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Some afterthoughts: Of course avoid the common MR problems - assigning wrong SG, saturating low resolution data etc etc.. 1) Any sequence search tool might have told you there was only a poor match available. 23% is very marginal for MR and with that degree of similarity you are very wise to start searching for exptl phase methods. However it is sometimes possible to get an MR solution which can at least be helpful as a guide while you build your model into the dexptlly phased map! BALBES does a very good job at analysing likely models - could your sequence suggestr a multimer? are there domains which fit well? etc etc. Then there are the other methods which can give answers - aligning multiple models, doing homology modelling etc. But even if you found a reasonable solution rebuilding and refinement can be difficult - much easier to have some exptl phases to guide that.. Eleanor Ashley Buckle wrote: > This is generally a good idea, but removal of residues is a subjective process, and a little trial and error. If your sequence searching finds multiple search models you can superimpose them and systematically remove the poorer fitting regions based upon RMSD. We have built a server for this at http://pxgrid.med.monash.edu.au:8080/mustangserver/ > Also see the paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010048 > > This can generate A LOT of search models, so you need a way of testing them all, and possibly varying other parameters (eg in PHASER varying RMSD, space groups to test, clashes). This can generate >100 runs, so best to be able to use a compute cluster, and some way of queing the jobs (eg MrBump, BALBES etc. Another solution is here: > > http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010049 > > hope that helps > Ashley > > On 25/05/2010, at 2:52 AM, Jürgen Bosch wrote: > >> You've also applied BRAIN 2.0 ? >> >> I mean looked at homologous structures, superimposed them and decided which parts are to be removed ? >> Never trust programs :-) There could be a flexible alpha helix which if you removed it would have given you in all programs a solution. >> >> it's Monday, >> >> Jürgen >> >> >> On May 24, 2010, at 10:24 AM, Paul Lindblom wrote: >> >>> The last molrep job just finished and it found only an odd solution. So I think I will try to get my phases elsewhere. But I am somewhat astonished that there are still enough cases you can't solve by MR. >>> >>> Thanks to all who replied. Here is a list of servers/programs to find a MR model: >>> >>> http://www.ebi.ac.uk/pdbe-srv/view/ >>> >>> http://www.ebi.ac.uk/Tools/fasta33/index.html >>> >>> http://meta.bioinfo.pl/submit_wizard.pl >>> >>> XtalPred >>> http://ffas.burnham.org/XtalPred-cgi/xtal.pl >>> >>> Balbes http://www.ysbl.york.ac.uk/~fei/balbes/ >>> >>> use the OCA browser for FASTA searches of the PDB >>> >>> Modeller or Rosetta (both also available as web servers) >>> >>> ensemble of many proteins with Phaser >>> >>> FFAS server maintained by the Godzik lab >>> >>> generate some models using the "Phyre" server ( http://www.sbg.bio.ic.ac.uk/~phyre/ ) and feed the best .pdbs into Mr Bump. >>> >>> >>> >>> >>> >> - >> Jürgen Bosch >> Johns Hopkins Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> Johns Hopkins Malaria Research Institute >> 615 North Wolfe Street, W8708 >> Baltimore, MD 21205 >> Phone: +1-410-614-4742 >> Lab: +1-410-614-4894 >> Fax: +1-410-955-3655 >> http://web.mac.com/bosch_lab/ >> > > Associate Professor Ashley M Buckle > NHMRC Senior Research Fellow > The Department of Biochemistry and Molecular Biology, > Faculty of Medicine > Monash University, Clayton, Vic 3800 > Australia > > http://www.med.monash.edu.au/biochem/staff/abuckle.html > iChat/AIM: blindcaptaincat > skype: ashley.buckle > Tel: (613) 9902 9313 (office) > Fax : (613) 9905 4699 > mobile: 0430 913031 > >