Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Hi Hui, I think most of us can't do much with rar archive files. This is a Windows thing I believe and my Linux system tells me Archive type not supported... Fred. hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Hi Fred You probably need to install package 'unrar-free', e.g. see: http://packages.ubuntu.com/hardy/i386/unrar-free/download . Cheers -- Ian On Fri, Jul 16, 2010 at 3:37 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi Hui, I think most of us can't do much with rar archive files. This is a Windows thing I believe and my Linux system tells me Archive type not supported... Fred. hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
rar and unrar are available for linux. Something similar to aptitude install unrar or zypper -i unrar, depending on the distribution, might even be faster than repacking the archive. Tim On Fri, Jul 16, 2010 at 04:37:04PM +0200, Vellieux Frederic wrote: Hi Hui, I think most of us can't do much with rar archive files. This is a Windows thing I believe and my Linux system tells me Archive type not supported... Fred. hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Dear Hui, I am not sure what you mean by the diffraction patterns looking all the same. They don't look the same to me, although they surely don't display any lunes. The diffraction goes quite a bit beyond 3.5A, but I don't know HKL2000 well enough to explain why it refuses to integration further than 4.4A. Why don't you try imosflm or xds instead of HKL2000? xprep reports an overall Rint (=Rmerge) of 18.9% when merging your data in P4(2)2(1)2, but you probably want to include the whole resolution range (beyond 4A) before you can be all sure about it. Cheers, Tim On Fri, Jul 16, 2010 at 11:30:31PM +0800, hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Pointless thinks it's P42 21 2 with a reasonably high confidence (though that doesn't exclude twinning) Phil data.log Description: Binary data On 16 Jul 2010, at 17:30, Tim Gruene wrote: Dear Hui, I am not sure what you mean by the diffraction patterns looking all the same. They don't look the same to me, although they surely don't display any lunes. The diffraction goes quite a bit beyond 3.5A, but I don't know HKL2000 well enough to explain why it refuses to integration further than 4.4A. Why don't you try imosflm or xds instead of HKL2000? xprep reports an overall Rint (=Rmerge) of 18.9% when merging your data in P4(2)2(1)2, but you probably want to include the whole resolution range (beyond 4A) before you can be all sure about it. Cheers, Tim On Fri, Jul 16, 2010 at 11:30:31PM +0800, hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Dear Hui, About the so-called weird pattern, it is not a surprise at all! You mentioned you had a long-spindle shaped crystal with large cell dimensions (208 A) and a very possible P4x2x2 SG (proved by Phil). It is very likely the longest dimension of the crystal (parallel to cell edge of 54.55 Å) was closely mounted parallel to the spindle orientation during your data collection. Such an un-inclined crystal mounting with high symmetry in this direction (4-fold), large cell constants perpendicular to this direction, and with big enough oscillation angle (could be small angle) caused this phenomenon--- weird pattern. You can check the crystal rotX and rotY (in your P1 case also rotZ) to easily see the mounting (crystal orientations). Also your images should also clearly tell you by human eyes. Though the changes of the spot positions in the weird pattern are hard to tell with human eyes, the changes in intensity of the spots should be easily seen. Have fun! Lijun On Jul 16, 2010, at 8:30 AM, hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang data.rar Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836
Re: [ccp4bb] Perfect crystal with weird diffraction pattern
Sorry, I think my reply was not case in the attached images! I happened to have the problem to see the image but I could now see all of them. I think Tim was correct, the patterns are not the same at all. Lijun On Jul 16, 2010, at 12:23 PM, Lijun Liu wrote: Dear Hui, About the so-called weird pattern, it is not a surprise at all! You mentioned you had a long-spindle shaped crystal with large cell dimensions (208 A) and a very possible P4x2x2 SG (proved by Phil). It is very likely the longest dimension of the crystal (parallel to cell edge of 54.55 Å) was closely mounted parallel to the spindle orientation during your data collection. Such an un-inclined crystal mounting with high symmetry in this direction (4-fold), large cell constants perpendicular to this direction, and with big enough oscillation angle (could be small angle) caused this phenomenon---weird pattern. You can check the crystal rotX and rotY (in your P1 case also rotZ) to easily see the mounting (crystal orientations). Also your images should also clearly tell you by human eyes. Though the changes of the spot positions in the weird pattern are hard to tell with human eyes, the changes in intensity of the spots should be easily seen. Have fun! Lijun On Jul 16, 2010, at 8:30 AM, hui yang wrote: Hi all, I just collected a data set from a long-spindle-shaped crystal. The data has been scaled to P1 space group with HKL2000, and the final overall Rmerge is 0.208. What is strange is that, the diffraction pattern looks all the same at different rotation angles, and the diffraction point outside the 4A cycle are excluded automatically and thus lead to a final resolution of 4.4A. I’m wondering 1) Whether this crystal is twinned? 2) What is the actual space group of it? A picture of the crystal, three images of the diffraction pattern (1, 90 and 180), the sca file and log file have been attached to this mail for your information. Any suggestions and comments will be highly appreciated. Thank you very much in advance for your inputs. Sincerely, Hui Yang data.rar Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836 Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836
