Dear Pramod, To run XDS, you could try to run it via the CPP4 procedure XIA2, or via autoPROC from Global Phasing. What also may help is to retype the line: NAME_TEMPLATE_OF_DATA_FRAMES=../images/WFTig1_???.mar2300 ! MAR345 I have had cases, where there were (I believe) hidden characters in there which caused XDS to fail. I would also check that the images XDS complains about, are really there and not empty. Your SPOT_RANGE line is commented out. I would remove the comment "!" and try different spot ranges, including all images. You may also want to play with STRONG_PIXEL, to find a value which finds your major diffraction pattern and ignores the minor pattern. Sometimes it helps, to specify the known(?) space group and cell dimensions, sometimes it is better to leave them out.
XDS output files are normally not multi-megabyte, so you could also consider to post the relevant output files (INIT.LP, COLSPOT.LP) to the bullitin board. Best, Herman ________________________________ Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Pramod Kumar Gesendet: Freitag, 21. Juni 2013 22:59 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] str solving problem Dear ... Francis Last I remember, HKL2000 bases its indexing on the 'strongest' spots on an image (though you could manually select spots). It could result in a misindex if the strongest spots come from separate lattices.. I have used both HKL2000 and mosflm giving the same results (although I have used manual selection of spots as a trial but results are identical). Try a program that uses all spots for indexing, across all images (XDS for example) and you might get the true space group.. I have given several efforts to the XDS but its giving error "data image of particular no. does not exist (initially it was saying 11th image than i change image range then it says 21st and so on) kindly check my data collection profile and XDS.INP file in attachment' Or if the crystal is big enough, you could try shooting it in different areas and 'searching' for a better spot to collect data. Or 'grow a better crystal'. raising the crystals and struggle is on the peak... Dear Eugene plz find the attached scale log file, scaling table of mosflm When you index spots in Mosflm, do your predictions agree with the spots? plz see the snapshot of predicted spots.. Dear Eleanor Yes both the molecule are visible in the ASU. Dear Pozharski Balbes pipeline hitting extremely high marks when fed into Phaser while being complete nonsense (it's a 150kDa multi-domain protein and resulting domain arrangement made absolutely no sense). Refinement was stuck with high R-values and I sadly gave up on it for now. I suspected that refmac step included in the pipeline artificially shifts the model so that it conforms to Patterson map better, which results in high score in Phaser. My domain arrangement is as expected, two molecules in ASU. thanks and regards pramod On Thu, Jun 20, 2013 at 3:50 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: As others say - the Rfactors look pretty good for MR, mine usually start over 50% even with a better model and one hopes they then decrease.. But you say you took the Balbes model into phaser? and I think Balbes automatically runs cycles of refinement so any comment on R factors may not mean much. Have you found both molecules in the asymmetric unit? You only give LLG for one? Eleanor On 19 June 2013 17:44, Eugene Valkov <eugene.val...@gmail.com<mailto:eugene.val...@gmail.com>> wrote: Yes, I would agree with Francis that diffraction shows contribution from several lattices, which could lead to misindexing. However, it should be feasible to get a model that refines from this sort of data. Pramod - could you please post your data processing statistics from your scaling program? Better if you have several for different spacegroups. Also, I have no idea how HKL200 does this, but could you please provide an indexing solution table from Mosflm that shows penalties associated with each type of space group? Was there a sharp penalty drop at some point or was it more gradual? When you index spots in Mosflm, do your predictions agree with the spots? Or is there a substantial portion that are missed? I would consider altering thresholds in Mosflm for indexing (see the manual). Eugene On 19 June 2013 17:34, Francis E. Reyes <francis.re...@colorado.edu<mailto:francis.re...@colorado.edu>> wrote: On Jun 17, 2013, at 12:36 PM, Pramod Kumar <pramod...@gmail.com<mailto:pramod...@gmail.com>> wrote: >> I have a crystal data diffracted around 2.9 A*, >> during the data reduction HKL2000 not convincingly showed the space group >> (indexed in lower symmetry p1), while the mosflm given C-centered >> Orthorhombic, and again with little play around HKL2000 given CO > > no ice ring is appeared, diffraction pattern looks ok, misindexing in any > direction is not conclusive to me (plz see the imj attachment) The diffraction does not look ok... there's hints of multiple lattices... which is not a problem if the two lattice orientations do not perfectly overlap (i.e. their spots are separable). Last I remember, HKL2000 bases its indexing on the 'strongest' spots on an image (though you could manually select spots). It could result in a misindex if the strongest spots come from separate lattices (and even worse if you have twinning/pseudosymmetry issues). Try a program that uses all spots for indexing, across all images (XDS for example) and you might get the true space group. Or if the crystal is big enough, you could try shooting it in different areas and 'searching' for a better spot to collect data. Or 'grow a better crystal'. F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder -- Dr Eugene Valkov MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. Email: eval...@mrc-lmb.cam.ac.uk<mailto:eval...@mrc-lmb.cam.ac.uk> Tel: +44 (0) 1223 407840<tel:%2B44%20%280%29%201223%20407840> -- ************************************************ Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657. ************************************************
