Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
Hi Folks, To follow up Harry's comments. We have a Pilatus 300K on I19 here at Diamond which is used from time to time for small molecule work. Processing with XDS has proved to be successful (I can send an example XDS.INP but you will need to make sure you have a good knowledge of the experimental geometry.) If these had been recorded properly with the full CBF format you would be able to process them with xia2 with XDS, which is what we have been using here. However Harry's report suggests that this is unlikely to work. XDS with a correctly crafted input file should work fine. BTW, in addition to Tim's comments above, I also set DELPHI=30 (relatively arbitrarily) to give enough reflections that the profile averaging could be useful. We have not tested this substantially however. Best wishes, Graeme On 6 February 2013 11:53, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Hi Tim I've looked at these images and they differ from the normal 6M images (miniCBF) in that they are a stab at writing fullCBF, i.e. with imgCIF style data content - unfortunately, there are a few syntax errors which need fixing before programs that use the header information (like Crysalis Pro, inter alia;-)) can do much useful with them. XDS (and any other programs that ignore header information) should be able to process these provided the correct beamline values are supplied. On 6 Feb 2013, at Wed6 Feb 11:19, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jose, it is odd the software should read 6M but not 0.3M Pilatus files - the format is probably the same, only the dimensions would differ - at least that's my guess. While you are waiting you might start processing your data with XDS, which is well suited also for small molecules crystals. If your cell is small, I recommend turning of refinement during the integration step (REFINE(INTEGRATE)=!) and only refine all parameters during the CORRECT step. You need to make sure the spots are correctly predicted on the FRAME.cbf, i.e. the cell from indexing is close enough to the correct one. Best wishes, Tim On 02/06/2013 11:35 AM, Jose Trincao wrote: Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFREjxFUxlJ7aRr7hoRAnT6AJoCPwjWp5eDrIQ0JevYl/98Bh2ixQCglIQ+ 7e+OerAR3x+GVUejoXmVcQM= =ZDOJ -END PGP SIGNATURE- Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jose, it is odd the software should read 6M but not 0.3M Pilatus files - the format is probably the same, only the dimensions would differ - at least that's my guess. While you are waiting you might start processing your data with XDS, which is well suited also for small molecules crystals. If your cell is small, I recommend turning of refinement during the integration step (REFINE(INTEGRATE)=!) and only refine all parameters during the CORRECT step. You need to make sure the spots are correctly predicted on the FRAME.cbf, i.e. the cell from indexing is close enough to the correct one. Best wishes, Tim On 02/06/2013 11:35 AM, Jose Trincao wrote: Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFREjxFUxlJ7aRr7hoRAnT6AJoCPwjWp5eDrIQ0JevYl/98Bh2ixQCglIQ+ 7e+OerAR3x+GVUejoXmVcQM= =ZDOJ -END PGP SIGNATURE-
Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
Hi Tim I've looked at these images and they differ from the normal 6M images (miniCBF) in that they are a stab at writing fullCBF, i.e. with imgCIF style data content - unfortunately, there are a few syntax errors which need fixing before programs that use the header information (like Crysalis Pro, inter alia;-)) can do much useful with them. XDS (and any other programs that ignore header information) should be able to process these provided the correct beamline values are supplied. On 6 Feb 2013, at Wed6 Feb 11:19, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jose, it is odd the software should read 6M but not 0.3M Pilatus files - the format is probably the same, only the dimensions would differ - at least that's my guess. While you are waiting you might start processing your data with XDS, which is well suited also for small molecules crystals. If your cell is small, I recommend turning of refinement during the integration step (REFINE(INTEGRATE)=!) and only refine all parameters during the CORRECT step. You need to make sure the spots are correctly predicted on the FRAME.cbf, i.e. the cell from indexing is close enough to the correct one. Best wishes, Tim On 02/06/2013 11:35 AM, Jose Trincao wrote: Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/ index.htm. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFREjxFUxlJ7aRr7hoRAnT6AJoCPwjWp5eDrIQ0JevYl/98Bh2ixQCglIQ+ 7e+OerAR3x+GVUejoXmVcQM= =ZDOJ -END PGP SIGNATURE- Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
