, size=39702
>>> Number of Miller indices: 39702
>>> Anomalous flag: False
>>> Unit cell: (175.17, 67.236, 119.246, 90, 121.416, 90)
>>>
>>>
>>> What am I missing?
>>>
>>> Thanks!
>>> Michael
>>>
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>>> phenixbb at phenix-online.org
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>>
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