Good advice above.. Someting extra - I would look at information about how the molecules might be arranged. Is there any non-crystallographic translation? ( One with a coordinate 0f say z= 0.5 could mean the spacegroup could be P21212 or P212121 )
Sometimes there is a sub-cell and you can search for fewer sites in that cell.. Eleanor On Thu, 18 Jul 2019 at 16:28, Mario Tyago Murakami < mario.murak...@lnbr.cnpem.br> wrote: > Dear Andy, Clemens and Michal > > The solution for orthrombic SG is very clear. P1 indexing results in a > very similar Unit cell parameters without appreciable deviations in angles > <0.1degrees. > > It seems more likely the problem pointed by Andy of a lot of sites. I will > try all the suggestions and hope to come back soon with good news. > > Thanks > Mario > > Em 18 de jul de 2019 11:44, THOMPSON Andrew < > andrew.thomp...@synchrotron-soleil.fr> escreveu: > > Dear Mario > > The data seem very good but you are looking for an awful lot of sites. > Keep trying with SHELX, but there are some keywords that you might use > which may help (see extract from SHELX doc). This worked for me for a > couple of structures with > 100 sites. You should also try with and without > Patterson seeding. You may need many thousand trials…. I would also start > with the data cutoff somewhere between 3.5 - 4 A (to get rid of anisotropy) > . You could also try manually modifying the Emin value to use just your > strongest signal. Don’t expect the solution to come out easily - you may > have to try different shelx runs for days before getting a single solution. > > At the same time, you really do need to be absolutely certain of the space > group ……any tests you can do > > Good luck > > Andy > > > > > > For large selenomethionine substructures (which behave more like equal > atom ab initiostructure solution of small molecules) it may be worth > increasing the number of Pattersonpeaks used for the Patterson seeding > (e.g. PATT 200; the default is 100) and adding theinstructions WEED 0.3 > (random omit maps) and SKIP 0.5 (uranium atom removal). Thelatter two are > the defaults when PLOP is present but are switched off by default if PLOP > isabsent. When PATS is used, WEED produces a much smaller additional > improvement in thehit ratio than when PATS is absent. For small > substructures (<10 sites), WEED and SKIP cando more harm than good by > eliminating too many correct sites at once. > > > > *De :* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *De la part de* > Mario Tyago Murakami > *Envoyé :* jeudi 18 juillet 2019 16:19 > *À :* CCP4BB@JISCMAIL.AC.UK > *Objet :* [ccp4bb] Se-SAD phasing > > > > 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 > > > > [image: cid:image001.png@01D53D5A.1C2140F0] > > > > 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 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
