Re: [ccp4bb] combine more than 9 datasets
It is limited to 9 input files, not datasets. If you have more than 9 files, you should be able to run CAD multiple times, to accumulate the datasets. If you want to play with the source code, it is parameter MAXFILES. This has NOT been tested for side effects. Martyn On Wed, 2009-06-24 at 21:38 +0200, Christian Roth wrote: Dear all, I want combine more than 9 datasets to compare them in respect to their isomorphism. CAD seems to be limited to 9 datasets. Is their an other program to do this? Or is it possible to modify CAD in a way that it except more than 9 datasets? The following scaling with SCALEIT would allow up to 20 derivatives, if I understood the manual correct. Best regards Christian -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319 -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] Coot installation on MacBook Pro
Hi! I have recently bought MacBook Pro and I have specific problem with installing coot on it. I already followed Scott lab's instructions but the problem still exists. All help and suggestions are most welcomed. Cheers! Mohinder
[ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Title: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. try hklview in CCP4 http://www.ccp4.ac.uk/dist/html/hklview.html best regards, Paul.. ### Dr. Paul A. McEwan Office B55 Centre for Biomolecular Science University of Nottingham Nottingham NG7 2RD UK Tel: 0115 8232010 (office) Tel: 0115 8232011 (lab) http://www.nottingham.ac.uk/pharmacy/research/medicinal-chemistry-structural-biology/structbio.php### From: CCP4 bulletin board on behalf of Francis E ReyesSent: Thu 25/06/2009 5:24 PMTo: CCP4BB@JISCMAIL.AC.UKSubject: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. Hi allIs there software that will take oscillation photographs and constructa precession-like photo of specific layers of the reciprocal lattice(say h0l), for inspection of the systematic absences, etc?ThanksFR-Francis Reyes M.Sc.215 UCBUniversity of Colorado at Bouldergpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Hi, HKLView in CCP4 will create a pseudo-precession photo from a reflection list (mtz-file) for the layer of choice. HTH, Esko On 25.6.2009, at 19.24, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D Esko Oksanen, M.Sc., researcher Macromolecular Structures Group Research Program in Structural Biology and Biophysics Institute of Biotechnology, University of Helsinki Viikinkaari 1 P.O. Box 65 FIN-00014 Helsinki FINLAND tel. +358-9-19158953 fax +358-9-19159940 mob. +358-40-4870835 Skype ejoksane esko.oksa...@helsinki.fi
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Thanks all who replied. Looks like HKLView is it.. Oddly I couldnt find it anywhere in the ccp4i interface (shouldn't it at least appear under Program List)? FR On Jun 25, 2009, at 10:24 AM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] Assistant Professor Level X-ray Crystallography Faculty Position
Posted on behalf of Dr. Issar Smith: The Public Health Research Institute at UMDNJ New Jersey Medical School invites applications for a faculty position at the assistant professor level. The successful candidate must possess a Ph.D., M.D., or equivalent degree and have extensive experience using X-ray crystallography to address questions of biomedical relevance. We are interested in candidates with a proven track record and a well- formulated research plan. The successful candidate will benefit from a stimulating and collaborative environment within the Institute. Advantages include competitive start-up funds and salaries, state-of-the-art facilities including a crystallization robot, an X-ray facility, and a new research building that is a short drive from the Brookhaven National Laboratory National Synchrotron Light Source. Evaluation of applicants will begin immediately. Please email your application including a curriculum vitae and a description of your current and future research program. Also indicate that you are applying for the assistant professor position. Candidates should also submit three references via email or mail to: Dr. Issar Smith, Chairman Faculty Search Committee Public Health Research Institute 225 Warren Street Newark NJ 07103 Email: smit...@umdnj.edu Tel. (973) 854-3260 Fax. (973) 854-3206 For more information about PHRI, visit: http://www.phri.org/index.asp The University of Medicine and Dentistry of New Jersey is an equal opportunity employer and encourages applications from minorities and women.
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! In the days when we had real precession cameras this was how you assigned the space group. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 25 June 2009 17:32 To: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. Thanks all who replied. Looks like HKLView is it.. Oddly I couldnt find it anywhere in the ccp4i interface (shouldn't it at least appear under Program List)? FR On Jun 25, 2009, at 10:24 AM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Hi, On Jun 25, 2009, at 6:41 PM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! This is actually how it is done in the Bruker software (Proteum2). It collects the relevant pixels from a whole series of xray images and generates a simulated precession image for a chosen zone. It can be very informative. Cheers, Martin On Jun 25, 2009, at 6:24 PM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR
[ccp4bb] crystal morphology and crystal system
Hi All, I am working with DNA-Protein complex and getting 3D crystals (~15% PEG 3350, 100mM Ca-acetate, pH 7.4) in Orthorhombic system. But in one case (different DNA length) it is always coming as a needle cluster or thin flake (20-25% PEG 3350). I took one needle and solved the structure (res 3.2A) in Triclinic system (half cell size that of Orthorhombic) two monomers in assym unit with little bit moderate R-values. Now my question is - would it be possible to play with the crystallization condition to get a 3D crystal? Though I have tried some. Any idea or suggestions will be appreciated. Regards Surajit
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Yep: the Oxford Diffraction 'CrysAlisPro' package includes a tool working in precisely the same way: generating 'pseudo-precession photos' through pixel-by-pixel analysis of all of the raw diffraction images... Marcus Winter (Oxford Diffraction) -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Martin Hallberg Sent: 25 June 2009 19:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. Hi, On Jun 25, 2009, at 6:41 PM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! This is actually how it is done in the Bruker software (Proteum2). It collects the relevant pixels from a whole series of xray images and generates a simulated precession image for a chosen zone. It can be very informative. Cheers, Martin On Jun 25, 2009, at 6:24 PM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Yes this is exactly what I wanted. I'm embarking on an educational pursuit of determining the space group from the diffraction images directly. Unfortunately it seems like all the solutions insofar are only commercially available as part of large packages that don't list their prices directly on the website and, therefore, are probably too much for a single person to afford for just this purpose. Cheers FR On Jun 25, 2009, at 10:41 AM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! In the days when we had real precession cameras this was how you assigned the space group. Cheers -- Ian - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
A long time ago, I wrote a little program for turning spot picks into a PDB file that you could load up and rotate around in a graphics program (such as O, at the time): http://bl831.als.lbl.gov/~jamesh/pickup/spt2xyz.com this one works on the *.spt files that comes out of MOSFLM. You can concatenate *.spt files for each of your images to get the full data set represented. I also wrote one that works on ADSC images if you have the DPS program installed: http://bl831.als.lbl.gov/~jamesh/pickup/adsc2pdb.com but it only works for the common coordinate system convention we use at ALS and SSRL. Not sure about other beamlines. The algorithm for converting spot positions into reciprocal space is not exactly new, as it is at the core of any and every autoindexing program. All you do is figure out the take-off angle of the diffracted ray from the crystal and then calculate the coordinate where this line intersects the Ewald sphere. Specifically, the distortion is: distortion = lambda*sqrt((Xdet)^2+(Ydet)^2+(dist)^2) where: lambda - the x-ray wavelength in A Xdet - X coordinate of the spot relative to the beam center (in mm) Ydet - Y coordinate of the spot relative to the beam center (in mm) dist- the crystal-to-film distance (from crystal to direct-beam spot, in mm) You then use this distortion to compute the x-y-z coordinate of the reciprocal-lattice point in reciprocal space: x' = Xdet/distortion y' = Ydet/distortion z' = dist/distortion - 1/lambda Yes, there are x-y-z coordinates in reciprocal space. They all have units of inverse Angstroms. Of course, these x',y',z' coordinates are at the phi value of the image you picked spots on. To get the coordinates at phi=0, you need to un-roate them: x = x'*cos(phi)-z'*sin(phi) y = y' z = x'*sin(phi)+z'*cos(phi) where some people can probably tell that in this convention the phi axis is right-handed and parallel to the Ydet axis of the detector. The last step is to multiply these x,y,z coordinates by some reasonable scale factor and put them into a PDB file. Maybe put the intensity in the B-factor column, so that you can color it. Then you need to find a display program that can handle a million-atom PDB. Does anyone have one of those? Ideally, what one would like to do is make an electron density map with pixel-to-pixel correspondence to the image. All you do is apply the above formulas to each pixel, do a Lorentz-Polarization correction, and then just render the data set as a map. Sounds like there are a couple of commercial programs that do this in 2 dimensions. Problem with doing it in 3D is there are no programs that can display an electron density map this big. In fact, I can't even get CCP4 to write out map or mtz files bigger than 2 GB. I get filesize limit exceeded errors (even though the filesystem can handle large files). Is this a limitation of the 32-bit binaries? Can anyone help me confirm that re-compiling CCP4 as 64-bit will fix this? This error can be reproduced by trying to make a 2 A data set for the largest unit cell in the PDB: unique hklout test.mtz EOF RESO 2 SYMM 1 CELL 687.900 687.900 1933.300 90 90 90 DEFAULT 1 LABOUT F=F END EOF Thanks! -James Holton MAD Scientist Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! In the days when we had real precession cameras this was how you assigned the space group. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: 25 June 2009 17:32 To: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. Thanks all who replied. Looks like HKLView is it.. Oddly I couldnt find it anywhere in the ccp4i interface (shouldn't it at least appear under Program List)? FR On Jun 25, 2009, at 10:24 AM, Francis E Reyes wrote: Hi all Is there software that will take oscillation photographs and construct a precession-like photo of specific layers of the reciprocal lattice (say h0l), for inspection of the systematic absences, etc? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
I think you should just grab a copy of Stout and Jensen, and use the oscillation photographs directly. What's so special about a precession image? You can still index the spots and follow along rl lines. Bernie Santarsiero On Thu, June 25, 2009 1:38 pm, Francis E Reyes wrote: Yes this is exactly what I wanted. I'm embarking on an educational pursuit of determining the space group from the diffraction images directly. Unfortunately it seems like all the solutions insofar are only commercially available as part of large packages that don't list their prices directly on the website and, therefore, are probably too much for a single person to afford for just this purpose. Cheers FR On Jun 25, 2009, at 10:41 AM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! In the days when we had real precession cameras this was how you assigned the space group. Cheers -- Ian - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Just to add on Bernard's comment: the best way of doing what he suggests is to add a few oscillation images (using for example the ccp4 idiffdisp). Now, how well you'll be able to detect zones that lead to proper indexing, a-la good old precession images, depends on the geometry of your data collection of course. If you collected around one oscillation axis with a randomly mounted crystal you should be very lucky to come across zones that really lead to proper indexing. Certainly you would be luckier if you recorded images around several zones. Still, it would be useful to do what Ian suggested, i.e. a program for obtaining precession like pictures from raw data (a non-commercial one, I mean). Cheers, Boaz - Original Message - From: Santarsiero, Bernard D. b...@uic.edu Date: Thursday, June 25, 2009 20:42 Subject: Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice. To: CCP4BB@JISCMAIL.AC.UK I think you should just grab a copy of Stout and Jensen, and use the oscillation photographs directly. What's so special about a precession image? You can still index the spots and follow along rl lines. Bernie Santarsiero On Thu, June 25, 2009 1:38 pm, Francis E Reyes wrote: Yes this is exactly what I wanted. I'm embarking on an educational pursuit of determining the space group from the diffraction images directly. Unfortunately it seems like all the solutions insofar are only commercially available as part of large packages that don't list their prices directly on the website and, therefore, are probably too much for a single person to afford for just this purpose. Cheers FR On Jun 25, 2009, at 10:41 AM, Ian Tickle wrote: But I thought what you wanted was to reconstruct the diffraction pattern (i.e. streaks, TDS, ice rings, zingers, warts all) as a pseudo-precession image, not just display a representation of the integrated intensities. That surely would be much more useful, then one could see whether the apparent systematic absence violations were just streaks from adjacent spots, TDS, ice spots etc that have fooled the integration algorithm. That would be much more useful! In the days when we had real precession cameras this was how you assigned the space group. Cheers -- Ian - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
On Thu, 25 Jun 2009 11:39:29 -0700 James Holton jmhol...@lbl.gov wrote: A long time ago, I wrote a little program for turning spot picks into a PDB file that you could load up and rotate around in a graphics program (such as O, at the time): http://bl831.als.lbl.gov/~jamesh/pickup/spt2xyz.com this one works on the *.spt files that comes out of MOSFLM. You can concatenate *.spt files for each of your images to get the full data set represented. I also wrote one that works on ADSC images if you have the DPS program installed: http://bl831.als.lbl.gov/~jamesh/pickup/adsc2pdb.com but it only works for the common coordinate system convention we use at ALS and SSRL. Not sure about other beamlines. The algorithm for converting spot positions into reciprocal space is not exactly new, as it is at the core of any and every autoindexing program. All you do is figure out the take-off angle of the diffracted ray from the crystal and then calculate the coordinate where this line intersects the Ewald sphere. Specifically, the distortion is: distortion = lambda*sqrt((Xdet)^2+(Ydet)^2+(dist)^2) where: lambda - the x-ray wavelength in A Xdet - X coordinate of the spot relative to the beam center (in mm) Ydet - Y coordinate of the spot relative to the beam center (in mm) dist- the crystal-to-film distance (from crystal to direct-beam spot, in mm) You then use this distortion to compute the x-y-z coordinate of the reciprocal-lattice point in reciprocal space: x' = Xdet/distortion y' = Ydet/distortion z' = dist/distortion - 1/lambda Yes, there are x-y-z coordinates in reciprocal space. They all have units of inverse Angstroms. Of course, these x',y',z' coordinates are at the phi value of the image you picked spots on. To get the coordinates at phi=0, you need to un-roate them: x = x'*cos(phi)-z'*sin(phi) y = y' z = x'*sin(phi)+z'*cos(phi) where some people can probably tell that in this convention the phi axis is right-handed and parallel to the Ydet axis of the detector. The last step is to multiply these x,y,z coordinates by some reasonable scale factor and put them into a PDB file. Maybe put the intensity in the B-factor column, so that you can color it. Then you need to find a display program that can handle a million-atom PDB. Does anyone have one of those? Ideally, what one would like to do is make an electron density map with pixel-to-pixel correspondence to the image. All you do is apply the above formulas to each pixel, do a Lorentz-Polarization correction, and then just render the data set as a map. Sounds like there are a couple of commercial programs that do this in 2 dimensions. Problem with doing it in 3D is there are no programs that can display an electron density map this big. In fact, I can't even get CCP4 to write out map or mtz files bigger than 2 GB. I get filesize limit exceeded errors (even though the filesystem can handle large files). Is this a limitation of the 32-bit binaries? Can anyone help me confirm that re-compiling CCP4 as 64-bit will fix this? This error can be reproduced by trying to make a 2 A data set for the largest unit cell in the PDB: The limit on file sizes using fopen and the like for 32 bit systems is 2^31 bytes, unless you use fopen64 or use _FILE_OFFSET_BITS == 64 passed to the compiler (assuming you have LFS support, etc, etc): http://www.gnu.org/software/libc/manual/html_node/Opening-Streams.html#index-fopen64-931 on 64 bit machines, the file size limit is 2^63 bytes (this also depends on the file system type, just to make things even more complicated). Here's another easy way to test it: dd if=/dev/zero of=bigfile bs=1024 count=3145728 Hope this helps! -Tim -- - Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -
Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.
Dear Francis, Unfortunately it seems like all the solutions insofar are only commercially available as part of large packages that don't list their prices directly on the website and, therefore, are probably too much for a single person to afford for just this purpose. As mentioned in a private mail - you (and anyone else) might try rsv_mapper.py which is in the ImageD11 package at fable.sourceforge.net. It is free, opensource, and transforms a series of images into a 3D reciprocal space volume that you can slice as you like. Beware that your computer should be big enough to hold the resulting volume, and you need a deep understanding of crystallography to do cell transformations when choosing a basis for the volume. Please just send me an email if you need help to get started (eg you didn't collect data at the beamline where I work :-) If there is some general interest I guess a user manual could be written with some examples. Best, Jon
