Re: [ccp4bb] AW: [ccp4bb] high Rfree

[Daniel Rigden]

Hi there

AMPLE works very well for coiled-coil structures, irrespective of 
parallel/anti-parallel etc


http://journals.iucr.org/m/issues/2015/02/00/lz5005/

Resolution permitting, SHELXE tracing and phase modification, built into 
the AMPLE pipeline, gives statistics that differentiate very clearly 
between success and failure.


I also understand that ARCIMBOLDO works very well for coiled-coils

Good luck

Daniel


On 21/07/17 08:37, herman.schreu...@sanofi.com wrote:


Hi ???,

Coiled coil structures can be very tricky with MR, so your solution 
may not be correct. You could try to split your search model and run 
MR with the separate coils. If you have high enough resolution (> ~2.3 
Å?) and your MR solution is basically correct, you may be able to 
solve your problem by rebuilding and refinement, but this may be a lot 
of work. Without any details (resolution of the data, current 
Rwork/Rfree etc.) it is difficult to give any more specific advice.


Best,

Herman

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag 
von *???

*Gesendet:* Freitag, 21. Juli 2017 03:17
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] high Rfree

Hi everyone

   I have got a anti-parallel coiled-coil structure in a short 
fragment recently, then I want to solve a longer fragment structure 
with phenix-MR using this short fragment structure as a model.The 
result is not good because of the Rwork and Rfree is high.So 
 
I think the longer fragment will be parallel coiled-coil which is 
different with the shorter one. I am wondering whether there are any 
other methods to handle this phenomenon besides heavy atom phasing? 
Thanks a lot!!!




--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.

[ccp4bb] AW: [ccp4bb] high Rfree

[Herman . Schreuder]

Hi ???,

Coiled coil structures can be very tricky with MR, so your solution may not be 
correct. You could try to split your search model and run MR with the separate 
coils. If you have high enough resolution (> ~2.3 Å?) and your MR solution is 
basically correct, you may be able to solve your problem by rebuilding and 
refinement, but this may be a lot of work. Without any details (resolution of 
the data, current Rwork/Rfree etc.) it is difficult to give any more specific 
advice.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ???
Gesendet: Freitag, 21. Juli 2017 03:17
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] high Rfree

Hi everyone

   I have got a anti-parallel coiled-coil structure in a short fragment 
recently, then I want to solve a longer fragment structure with phenix-MR using 
this short fragment structure as a model.The result is not good because of the 
Rwork and Rfree is 
high.So
 I think the longer fragment will be parallel coiled-coil which is different 
with the shorter one. I am wondering whether there are any other methods to 
handle this phenomenon besides heavy atom phasing? Thanks a lot!!!