9781555819217
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vipul Panchal
[panchal.vi...@igib.in]
Sent: Sunday, July 02, 2017 12:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement
I do agree with Eleano
Of course - none of us has given the best advice of all! Try to find a
better ordered crystal!
Eleanor
On 2 July 2017 at 19:59, Matthias Barone wrote:
> Beside the good propositions of fixing the environment, flip the peptide,
> or using PDB_REDO, I would suggest the following additional attem
Beside the good propositions of fixing the environment, flip the peptide, or
using PDB_REDO, I would suggest the following additional attempts:
Try
1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate
directly to Ala. See which ones remain visible in a diff map and bring them
I do agree with Eleanor. When I was solving structure at 2.16A resolution,
outlier residues were having stearic clash or required side chain flipping.
At 2.76A resolution, hydrogen bonds would be difficult to visulize.
I found phenix.refine more user friendly. You may too find it useful.
Vipul P
Just remember - most Ramachandran outliers are due to errors in the
environment - eg: maybe some side chains clash hence refinement tries to
move things to accommodate that bad feature, etc etc etc...
At that resolution it is inevitable you will have some level of
mis-interpretation ..
4% outliers
Dear Meytal,
PHENIX-REFINE has an option for Ramachandran outlier refine. If you check
this on, it will do the work. But after this refinement, you must check
every residues to make sure residues are in the density.
Thank you
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm La
Van: Meytal Galilee<mailto:meytal.gali...@gmail.com>
Verzonden: zondag 2 juli 2017 13:26
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: [ccp4bb] Ramachandran oultliers increase upon restrained refinement
Dear all,
I am refining a 2.76A structure using refmac5.
I
Dear all,
I am refining a 2.76A structure using refmac5.
I keep fixing the Ramachandran outliers down to 18 (1.9%), however, upon
restrained refinement, the outliers increase back to 35.
Do you have any suggestions how can I fix my structure?
Thanks,
Meytal Galilee
