[phenixbb] unit cell discrepancies

Jacob Keller j-keller2 at fsm.northwestern.edu
Thu Apr 21 11:21:02 PDT 2011


Actually, this thread raises an interesting issue: do refinement
programs ever refine cell parameters (I think they do not.) I wonder
whether it would make any difference, especially in things like bond
lengths? Should be easy enough to include, but I guess the gains might
not be so significant? I would imagine, though, that once one had a
working model, one could make a histogram of observed bond lengths and
their orientations, and scale the cell parameters accordingly to make
the bond-length distribution be centered on the ideal lengths. This
might perhaps be another source of "missing R"?

Jacob

On Thu, Apr 21, 2011 at 11:47 AM, Michael Hothorn <michael at hothorn.de> wrote:
> 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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>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
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-- 
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-keller2 at northwestern.edu
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