[phenixbb] unit cell discrepancies

Dale Tronrud det102 at uoxray.uoregon.edu
Thu Apr 21 11:53:15 PDT 2011



On 04/21/11 11:21, Jacob Keller wrote:
> 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

   If you try to refine a model with the cell "constants" allowed to vary
you will find that they are not well determined.  You can change them by
huge amounts and refine the model down to pretty much the same R value.
The truth is that there is little in our calculation of the scattering
of a crystal that is tied to an absolute scale.  The scattering factor is
on such a scale but you can inflate all the B values and correct for a
cell constant that has become too large.  The only thing that ties down
the scale are the bond length restraints, and of course you are restraining
them.  If you inflate your cell constants the bonded atoms will move a
little big apart but the rest of the slack will be taken up in the space
between the chains.  Tight or sloppy packing is the tool to use, but
we don't restrain those so they don't help if you want to determine the
cell lengths.

  The location of the spots on the images give a wealth of information
about the cell constants leading to very precise values, if you know
your wave length and crystal to detector distance.  Intensities, not so much.

Dale Tronrud
> 
> 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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>>>>>
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