Re: [ccp4bb] Point group
On 05/21/15 11:56, Mohamed Noor wrote: Dear all I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. MR searches and refinement in SG P41 and P41212 results in R/Rfree of around 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to complain but Xtriage suggests 25 % twinning in the former (refinement was done without twin law) and that the true point group could be P422. So do I go with P422? Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The statistics are slightly better but I prefer to confirm it visually. I recently had a case of pseudosymmetry which makes me suspicious of automated processing suggestions. Thanks. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Point group
>> I can process my 3.8 A dataset in either P4 or P422 point groups. >Do the scaling statistics look similar for both? If so, go with P422. >Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Point group
On 05/21/2015 05:23 PM, Keller, Jacob wrote: I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I say try out P4 with twin refinement, see how your stats go. JPK Or eventually even to further lower symmetry... I had once an example of true P21212 crystals that processed nicely as P4212, due to a twinning two-fold axis parallel to the a,b diagonal Carlos -- ** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666/609 FAX:(351)-214433644 e-mail: fra...@itqb.unl.pt www.itqb.unl.pt
Re: [ccp4bb] Point group
Even I have the same problem my crystals get processed in to P212121 as well as P4212 and I am currently analysing the data but not able to conclude the space group. Any idea? Both structure while refining is giving around same R/Rfree. Any help will be appreciable. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of Advanced Research +91-9925450504 On Thu, May 21, 2015 at 10:57 PM, frazao wrote: > On 05/21/2015 05:23 PM, Keller, Jacob wrote: > >> I can process my 3.8 A dataset in either P4 or P422 point groups. >>> Do the scaling statistics look similar for both? If so, go with P422. >>> Trying to enforce an incorrect symmetry operator would blow up your >>> stats. >>> >> ...But in the case of twinning, lower space groups can masquerade as >> higher ones. I say try out P4 with twin refinement, see how your stats go. >> >> JPK >> > Or eventually even to further lower symmetry... I had once an example of > true P21212 crystals that processed nicely as P4212, due to a twinning > two-fold axis parallel to the a,b diagonal > > Carlos > > -- > ** > Dr. Carlos Frazao > Structural Biology Laboratory - > Macromolecular Crystallography Unit > ITQB-UNL, Av Republica, Apartado 127 > 2781-901 Oeiras, Portugal > > Phone: (351)-214469666/609 > FAX:(351)-214433644 > e-mail: fra...@itqb.unl.pt > www.itqb.unl.pt >
Re: [ccp4bb] Point group
Dear Mohamed You can get the equivalent of frame.CBF by using the duals image viewer with datablock or experiments.json and integrated.pickle. this will allow you to step through the frames looking at the actual integration boxes. Best wishes Graeme On 21 May 2015 17:02, "Mohamed Noor" wrote: > Dear all > > I can process my 3.8 A dataset in either P4 or P422 point groups. MR > searches and refinement in SG P41 and P41212 results in R/Rfree of around > 30/35 % with 8 and 4 NCS copies, respectively. Pointless doesn't seem to > complain but Xtriage suggests 25 % twinning in the former (refinement was > done without twin law) and that the true point group could be P422. So do I > go with P422? > > Secondly, where can I find the DIALS equivalent to XDS FRAME.cbf? The > statistics are slightly better but I prefer to confirm it visually. I > recently had a case of pseudosymmetry which makes me suspicious of > automated processing suggestions. > > Thanks. >
Re: [ccp4bb] point group...321
Yes, several, but it's only important when merging multiple data sets. And it's not really ambiguities but alternatives. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gihan Ketawala Sent: Thursday, March 29, 2018 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] point group...321 Hi, Can the point group 321 show indexing ambiguities? if not since I'm dealing with non-anomalous dataset can I use 3m1 instead? Thank you, Best, Gihan
Re: [ccp4bb] point group...321
Look at CCP4 v7.0 Program Documentation reindexing Yes PG 321 has two indexing options.. - *i.e.* reindex (h,k,l) to (k,h,-l) which is equivalent here to reindexing (h,k,l) to (-h,-k,l). On 29 March 2018 at 21:26, Gihan Ketawala wrote: > Hi, > Can the point group 321 show indexing ambiguities? if not since I'm > dealing with non-anomalous dataset can I use 3m1 instead? > > Thank you, > Best, > Gihan >
