Re: [phenixbb] unit cell discrepancies

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 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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