Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
Scale constant in Aimless or Scala should do it. I should probably make that automatic. I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
On Tuesday, February 12, 2013 12:39:57 am Phil wrote: Scale constant in Aimless or Scala should do it. I should probably make that automatic. scale constant did indeed persuade aimless/scala to run. However, what seems to have happened is that aimless/scala expanded the original [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were filled in as zero. When ctruncate runs, it segfaults on a divide by zero error. If I filter out the +/- columns and run ctruncate again, all is well. So aside from anything else, I think ctruncate needs some sanity checks for all-zero columns. Ethan I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
Ah I'm not sure about that. It may be possible to tell ctruncate not to do this. Actually if you started with Fs you don't want to truncate the data. Maybe use old truncate with the notruncate option Phil Sent from my iPad On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, February 12, 2013 12:39:57 am Phil wrote: Scale constant in Aimless or Scala should do it. I should probably make that automatic. scale constant did indeed persuade aimless/scala to run. However, what seems to have happened is that aimless/scala expanded the original [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were filled in as zero. When ctruncate runs, it segfaults on a divide by zero error. If I filter out the +/- columns and run ctruncate again, all is well. So aside from anything else, I think ctruncate needs some sanity checks for all-zero columns. Ethan I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
On Tuesday, February 12, 2013 09:52:19 am Phil wrote: Ah I'm not sure about that. It may be possible to tell ctruncate not to do this. Actually if you started with Fs you don't want to truncate the data. Pointless changes the Fs to Is, so you need to get back to Fs somehow. Ethan Maybe use old truncate with the notruncate option Phil Sent from my iPad On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, February 12, 2013 12:39:57 am Phil wrote: Scale constant in Aimless or Scala should do it. I should probably make that automatic. scale constant did indeed persuade aimless/scala to run. However, what seems to have happened is that aimless/scala expanded the original [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were filled in as zero. When ctruncate runs, it segfaults on a divide by zero error. If I filter out the +/- columns and run ctruncate again, all is well. So aside from anything else, I think ctruncate needs some sanity checks for all-zero columns. Ethan I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
Hi Phil, what I tend to do if I want to stay as close as possible to the original data: scala hklin some.mtz hklout tmp.mtz end_ip RUN 1 BATCH 1 TO ONLYMERGE ANALYSE NONORMAL NOPLOT SDCORR NOREFINE FIXSDB NOADJUST BOTH 1.0 0.0 0.0 INITIAL UNITY REJECT 999.9 ALL 999.9 END end_ip truncate hklin tmp.mtz hklout other.mtz end_ip SCALE 1.0 ANOM NO END end_ip ... maybe with NOTRUNCATE as well. This is a bit older ... so there might be a way of achieving the same with the more modern aimless and ctruncate? Cheers Clemens On Tue, Feb 12, 2013 at 06:52:19PM +0100, Phil Evans wrote: Ah I'm not sure about that. It may be possible to tell ctruncate not to do this. Actually if you started with Fs you don't want to truncate the data. Maybe use old truncate with the notruncate option Phil Sent from my iPad On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, February 12, 2013 12:39:57 am Phil wrote: Scale constant in Aimless or Scala should do it. I should probably make that automatic. scale constant did indeed persuade aimless/scala to run. However, what seems to have happened is that aimless/scala expanded the original [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were filled in as zero. When ctruncate runs, it segfaults on a divide by zero error. If I filter out the +/- columns and run ctruncate again, all is well. So aside from anything else, I think ctruncate needs some sanity checks for all-zero columns. Ethan I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Any tool to calculate surface accessible by ... another protein?
Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Thanks in advance for any hint, All the best, Emmanuel
Re: [ccp4bb] Which program sequence to use in transforming from P1 to orthorhombic?
You can do much the same with Aimless but I'm not sure about ctruncate. No access to documentation at present If the Is came from Fs by squaring them in Pointless then it is important not to truncate them, just square root them Phil Sent from my iPhone On 12 Feb 2013, at 19:46, Clemens Vonrhein vonrh...@globalphasing.com wrote: Hi Phil, what I tend to do if I want to stay as close as possible to the original data: scala hklin some.mtz hklout tmp.mtz end_ip RUN 1 BATCH 1 TO ONLYMERGE ANALYSE NONORMAL NOPLOT SDCORR NOREFINE FIXSDB NOADJUST BOTH 1.0 0.0 0.0 INITIAL UNITY REJECT 999.9 ALL 999.9 END end_ip truncate hklin tmp.mtz hklout other.mtz end_ip SCALE 1.0 ANOM NO END end_ip ... maybe with NOTRUNCATE as well. This is a bit older ... so there might be a way of achieving the same with the more modern aimless and ctruncate? Cheers Clemens On Tue, Feb 12, 2013 at 06:52:19PM +0100, Phil Evans wrote: Ah I'm not sure about that. It may be possible to tell ctruncate not to do this. Actually if you started with Fs you don't want to truncate the data. Maybe use old truncate with the notruncate option Phil Sent from my iPad On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote: On Tuesday, February 12, 2013 12:39:57 am Phil wrote: Scale constant in Aimless or Scala should do it. I should probably make that automatic. scale constant did indeed persuade aimless/scala to run. However, what seems to have happened is that aimless/scala expanded the original [I, SIGI] into [I+, SIGI+] [I-, SIGI-], but all the [I-, SIGI-] entries were filled in as zero. When ctruncate runs, it segfaults on a divide by zero error. If I filter out the +/- columns and run ctruncate again, all is well. So aside from anything else, I think ctruncate needs some sanity checks for all-zero columns. Ethan I should probably also add a CIF reader to Pointless. Is there a good (easy) C++ one out there? Phil Sent from my iPad On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote: Ethan, The last time I attempted similar things, I had to run rotaprep to convince scala of using most things that did not come directly out of mosflm, but that was before the pointless days. As the reflections are already scaled in P1, I would consider it safe to rely on the Pointless Rmerge -- but that's just a guess (and you can't do much with the data downstream). I would assume sftools might be able to merge the reindexed file output by pointless. Nevertheless, if I were faced with the same problem nowadays, I would convert to a shelx hkl file and use xprep for the merging and statistics -- that's painless. Cheers, Jens On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote: Hi all, I've downloaded a structure factor file from the PDB that presents itself as being triclinic. It contains F, sig(F), and Rfree only. The P1-ness of this structure is dubious, however. Pointless is 99.6% sure it's orthorhombic and puts out an mtz file in P212121 containing I SIGI BATCH M/ISYM where the batch numbers are all 1 and ISYM runs from 1 to 8. So far so good, but now I'm stuck. I can't persuade Scala or Aimless to merge the symmetry mates and report a merging R factor.Is there a trick to this? Some other program sequence? Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Postdoc position: structural biology of microtubule dynamics
A postdoctoral position is available immediately in Luke Rice’s lab at the University of Texas Southwestern Medical Center in Dallas, TX. The Rice lab is broadly interested in questions relating to the molecular mechanisms of microtubule polymerization dynamics and the mode of action of regulatory factors. Our studies (e.g. Biochemistry 50:8636-44, 2011; Science 337:857-60, 2012) take advantage of our ability to prepare recombinant alpha/beta-tubulin and draw on experimental techniques including but not limited to X-ray crystallography and solution biochemistry/biophysics, computational modeling, time-lapse microscopy, and yeast genetics. The laboratory is part of the supportive and intellectually vibrant Department of Biophysics. Self-motivated and recently minted PhD's from a wide variety of backgrounds will be considered, and a number of different projects are available. To apply please email a CV, contact information for 3 references, and a brief statement explaining your interest to luke.r...@utsouthwestern.edumailto:luke.r...@utsouthwestern.edu. Please put ‘Application for Postdoc’ in the subject field. Regards, Luke - Luke M. Rice Assistant Professor and Thomas O. Hicks Scholar in Medical Research Departments of Biophysics and Biochemistry, ND10.300 UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8816 phone: (214) 645-5931tel:%28214%29%20645-5931 email: luke.r...@utsouthwestern.edumailto:luke.r...@utsouthwestern.edu UT Southwestern Medical Center The future of medicine, today.
Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?
On 02/13/2013 04:51 AM, Emmanuel Levy wrote: Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Without any guarantee, you may try Voroprot: http://code.google.com/p/baltymus/wiki/Tutorial I think it would never crash, whatever the probe size. Thanks in advance for any hint, All the best, Emmanuel