I agree with Kay that, with a good model, solving in P1 is likely to be the easiest comprehensive solution. If that doesn’t work, Phaser starts every MR_AUTO job by making a list of all the subgroups, including the different potential indexings (represented by Hall symbols), so you could also work through those systematically. You provide a “SPACEGROUP HALL” command with one of the Hall symbols for each possibility, and Phaser will expand the data from the higher symmetry and reindex as required.
Best wishes, Randy Read > On 9 Jun 2021, at 09:37, Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > > Hi Almudena, > > if it is a packing problem, you need to find the correct subgroup of P6522 > (179). > Take a look at > https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups > . > Subgroups of 179 are 20, 153, 154, 170, and recursively each of these has > subgroups: > 20 has 4 and 5 as subgroups, 153 and 154 both have 5 and 145 as subgroups, > 170 has 4 and 145 as subgroups - taken together, 4, 5 and 145. > These have 1 as subgroup. > So the true space group could be P1, P21, C2, P32, C2221, P3212, P3221, P65. > You could run molecular replacement with all of these. Unfortunately, there > may be several ways to index the data in some of these space groups, and they > may not be equivalent. For example, I think there are 3 non-equivalent ways > to index in C2 or P21 if the Laue class is 6/m . > > If there is twinning, the intensity statistics should tell about that - but > they may be set off by tNCS. > > One way to overcome the mess of possible space groups and settings plus the > twinning possibility is to index and solve the structure in P1. That should > allow a packing without clashes, and one could identify the correct space > group by running POINTLESS on the Fcalc, and/or Zanuda. Since you have a good > model, I'd try that. > > Hope this helps, > Kay > > On Tue, 8 Jun 2021 17:14:30 +0200, Almudena Ponce Salvatierra > <maps.fa...@gmail.com> wrote: > >> Hello everyone, >> >> I am working with an RNA-only structure, data are at 3 Angstroms, and at >> first, I thought was in the C2 space group (with 6 molecules in the AU). >> >> I can't finish building! it, because the structure seems to get in the way >> of its neighbor symmetrically! See the attached picture, please! The only 4 >> residues that the structure is missing "have to go there", where one >> structure meets the other one. The R factors for this spacegroup are around >> 0.3. >> >> However, Phenix Xtriage suggests the symmetry may be higher. So I reindex >> in P622, do MR with Phaser (trying all possible space groups in that point >> group), and it finds a unique solution in space group P 65 2 2 with TFZ of >> 50 and LLG >3000. Of course, the problem persists (one molecule sort of >> interfering with the neighbor), not only that but also the refinement >> R-factors are substantially higher, 0.37. >> >> I have to say that the refinement maps look better when I am working with >> the C2 spacegroup. I can't understand, though, what is happening at that >> "supposedly interface" between the two molecules. Has anybody experienced >> anything like this in the past? Can it be a twin? Is it something else? >> and... how to fix it? >> >> Thank you very much in advance. >> >> Best wishes, >> >> Almudena >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
