Thanks for all the good suggestions. This gives me a lot more things to try.
Ursula On Sat, Dec 13, 2014 at 2:44 AM, Claudia Millán Nebot <[email protected]> wrote: > > Dear Ursula, > > If you have a resolution around 2.0 A you can try some of the following: > > - Expand the partial solution with shelxe autotracing feature. > > - Do a search with ARCIMBOLDO_LITE using the partial solution. You can fin > the program at http://chango.ibmb.csic.es/arcimboldo_lite. Then, instead > of searching for ideal alpha helices, you can input your solution and > search for 2 copies. > > Hope it helps. Best, > > Claudia > > > ---------------------------------------------------------------------------------------- > > Claudia Millán ([email protected]) > > Crystallographic Methods Group > > http://chango.ibmb.csic.es > > Institut de Biologia Molecular de Barcelona (IBMB-CSIC) > > Barcelona, Spain > > LinkedIn: es.linkedin.com/in/claudiamillan/ > <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> > > ResearchGate: > https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf > > > > 2014-12-12 22:38 GMT+01:00 Ursula Schulze-Gahmen <[email protected]> > : >> >> I am trying molecular replacement with a very poor model. The model >> consists mainly of 1 long helix and two slightly bent antiparallel helices. >> After dividing it into 2 fragments, I was able to find a solution for one >> of the fragments ( at least I think so after looking at maps, packing, >> refinement etc). But even if I place the first solution as fixed ensemble >> in phaser, I cannot find a solution for the second fragment ( 18% sequence >> identity). From the structure of the model and the packing it seems clear >> where the fragment should go roughly. >> >> Are there any other programs other than phaser that might be able to >> solve this problem? I tried already epmr and mr_rosetta without success. >> I also tried to just superimpose the complete model onto the partial >> solution. This results in quite nice packing, but doesn't refine. Is there >> a rigid program refinement program with very large convergence? >> >> Ursula >> >> -- >> Ursula Schulze-Gahmen, Ph.D. >> Project Scientist >> UC Berkeley, QB3 >> 360 Stanley Hall #3220 >> Berkeley, CA 94720-3220 >> (510) 643 9491 >> > -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
