I'll also recommend Buccaneer. You might try using a combination of
PARROT for density modification and NCS averaging followed by
autobuilding with BUCCANEER using initial phases from your MR solution.
You only have two copies of the protein in the ASU, so you only get a
modest boost in electron density averaging, but maybe every little bit
helps. This approach was very successful for me with 8-fold NCS and a
29% identity search model that gave poor but usable initial MR phases
for 2.4A data.
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 10/25/2016 9:19 AM, Dmytro Guzenko wrote:
Hi Vikram,
Try Buccaneer, it works much better at such resolution than Arp/Warp.
Launch it several times with different parameters (e.g. use original
structure as seed/initial/nothing), then open the results together and
merge the pieces that look best and have lowest b-factors. Use Buster
for refinement of the merged model and iterate with Buccaneer again.
That's what worked for me once to bootstrap a poor MR solution (~20%
of the structure originally) to a near-complete model at 2.7A.
You are in a sense replicating what phenix.autobuild attempts to do,
but you'll be able to do it better (and probably faster) manually.
Kind regards,
Dmytro.
On 25/10/16 14:16, Vikram Dalal wrote:
Hi everyone,
We are trying to solve a protein structure of 2.6 A. We have
processed it with HKL2000. We have even tried processing with mosflm
and xia2. It is in C2221 space group (checked by pointless) and data
is not twinned. It has 31% identical with a search model and has 57%
sequence coverage. There are 2 subunits in asu.
I did not get proper phases with MOLREP and phaser. I have tried
Balbes (R free 50) and Mr BUMP (R free 54).But, density from balbes
look some reasonable.
So i have refined it in ccp4i and phenix differently and then model
build it by coot. My protein has 377 Amino acid. But, I stucked at R
free 41 and now i have amino acid 50 to 369 in both chains, still 49
amino acid at N terminal and 8 amino acid at C terminal are missing
and some loops are missing in between too.
*I have tried the ARP/wARP, but it does not work for it. *
*
*
*I have even tried phase and build of phenix but condition remain
same. i got stuck at R free at 42 and same around 49 amino acids at N
terminal and 8 amino acids at C terminal and some internal loops
still absent.*
*
*
*Thank you in advance.*
*
*
