[phenixbb] unit cell discrepancies

Michael Hothorn michael at hothorn.de
Thu Apr 21 09:47:44 PDT 2011


I found my mistake. The cell parameter definition in the .def file 
apparently overrules the definition in either the input .mtz or in the 
input .pdb CRYST1 card. Is that correct like this: .def file definition 
 > .mtz definition > CRYST1 card definition?

best wishes
Michael



On 04/20/2011 09:35 PM, Pavel Afonine wrote:
> 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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