Dear AK, if you just need the Se positions, you can run Phaser MR-SAD (available from the GUI) using your partial model as a starting point, together with the Se-Met data. Dependending on the model quality (and the model does not have to be very good), it may be able to locate the Se-sites. BW, Gabor On Sep 6 2012, ash.k@aol.com wrote: > Satisfactory map means: I am expecting a coiled coil or helix bundle type > of assembly and I could see some densities appropriate for helices. There > are proper solvent channels and continuous stretches of densities. > > More to add about data on this: the data is anisotropic and the longer > 'c' axis and alignment of helical density along c axis support this. This > also makes me think that perhaps map is sensible. > > Few rounds of model building, refinement and DM has been successful to > assign around 10 polyala helices and their distribution looks sensible > from packing point of view. Now the problem is to assign the side chain. > I was hoping to make use of Se locations for this. R and Rfree are still > random, in the range of 50%. I am not sure, but it could be perhaps > because most of the scattering material is still unassigned. > > > > > > >-----Original Message----- >From: Francis E Reyes <Francis.Reyes@colorado.edu> >To: PHENIX user mailing list <phenixbb@phenix-online.org> >Cc: phenixbb <phenixbb@phenix-online.org> >Sent: Thu, Sep 6, 2012 8:07 am >Subject: Re: [phenixbb] Autosol: MIRAS > > > This one is solvable, but with extreme difficulty. I recently completed a > structure solution with experimental phases starting at 5.0 A using phase > information from multiple derivatives. > > >How would you describe a somewhat satisfactory map? > > >F > >On Sep 5, 2012, at 7:08 PM, ash.k@aol.com wrote: > > > > > > > >Hi Shya, > > I did wavelength scan, got a good signal for Se and used appropriate > wavelengths for data collection and also used experimental f' and f'' > values for phasing. I think the reasons SAD or MAD for SeMet data is not > working are (i) low resolution: 3.7 for SeMet (Anomalous data is up to > 4.8A) (ii) I should have mentioned this earlier: 3 out of 6 Se are very > close to N-terminus, possible they are disordered. Unit cell is also some > what big..100, 120 and 320A; F222 space group. > >AK > > > >-----Original Message----- >From: Shya Biswas <shyabiswas@gmail.com> >To: PHENIX user mailing list <phenixbb@phenix-online.org> >Sent: Thu, Sep 6, 2012 7:29 am >Subject: Re: [phenixbb] Autosol: MIRAS > > >Hi AK, >Did you do a wavelength scan when you collected the SE dataset you >need to put the values of f' and f'' from your wavelength scan in >order to locate the heavy atom sites, 6 methionine should be enough to >phase your molecule. >Shya > >On Wed, Sep 5, 2012 at 9:25 PM, <ash.k@aol.com> wrote: >> Hi all, >> >> I am trying to solve a structure through experimental phasing using >> AUTOSOL. I have a couple of heavy atom derivative datasets (Hg, La, Eu, >> Cd) and also a SeMet data. Unfortunately all the datasets are of low >> resolution (3.7-4.2A) and there are possibly 4-8 molecules in the asu. >> MIR, SAD and MAD alone did not give any convincing solution. >> >> However, MIRAS, with a combination of few heavy atom datasets and the >> anomalous data from SeMet crystals, gave a somewhat satisfactory map. >> But the heavy atom site picked by AUTOSOL list only one of the heavy >> atoms i.e. Lanthanum. In another set of run, the solution of which was >> not convincing, the heavy atom substructure had only Hg. There are 6 Met >> out of 200 residues in one molecule and mass spec results show that Se >> incorporation is 100%. >> >> Now, my doubt is that why does the heavy atom substructure contain only >> La and how can I get the substructure involving Se from this solution >> (or the datasets used)? Se location is going to help me a lot for >> finding a starting point to assign side chains. >> >> Any suggestion would be greatly appreciated. >> >> Thanks >> AK >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb@phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >_______________________________________________ >phenixbb mailing list >phenixbb@phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > > > > >_______________________________________________ >phenixbb mailing list >phenixbb@phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > > > >_______________________________________________ >phenixbb mailing list >phenixbb@phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > > > -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ################################################## _______________________________________________ phenixbb mailing list phenixbb@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb