Dear Ursula
AMPLE is also worth trying, especially but not exclusively for smaller
and predominantly helical targets. It was originally conceived for
novel folds but you may well find ab initio modelling methods get closer
to the real structure of distant homologs than the nearest available
templates. AMPLE will produce a range of search models of different
sizes, through clustering and truncation of a model set, and this
sampling can be helpful. You can install Rosetta for the modelling or,
thanks to Yang Zhang's efforts, take a tar file direct from his Quark
server (http://zhanglab.ccmb.med.umich.edu/QUARK/) and give it to AMPLE.
Higher resolution helps generally, but we have had success out to 2.9A.
Good luck
Dan
On 13/12/14 10:44, Claudia Millán Nebot 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 (cmn...@ibmb.csic.es <mailto:cmn...@ibmb.csic.es>)
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/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
<uschulze-gah...@lbl.gov <mailto:uschulze-gah...@lbl.gov>>:
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
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Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220 <tel:94720-3220>
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