Hi, I have had twinning with P61, which makes it look like P6122. This is with slightly asymmetric dimer. You could try mol replacement in P65, and refine with twinning on. Maps should look better if correct. Ben
Sent from my iPhone > On 9 Jun 2021, at 10:13, Randy John Read <rj...@cam.ac.uk> wrote: > > 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/ ######################################################################## 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/
