Re: [ccp4bb] tNCS: indexing and EP problems
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nicolas, you need to make sure the SPACE_GROUP_NUMBER is set (not commented out) and different from 0 in order for UNIT_CELL_PARAMETERS to be taken into account. Additionally you can unset the refinement of the CELL in the respective REFINE(IDXREF) instruction. Regards, Tim On 09/23/2013 05:51 PM, Nicolas Soler wrote: Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSQTmOUxlJ7aRr7hoRAmcZAKDR7j+rt/z408FXlN92EW64fjhRNgCfTo0v UYe3fqRklf6llglhUJbumgA= =q1BH -END PGP SIGNATURE-
[ccp4bb] tNCS: indexing and EP problems
Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas
Re: [ccp4bb] tNCS: indexing and EP problems
Hi Boaz, I'm looking for one or several XDS keyword(s) to configure, in order to find the same unit cell that Mosflm found. Thanks, Nicolas On 23/09/2013 15:04, Boaz Shaanan wrote: Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas Soler [nso...@mrc-lmb.cam.ac.uk] Sent: Monday, September 23, 2013 5:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tNCS: indexing and EP problems Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
Re: [ccp4bb] tNCS: indexing and EP problems
Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas Soler [nso...@mrc-lmb.cam.ac.uk] Sent: Monday, September 23, 2013 5:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tNCS: indexing and EP problems Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas
Re: [ccp4bb] tNCS: indexing and EP problems
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1+MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
Re: [ccp4bb] tNCS: indexing and EP problems
In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. The new XDS gui can also serve for that these days, I guess. Boaz
[ccp4bb] השב: Re: [ccp4bb] tNCS: indexing and EP problems
Hi Nicolas, You may want to make sure that all other parameters in XDS are the same as in mosflm and particularly the origin. Otherwise, how does the xds indexing/integration look? Perhaps pointless will give a clue about the relation between the xds and mosflm cells/spacegroup? Cheers, Boaz הודעה מקורית מאת Nicolas Soler nso...@mrc-lmb.cam.ac.uk תאריך: 23/09/2013 18:40 (GMT02:00) אל CCP4BB@JISCMAIL.AC.UK נושא Re: [ccp4bb] tNCS: indexing and EP problems Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla -http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
Re: [ccp4bb] tNCS: indexing and EP problems
Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla -http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1+MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
