Re: [ccp4bb] 2Theta data set solving problem
Dear Navin, Maybe a little more explanation: the merging of different runs is done by the scaling program. There is nothing special with different 2theta angles, the only thing is that the scaling program should know about it for applying absorption corrections etc. This is handled automatically and should not require user intervention. For XSCALE you can read in multiple HKL files, for scala/aimless, as Tim pointed out, you first have to combine the different mtz files into one. Scale/aimless should also automatically detect the different runs. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Tuesday, April 09, 2013 6:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 2Theta data set solving problem -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Navin, what happens when you read them both into pointless, followed by aimless? Once processed, the data should scale irrespective of the 2theta. If they don't they might be indexed differently, but pointless would fix this. Best, Tim On 04/09/2013 06:15 PM, navin narayanan wrote: hello everybody, Thank you for all your suggestions. I am able to process the 2 data sets separately. But the problem is that I dont have an idea as to how can i merge the 2 data sets with different 2theta values. On Tue, Apr 9, 2013 at 5:48 PM, herman.schreu...@sanofi.com wrote: ** Dear Navin, As others have pointed out, it is not clear where your problem exactly lies: Are you not able to process the 2theta=20° run, or are you not able to merge it with the 2theta=0° run? Anyways, I and others have had similar problems with merging high and low resolution runs, see a very recent thread below: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg30764.html In my case, Scala would fail with low redundancy data or when there are too few reflections in common between both runs. What worked for me is to process with XDS and scale with XSCALE. For this you can use the autoProc procedure of global phasing, or teh Xia2 pipeline which seems to be part of CCP4. Using one of these pipelines will probably also solve your problem if you are not able to process the swing-out run. Good luck! Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *navin narayanan *Sent:* Tuesday, April 09, 2013 1:49 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] 2Theta data set solving problem Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan - -- 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/ iD8DBQFRZEO4UxlJ7aRr7hoRAv02AKC9ty1xv0Qq6Pd0dwjOpd9uM1Va9QCgyz6e ipQwR9GT3DW8EyvSqIt0MY8= =nxDA -END PGP SIGNATURE-
[ccp4bb] 2Theta data set solving problem
Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
Navin, You mean that you can not PROCESS your data set? What diffraction data processing program are you use? What is your source, goniostat, diffractometer, area detector? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 9, 2013, at 14:41 , navin narayanan navi...@gmail.com wrote: Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
Hi Navin I'll assume you are using iMosflm from the CCP4 suite. Have you tried increasing the resolution in the Processing Options window, under the Processing tab? The option to display resolution rings and change the resolution by dragging the ring does not work at present in iMosflm. On 9 Apr 2013, at Tue9 Apr 12:41, navin narayanan wrote: Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] 2Theta data set solving problem
Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
I thought imosflm recognizes automatically the 2theta offset ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Apr 9, 2013, at 7:51, navin narayanan navi...@gmail.commailto:navi...@gmail.com wrote: Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
Hello, Navin Not enough information. What do you mean by picking up? Low I/s, high Rmeas, too many alien spots? May be your crystals are twins with high mosaicity, with ice rings and high background noise. Please, share your processing log file (Mosflm?DENZO?) Some home sources have additional axis (kappa) and data sets must be processed by its own software. Please, provide more information 09.04.2013 15:41, navin narayanan ?: Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] 2Theta data set solving problem
Dear Navin, As others have pointed out, it is not clear where your problem exactly lies: Are you not able to process the 2theta=20° run, or are you not able to merge it with the 2theta=0° run? Anyways, I and others have had similar problems with merging high and low resolution runs, see a very recent thread below: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg30764.html In my case, Scala would fail with low redundancy data or when there are too few reflections in common between both runs. What worked for me is to process with XDS and scale with XSCALE. For this you can use the autoProc procedure of global phasing, or teh Xia2 pipeline which seems to be part of CCP4. Using one of these pipelines will probably also solve your problem if you are not able to process the swing-out run. Good luck! Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of navin narayanan Sent: Tuesday, April 09, 2013 1:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 2Theta data set solving problem Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
hello everybody, Thank you for all your suggestions. I am able to process the 2 data sets separately. But the problem is that I dont have an idea as to how can i merge the 2 data sets with different 2theta values. On Tue, Apr 9, 2013 at 5:48 PM, herman.schreu...@sanofi.com wrote: ** Dear Navin, As others have pointed out, it is not clear where your problem exactly lies: Are you not able to process the 2theta=20° run, or are you not able to merge it with the 2theta=0° run? Anyways, I and others have had similar problems with merging high and low resolution runs, see a very recent thread below: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg30764.html In my case, Scala would fail with low redundancy data or when there are too few reflections in common between both runs. What worked for me is to process with XDS and scale with XSCALE. For this you can use the autoProc procedure of global phasing, or teh Xia2 pipeline which seems to be part of CCP4. Using one of these pipelines will probably also solve your problem if you are not able to process the swing-out run. Good luck! Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *navin narayanan *Sent:* Tuesday, April 09, 2013 1:49 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] 2Theta data set solving problem Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] 2Theta data set solving problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Navin, what happens when you read them both into pointless, followed by aimless? Once processed, the data should scale irrespective of the 2theta. If they don't they might be indexed differently, but pointless would fix this. Best, Tim On 04/09/2013 06:15 PM, navin narayanan wrote: hello everybody, Thank you for all your suggestions. I am able to process the 2 data sets separately. But the problem is that I dont have an idea as to how can i merge the 2 data sets with different 2theta values. On Tue, Apr 9, 2013 at 5:48 PM, herman.schreu...@sanofi.com wrote: ** Dear Navin, As others have pointed out, it is not clear where your problem exactly lies: Are you not able to process the 2theta=20° run, or are you not able to merge it with the 2theta=0° run? Anyways, I and others have had similar problems with merging high and low resolution runs, see a very recent thread below: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg30764.html In my case, Scala would fail with low redundancy data or when there are too few reflections in common between both runs. What worked for me is to process with XDS and scale with XSCALE. For this you can use the autoProc procedure of global phasing, or teh Xia2 pipeline which seems to be part of CCP4. Using one of these pipelines will probably also solve your problem if you are not able to process the swing-out run. Good luck! Herman -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *navin narayanan *Sent:* Tuesday, April 09, 2013 1:49 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] 2Theta data set solving problem Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan - -- 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/ iD8DBQFRZEO4UxlJ7aRr7hoRAv02AKC9ty1xv0Qq6Pd0dwjOpd9uM1Va9QCgyz6e ipQwR9GT3DW8EyvSqIt0MY8= =nxDA -END PGP SIGNATURE-
