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
