Dear Mario, you probably want to run more than NTRY 1000. With today's computers, NTRY 5000 or NTRY 10000 should not take very long.
You high resolution cut-off in shelxd, 2.7A, is the default, as shelxc adds 0.5A to the high resolution limit of the full data set. In your case this seems reasonable, as CC(1/2) drops below 30% at about 2.75A. You are looking for Se incorporated into SeMet, i.e. your scatterers cannot have a special position. Set the second number of MIND to e.g. 3.5 (>0!) to reject the possibility that heavy atoms have special positions. The main reason. why you may not have found a solution could the the FIND 8 command. This tells shelxd to look for 8 Se-atoms. You describe yourself that you are expecting 80-120 Se-atom. So set with FIND 100 I strongly recommend using the GUI hkl2map by Fabio Dall'Antonio, http:// webapps.embl-hamburg.de/hkl2map/ It guides your very well through the steps of shelx c/d/e As for the space group, your indexing in XDS looks reasonable, I don't think that XDS accidentally doubled one of the unit cell axes. However, from pointless.log, the decision for the 2(1) b-axis is based on 26 reflections. I would normally trust pointless, and expect that you get as solution by properly setting the parameters in shelxd and trying autobuilding in shelxe (your resolution limit for shelxe is probably 1.9-2.0; 2.2 was quite a cautious resolution cut-off). However, you may want to re-run the CORRECT steps with SPACE_GROUP_NUMBER=16 UNIT_CELL_CONSTANTS= 118.836 167.150 151.908 90 90 90 REIDX= -1 0 0 0 0 0 1 0 0 1 0 0 and run shelx c/d/e with spacegroup P2(1)2(1)2 (sorry, I am not sure wether conventionally a<b or b<a in P2(1)2(1)2) Good luck, Tim On Thursday, July 18, 2019 7:53:03 PM CEST Mario Tyago Murakami wrote: > Sure, it follows attached. I am also attaching the pointless log and > IDXREF.LP from xds. > -----Mensagem original----- > De: Tim Grüne <tim.gru...@univie.ac.at> > Enviada em: quinta-feira, 18 de julho de 2019 13:06 > Para: Mario Tyago Murakami <mario.murak...@lnbr.cnpem.br> > Cc: CCP4BB@jiscmail.ac.uk > Assunto: Re: [ccp4bb] Se-SAD phasing > > Dear Mario, > > you may want to post the shelxc log file and the shelxd input file to get a > bit more quantitative advice with shelxd. For the spacegroup, it is worth > reading the pointless log file carefully about how many expected absences > you have per screw axis, although pointless is quite careful and does not > suggest a screw axes when the respective axis was not recorded. > > > From your CCanom, you could cut your resolution to 2.8A for shelxd (your > native data probably goes to 2.0'ish A, by the way). > Best regards, > Tim > > Am 18.07.2019 16:19, schrieb Mario Tyago Murakami: > > > Dear all, > > > > I am trying to solve the phases of the following SeMet data, but so > > far unsuccessfully. Suggestions are very welcome. Please see below > > some details about the case. > > > > The statistics below is from a merged data from different kappas of > > the same crystal to increase redundancy. We used the fixed energy > > 12675 eV since the fluorescence detector was not working at the used > > beamline to get best energy values for this crystal. > > > > Xtriage did not indicate any crystallographic pathology, except > > moderate anisotropy. > > > > The unit cells parameters are 118.72 151.82 167.05 90.000 90.000 > > > > 90.000 (P212121) containing from 8 to 12 molecules in the asymmetric > > > > unit. The protein has ~28.5 kDa and 10 Met residues, excluding those > > from the N- and C-termini, probably with low occupancy. Thus, > > something 80 to 120 scatterers are expected. > > > > Phenix_anomalous_signal indicates a probability of 99% to solve it and > > the anomalous signal is theoretically in a very good range. > > > > I have tried SHELXD with different resolutions and number of sites. I > > have also used Hyss. But all attempts failed. > > > > Thanks in advance > > > > Mario > > > > Aviso Legal: Esta mensagem e seus anexos podem conter informações > > confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e > > considere eventual consulta ao remetente antes de copiá-la, divulgá-la > > ou distribuí-la. Se você recebeu esta mensagem por engano, por favor > > avise o remetente e apague-a imediatamente. > > > > Disclaimer: This email and its attachments may contain confidential > > and/or privileged information. Observe its content carefully and > > consider possible querying to the sender before copying, disclosing or > > distributing it. If you have received this email by mistake, please > > notify the sender and delete it immediately. > > > > ------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry > University of Vienna > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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