Re: [ccp4bb] data processing with XDS
Thank you very much for useful suggestions! :-) Best, Almu 2014-05-20 9:44 GMT+02:00 Kay Diederichs kay.diederi...@uni-konstanz.de: Dear Almudena, if you follow the recommendations given in the Difficult datasets article on XDSwiki, your problem would have a good chance to be solved. best wishes, Kay On Mon, 19 May 2014 18:18:46 +0200, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, I am looking for some suggestions here. I have lately collected some datasets but the spots are very very weak... it is very difficult to process them. At times it looks like XDS is stalled or at times it just says that it can not interpret the lattice parameters... also while running integrate I have such a message after each range of images: !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 9.1E-03 (should be 1.0E-03) I guess this is not good at all. And I wonder what to do? Is there any info that I can get out from these data at all? or rather not? I wonder if the problem is to find the spots, I have tried with HKL2000 and it can't even find enough of them for indexing. Any ideas are welcome. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] data processing with XDS
Dear Almudena, if you follow the recommendations given in the Difficult datasets article on XDSwiki, your problem would have a good chance to be solved. best wishes, Kay On Mon, 19 May 2014 18:18:46 +0200, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, I am looking for some suggestions here. I have lately collected some datasets but the spots are very very weak... it is very difficult to process them. At times it looks like XDS is stalled or at times it just says that it can not interpret the lattice parameters... also while running integrate I have such a message after each range of images: !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 9.1E-03 (should be 1.0E-03) I guess this is not good at all. And I wonder what to do? Is there any info that I can get out from these data at all? or rather not? I wonder if the problem is to find the spots, I have tried with HKL2000 and it can't even find enough of them for indexing. Any ideas are welcome. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] data processing with XDS
Dear all, I am looking for some suggestions here. I have lately collected some datasets but the spots are very very weak... it is very difficult to process them. At times it looks like XDS is stalled or at times it just says that it can not interpret the lattice parameters... also while running integrate I have such a message after each range of images: !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 9.1E-03 (should be 1.0E-03) I guess this is not good at all. And I wonder what to do? Is there any info that I can get out from these data at all? or rather not? I wonder if the problem is to find the spots, I have tried with HKL2000 and it can't even find enough of them for indexing. Any ideas are welcome. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] data processing with XDS
Hi Almudena Have you tried Mosflm (since this is the CCP4 BB...)? On 19 May 2014, at 17:18, Almudena Ponce Salvatierra wrote: Dear all, I am looking for some suggestions here. I have lately collected some datasets but the spots are very very weak... it is very difficult to process them. At times it looks like XDS is stalled or at times it just says that it can not interpret the lattice parameters... also while running integrate I have such a message after each range of images: !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 9.1E-03 (should be 1.0E-03) I guess this is not good at all. And I wonder what to do? Is there any info that I can get out from these data at all? or rather not? I wonder if the problem is to find the spots, I have tried with HKL2000 and it can't even find enough of them for indexing. Any ideas are welcome. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany 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)
Re: [ccp4bb] data processing with XDS
Hi Almudena, you can also try mosflm as said Harry. And you can try different setting in the XDS.INP, you can try to reduce the STRONG_PIXEL (because you said spots are weak) number or/and MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT (if the spot are small). Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Almudena Ponce Salvatierra [maps.fa...@gmail.com] Envoyé : lundi 19 mai 2014 18:18 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] data processing with XDS Dear all, I am looking for some suggestions here. I have lately collected some datasets but the spots are very very weak... it is very difficult to process them. At times it looks like XDS is stalled or at times it just says that it can not interpret the lattice parameters... also while running integrate I have such a message after each range of images: !!! WARNING !!! REFINEMENT DID NOT CONVERGE LAST CORRECTION SHIFT WAS 9.1E-03 (should be 1.0E-03) I guess this is not good at all. And I wonder what to do? Is there any info that I can get out from these data at all? or rather not? I wonder if the problem is to find the spots, I have tried with HKL2000 and it can't even find enough of them for indexing. Any ideas are welcome. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
