5 degrees per image may be problematic for some algorithms since the diffraction spots have uncertain positions in three dimensions. Two dimensions will come from the position of the spot on the detector and the position of the detector. The third dimension will come from the rotation angle value of the image which will have a large uncertainty. There are ways around this and d*TREK uses some of them.
________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Niu Tou [[email protected]] Sent: Thursday, March 14, 2013 6:01 PM To: [email protected] Subject: Re: [ccp4bb] Diffraction data with big rotation angle Hi Tim, I only tried HKL2000, and index with different resolution and different number of images. I am not quite familiar with XDS or d*trek. One thing I am not sure is if this large oscillation angle will cause problem in indexing? If this is true, any method to overcome it? The situation I met was when I chose different settings to do index, HKL2000 would give different cell dimensions while most of them were not small enough for a peptide crystal. The unit cell should be pretty small since even collecting data with 5 degree oscillation angle, the spots in one image were still fewer than a normal protein crystal case, so there is no spots overlap. Best, Yang On Thu, Mar 14, 2013 at 5:20 AM, Tim Gruene <[email protected]<mailto:[email protected]>> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Niu, could you let us know more about what you have already tried? - - use more images, maybe all images for indexing - - try a different program: xds instead of mosflm instead of hkl200 instead of d*trek instead of xds .... depending what you have tried. - - try to find the unit cell dimensions manually from adxv - - try cell_now with the SPOTS.XDS in XDS I would check the output of IDXREF.LP to figure out if indexing seems possible, i.e. if the input parameters seem stable or if they are just floating around and many more - it depends on the data set, really! Best, Tim On 03/13/2013 09:12 PM, Niu Tou wrote: > Dear colleagues, > > We have some diffraction data from small peptide crystals, the > shape of diffraction spots looks normal, and resolution is beyond > 2A. The data were collected with 5 degree rotation per image. Later > on we found it is hard to do index. Does anybody know some skills > to figure this problem? > > Best wishes, Niu > - -- - -- 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/ iD8DBQFRQZZFUxlJ7aRr7hoRAmr3AKD28Mml3XY2LIWkDknKrkJFToLDvwCgu1DI LDaPuAMfGlEIEObuWcckM7Y= =yuwC -----END PGP SIGNATURE-----
