P4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> ???
> Sent: Thursday, June 20, 2019 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] RAMACHANDRAN outlier of Thr
>
> Dear all
>
> The problem is when I check RAMACHANDRAN outlier with coot, it shows
>
Dear all
The problem is when I check RAMACHANDRAN outlier with coot, it shows zero,
while it become one Thr outlier in phenix.vadition. so I am confusing about the
standard of RAMACHANDRAN outlier in coot and phenix.validation, any difference
between them? Thanks
yours
shijun
##
But turn on the Ramachandran restraints in the box..
And ALWAYS make sure there is no obvious error before trying it - CISPEP? -
missing density etc..
Eleanor
On 21 January 2015 at 06:23, Dialing Pretty <
03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear All,
>
> Real space refinem
Dear All,
Real space refinement in COOT is one important strategy to reduce Ramachandran
outlier, right?
Dialing
I don't think, online server of autobuster is available. It is freely
available, you can install it and run locally.
https://www.globalphasing.com/buster/manual/autobuster/manual/index.html
Atul
On 1/13/15, rohit kumar wrote:
> Hi,
> Is Autobuster a online server?
> On 13-Jan-2015 2:27 pm, "Atu
Hi,
Is Autobuster a online server?
On 13-Jan-2015 2:27 pm, "Atul Kumar" wrote:
> Dear Rohit,
>
> You can follow the way Tim suggested. At low resolution and for disordered
> regions, autobuster works well for refinement.
>
> Atul
>
> On Tue, Jan 13, 2015 at 7:47 AM, Tim Gruene
> wrote:
>
>> Dea
Dear Rohit,
You can follow the way Tim suggested. At low resolution and for disordered
regions, autobuster works well for refinement.
Atul
On Tue, Jan 13, 2015 at 7:47 AM, Tim Gruene wrote:
> Dear Rohit Kumar Singh,
>
> you can remove a couple of residues before and after the outlier and
> reb
Dear Rohit Kumar Singh,
you can remove a couple of residues before and after the outlier and
rebuild it. You can also switch on Ramachandran restraints in Coot and
run real-space refinement. If this does not help, I would delete a
single residue within the region in question, run real-space refine
Hello all,
if outlier is in between 5 to 6 %, how someone can fix it.
As the resolution is low (3.0-3.5 A).
On Mon, Jan 12, 2015 at 7:53 PM, Robbie P. Joosten wrote:
> Hi Dialing,
>
> 86% favoured can actually be quite okay for an initial model. As long as
> it doesn't have 14% in the disallowe
Hi Dialing,
86% favoured can actually be quite okay for an initial model. As long as
it doesn't have 14% in the disallowed region, the vast majority of
residues will be correct, or close enough to the correct answer that
they can be fixed easily. Of course, such a model will need tweaking,
bu
Dear All，
If an initial PDB has only 86% residues in the Ramachandran favored region, it
would mean there is a significant error (for example significant length of
protein fragment in the total protein assigned to the wrong electron density
map position) , right?
Dialing
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