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
... only in the [0kl] plane. ... I'm sure you've already checked, but if during data collection the [0kl] axis was nearly perpendicular to the rotation axis, then you may only have to superimpose (with ipdisp) few suitably selected images to obtain a small (low resolution) portion of what you are after. -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
[ccp4bb] software to represent raw reflections in hkl zones
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] software to represent raw reflections in hkl zones
hklview will generate pseudo precession images Sent from my iPhone On 05/05/2010, at 11:03 PM, Tillmann Heinisch tillmann.heini...@unibas.ch 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] software to represent raw reflections in hkl zones
to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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] software to represent raw reflections in hkl zones
Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] software to represent raw reflections in hkl zones
I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] software to represent raw reflections in hkl zones
As Phil says, constructing an undistorted slice through reciprocal space is much harder than displaying integrated intensities. The Bruker APEX2 software does this nicely and I understand that they can also convert MAR CCD and possibly some other frame formats to Bruker format, which presumably would be necessary to apply it to your data. Although intended for - and widely used by - small molecule crystallographers this should work equally well for macromolecules. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 5 May 2010, Phil Evans wrote: I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] software to represent raw reflections in hkl zones
Hi this is what I thought. I would imagine that you'd want to combine the 2D information in the X-ray images in a dataset into a 3D solid figure, then look at slices through this for the RL projection you were interested in. If you indexed the dataset first you should be able to get the right orientations... I don't know anything that does this for single crystal X-ray work, but maybe something from cryo EM single particle reconstruction could be adapted? On 5 May 2010, at 17:10, Phil Evans wrote: I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] software to represent raw reflections in hkl zones
This 'much harder job' is accomplished, too, in the comprehensive CrysAlisPro data-analysis suite from Oxford Diffraction. Again: not just from images in the OD format, but from a wide variety of others, also. So, if we could assist in this case, Tillmann, then we would be pleased to... Marcus Winter. (Oxford Diffraction Ltd.) -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George M. Sheldrick Sent: 05 May 2010 17:20 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] software to represent raw reflections in hkl zones As Phil says, constructing an undistorted slice through reciprocal space is much harder than displaying integrated intensities. The Bruker APEX2 software does this nicely and I understand that they can also convert MAR CCD and possibly some other frame formats to Bruker format, which presumably would be necessary to apply it to your data. Although intended for - and widely used by - small molecule crystallographers this should work equally well for macromolecules. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 5 May 2010, Phil Evans wrote: I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] software to represent raw reflections in hkl zones
Storing a complete 3D image set in memory is moderately challenging even for today's computers (probably several to several 10s of gigabytes, though you could perhaps cheat a bit), so programs would probably have to use old-fashioned double sort techniques to extract a zone. I wonder how the Bruker program does it Phil On 5 May 2010, at 17:20, George M. Sheldrick wrote: As Phil says, constructing an undistorted slice through reciprocal space is much harder than displaying integrated intensities. The Bruker APEX2 software does this nicely and I understand that they can also convert MAR CCD and possibly some other frame formats to Bruker format, which presumably would be necessary to apply it to your data. Although intended for - and widely used by - small molecule crystallographers this should work equally well for macromolecules. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 5 May 2010, Phil Evans wrote: I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM +0200, Tillmann Heinisch wrote: to my knowledge hklview just works with integrated data whereas I need to plot raw intensities along h, k and l to investigate reflection streakings. I heard such software is routinely used in small molecule crystallography. Tillmann On May 5, 2010, at 3:18 PM, David Briggs wrote: Hi Tillmann Will the CCP4 program HKLview do what you want? http://www.ccp4.ac.uk/html/hklview.html Cheers, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 5 May 2010 14:03, Tillmann Heinisch tillmann.heini...@unibas.ch 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 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] software to represent raw reflections in hkl zones
I wrote a little jiffy for doing this some years ago: http://bl831.als.lbl.gov/~jamesh/pickup/adsc2pdb.com However, I should note that this program relies on the DPS program: dps_peaksearch to pick spots on each image in your data set. These spots are then transformed into reciprocal space coordinates in the form of a PDB file, which you can view and rotate around with your favorite graphics program. At the time I wrote it, the most popular program was O, and so the jiffy writes input files for that program. If you don't have DPS, then a similar jiffy for converting the *.spt files that MOSFLM generates during the autoindexing process is here: http://bl831.als.lbl.gov/~jamesh/pickup/spt2xyz.com This is not exactly the 2D-3D-2D re-binning program that is now being discussed as the much harder job, but I have found that transforming peaks will do in most cases. After all, you are generally looking for how the spots transform anyway. Even this will make a very large PDB file in typical cases. The main caveat here is that my jiffy is only set up by default to work with a particular image type (ADSC) from a detector and spindle set up in the usual way (the way it is at my beamline). This is because I very rarely have access to other kinds of images. I think this underlies the reason why a general program for converting any diffraction image into reciprocal space does not exist: you have to know the camera geometry, and camera geometries are poorly documented. Specifically, given the fast and slow dimensions of the image file, you need to know not just the pixel size, but the beam center. The latter has at least 32 different conventions to represent it. Nearly all are used by one facility or another, but no image file format tells you which one it is using. For example, the beam center is usually given as two numbers, but 0 0 can be any of the four image corners (depending on the beamline), and X and Y could be fast or slow. You also need to know if you are in cameraman view or sample view. Both are popular, but invert the hand of the world if you get it wrong. Oh yes! and you also need to know the orientation and rotation direction of the spindle. This is often given as vertical vs horizontal and clockwise vs anticlockwise (which is not enough information), but most spindles are not precisely 90 degrees to the x-ray beam, and yes that does impact precisely where the spots fall. The detector is also not usually perfectly square with the beam either, and is even sometimes purposefully offset at a 2theta angle. Add to all this the heated debates over which direction is X, Y or Z (some think that X is the spindle axis, others (like me) think that X is the X-ray beam), and I think you can see the scope of this problem. Phil makes a good point about memory management problems, but I think that pales in comparison to the headaches of getting a poor, defenseless biologist with a stack of images to come up with the 14 numbers needed to uniquely describe the camera geometry. This is probably why most people just write a program for their favorite image format (the one down the hall). Part of the problem, I think, is that there are more combinations of conventions than there are degrees of freedom in the camera. You really only need 14 numbers (4 vectors and two scales) to completely describe an image file from a flat 2D detector and spindle (independent of XYZ conventions). But that is a topic for another time -James Holton MAD Scientist George M. Sheldrick wrote: As Phil says, constructing an undistorted slice through reciprocal space is much harder than displaying integrated intensities. The Bruker APEX2 software does this nicely and I understand that they can also convert MAR CCD and possibly some other frame formats to Bruker format, which presumably would be necessary to apply it to your data. Although intended for - and widely used by - small molecule crystallographers this should work equally well for macromolecules. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Wed, 5 May 2010, Phil Evans wrote: I think he's looking for a program which will extract a plane from the raw 3D reciprocal space, as sampled by the raw images (ie before integration, but with the plane defined by the indexed lattice). That's a much harder job Phil On 5 May 2010, at 16:50, Tim Gruene wrote: Hi Tillmann, what do you mean by 'raw intensities' as opposed to integrated data? Would xprep be an option for you? It reads XDS_ASCII.HKL, but that's of course after integration. But it should be easy to convert any (non-binary) file containing raw intensities into an hkl-file that you can read with xprep!? rlatt might be another program you are looking for. Tim On Wed, May 05, 2010 at 03:33:40PM
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
