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) ***
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] Which program sequence to use in transforming from P1 to orthorhombic?
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?
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
