Re: [ccp4bb] molecule on symmetry axis
Phenix can refine a tartaric acid on the twofold if you set the occupancy to 0.5 AND set the custom-nonbonded-symmetry-exclusion selection to the tartaric acid. It's a new feature. Nick Sent from my iPhone Nicholas K. Sauter (510)847-1592 cell (510)486-5713 desk On Oct 16, 2010, at 1:25 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hello Jackie Vitali, What happens if you model the tartaric acid as if it were not on a symmetry axis and then let phenix deal with the symmetry? I once had a water of which refmac stubbornly lowered the occupancy to 0.5 even though i kept on bringing it back to 1.0 until I realised that it was on a 2-fold axis. And this was seven years ago, so by now programs might be able to deal with more complicated molecules than just an oxygen. As for the SO4, you should set the occupancy of S and O to 0.33 because you only have one third per asymmetric unit. Now since the other oxygens belong to the same molecule, their occupancies should also be 0.33. But again, of you leave it at 1 and feed it into phenix, that should be corrected for. If it's not, try refmac! Cheers, Tim On Fri, Oct 15, 2010 at 06:28:52PM -0400, Jacqueline Vitali wrote: Dear colleagues, I have a tartaric acid on a two fold axis with its two halves related by the two fold. How do I refine this in Phenix? Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The other 3 oxygens are related by the 3-fold. How do I refine this in phenix? I can put S and one O occupancy 1, what occupancy do I put for the 3 oxygens that overlap their symmetry mates? And how do I maintain stereochemistry around the symmetry axis? These are not just one atom. For the tartaric acid the 2 fold goes through the middle of the bond. I could split it in two halves but I do not see how to keep stereochemistry. I would appreciate all suggestions. I apologize because the question should go to another newsgroup but I am still working with my subscription in phenixbb. Jackie Vitali -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] software to represent raw reflections in hkl zones
Tillmann,
I've added a jiffy script to synthesize pseudo-precession photos from a
rotation dataset, to the latest PHENIX package. We build this package
nightly, so any PHENIX bundle with a version number greater than
dev-402 will workhowever I see that dev-402 is not yet on the
public Web site (http://www.phenix-online.org) so I'll attach the python
script to this email for standalone use.
Here's what you'll need:
1) Make sure any recent PHENIX is installed and on path.
2) Make sure Mosflm is on path as ipmosflm
3) Index using two frames in the dataset:
labelit.index /data/project/dataset1_1_E1_###.img 1 90
4) Generate the precession photo:
labelit.python precession_photo.py bravais_choice=1 \ #id number for
the bravais setting as listed by labelit.index
pixel_width=600 resolution_outer=3.0 intensity_full_scale=1000 \
plot_section=H,K,0 image_range=1,90 pdf_output.file=HKL.pdf
5) These command line options should be self explanatory, but --help
gives a fuller description.
Nick Sauter
Tillmann Heinisch wrote:
Hi,
I have problems solving the structure of a protein crystal which seems to be
disordered. In order to investigate the disorder it would be useful to have a
precision photograph that shows reflections only in the [0kl] plane. Does
anyone know software that can transform raw data to give intensity distribution
in distinct zones of hkl?
Many Thanks for your help,
Tillmann
def usage():
return Python script to generate a synthetic photograph.
Requirements: Phenix must be installed and on path.
Mosflm must be installed and ipmosflm on path.
Usage:
1. First index the dataset using labelit.index. Typical syntax to index two
images is
labelit.index /home/data/project/dataset1_1_E1_###.img 1 90
2. Then
labelit.precession_photo command line arguments
Example:
labelit.precession_photo bravais_choice=1 \\
pixel_width=600 \\
resolution_outer=3.0 \\
intensity_full_scale=1000 \\
plot_section=H,K,0 \\
image_range=1,90 \\
pdf_output.file=HKL.pdf
3. Command line arguments explained:
labelit.precession_photo --help
Known limitations:
a) Since the source images are rotation photographs, there is an inherent
approximation in assuming that the data was obtained at the central
rotation angle (0.5 degree in a 0.0 to 1.0 rotation).
b) Real precession photographs are obtained with a finite-width annulus;
however the approximation here is one of an infinitesmal-width opening.
c) This is a naive implementation that reads all of the data into memory
first before calculating the image. More efficient algorithms will be
implemented later.
Author: Nick Sauter, LBNL; May 8, 2010.
Released under the CCTBX license; see cctbx.sf.net.
import math,pickle,os
import libtbx.phil
precession_master_phil = libtbx.phil.parse(
labelit_precession {
pixel_width = 1500
.type = int
.help = Width of pixel grid on which to calculate the synthesized image;
must be sufficiently large to sample the Bragg spots
resolution_outer = 4.0
.type = float
.help = The high-resolution limit (Angstroms) for the synthesized image
bravais_choice = None
.type = int
.help = Crystal setting (integer ID#), as enumerated in labelit.index
output, chosen for the synthesized section; print a list with
labelit.stats_index
plot_section = None
.type = str
.help = Miller indices of the section to be synthesized, comma separated,
no spaces, such as H,0,L
image_range = None
.type = ints(size=2)
.help = Range of data frames (inclusive) to be used for synthesized image,
i.e., min frame no.,max frame no., no spaces
intensity_full_scale = 255
.type = int
.help = Image intensity to be used as full scale (black)
pdf_output {
file = None
.type = str
.help = File name for pdf output
}
}
)
from scitbx import matrix
from scitbx.array_family import flex
from cctbx.crystal_orientation import crystal_orientation
from cctbx.uctbx import unit_cell
from spotfinder.diffraction.imagefiles import
Spotspickle_argument_module,image_files
from labelit.dptbx import AutoIndexEngine, Parameters
from labelit.command_line.imagefiles import QuickImage
from annlib_ext import AnnAdaptor
def get_precession_parameters(sources=[]):
parameters = precession_master_phil.fetch(sources=sources)
#validation not done here
return parameters
def ai_factory(inputpd):
subpd = inputpd[best_integration]
ai =
AutoIndexEngine(inputpd[endstation],inputpd[recommended_grid_sampling])
P = Parameters(xbeam=float(inputpd[xbeam]),ybeam=float(inputpd[ybeam]),
distance=float(inputpd[distance]),twotheta=float(inputpd[twotheta]))
ai.setBase(P)
ai.setWavelength(float(inputpd['wavelength']))
ai.setMaxcell(float(inputpd['ref_maxcel']))
ai.setDeltaphi(float(inputpd['deltaphi'])*math.pi/180.)
Re: [ccp4bb] software to represent raw reflections in hkl zones
Tillmann, I wrote a little jiffy some months ago, to go from raw images to a pseudo-precession photo, in the context of labelit.index. I'll dig it out and post a link to the program... Nick Tillmann Heinisch wrote: Hi, I have problems solving the structure of a protein crystal which seems to be disordered. In order to investigate the disorder it would be useful to have a precision photograph that shows reflections only in the [0kl] plane. Does anyone know software that can transform raw data to give intensity distribution in distinct zones of hkl? Many Thanks for your help, Tillmann
Re: [ccp4bb] X-ray diffraction image -- .jpg
Andy, Why not try labelit.png filename output.png [-large]? Labelit is availale at http://cci.lbl.gov/labelit Nick Sauter On 10/21/2009 7:53 AM, Andy Torelli wrote: Hi everyone, Is there a free utility that can convert an x-ray diffraction image collected with an ADSC detector to a standard image file format e.g. .jpg, png, etc.? I'm looking for something more elegant than a screen-capture that will yield a higher (graphics) resolution image. I'm sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli
Re: [ccp4bb] Reindexing Orthorhombic
James, If you still have the raw images on line, you can use a new feature in LABELIT to take care of matching the 2nd dataset indexing solution against the isomorphous atomic model from data set 1, and then re-integrate. Usage: labelit.index data set 2 first image data set 2 90-degree image compatibility_file=structure1.pdb The process requires ipmosflm to be in your executable path. Full details are at http://cci.lbl.gov/labelit Nick Sauter James Stroud wrote: Hello All, I have two crystals (that I'll call data set 1 and data set 2) that seem to be isomorphic, but y and z are transposed between the two data sets. Reindexing data set 2 with the operators h = -h k = l l = k makes the axes match data set 1, but running MR with the previous data set 2 solution on the newly reindexed data set 2 yields a solution rotated 180 about z with respect to the data set 1 solution. What is the operation to reindex such that real space is rotated 180 about z? These are in P212121. James -- Nicholas K. Sauter, Ph.D. Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley, CA 94720 nksau...@lbl.gov Voice: 510-486-5713 Fax: 510-486-5909
Re: [ccp4bb] Unmerged output from Scala
Phil, Labelit.rsymop relies on OUTPUT UNMERGED ORIGINAL to access scaled intensities with original Miller indices. However, the data are not fed back into Scala, so the changes you propose would be OK. Nick Phil Evans wrote: Is anyone using the OUTPUT UNMERGED option in Scala? This file contains columns called SCALE SIGSCALE which are the applied scale and its SD I propose to change the names of these columns so that if you put the file back into Scala the scales do not get re-applied by default (which is wrong since they have been applied already) Will this cause anyone problems? I suspect that very few people or programs are using this file Phil Evans -- Nicholas K. Sauter, Ph.D. Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley, CA 94720 [EMAIL PROTECTED] Voice: 510-486-5713 Fax: 510-486-5909
Re: [ccp4bb] mosflm orientation matrix and symmetry
Bryan, I think it would be more correct to say that the orientation matrix file applies to the Bravais type (e.g., hP--hexagonal primitive). Within the Bravais type you can substitute a different space group prior to integration. Nick From: Bryan W. Lepore [EMAIL PROTECTED] does the mosflm orientation matrix specify the crystal system and only the crystal system? i.e, given an orientation matrix from autoindexing, it would be correct to simply use keyword 'SYMMETRY SPACEGROUP' in mosflm to refine then integrate in any of the spacegroups within a given crystal system from autoindexing? -bryan
