Hi Uma,
Altering sigma affects the strength of geometry restraints throughout the model
- bonds, angles, etc. Choosing a very low sigma will cause geometry to be more
tightly restrained towards ideal values, which is why you observe
improvements in Coot validation. Note that strengthening the
to relax the geometric
restraints too much.
Best regards,
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert
Nicholls
Sent: Friday, April 27, 2012 9:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and sigma value
Hi Uma,
Altering sigma affects
not prove that your model
is optimal. If you use too tight restraints you can end up hiding genuine
fitting errors.
Cheers,
Robbie
--
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4bb] Refmac and sigma value
To: CCP4BB
up hiding
genuine fitting errors.
Cheers,
Robbie
--
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4bb] Refmac and sigma value
To: CCP4BB@JISCMAIL.AC.UK
It all will depend on the resolution. At low resolution
Dear All:
I use Refmac5 to refine my structure model.
When I set the sigma value to 0.3 (as recommended from tutorial), the
resulted model has many red-bars by coot validation (geometry, rotamer,
especially, Temp Facotr).
I then lower the sigma value to 0.1, the resulted model is much improved
Hi, Alex:
Which sigma do you mean?
The one for automatic weight, not for Jelly-body refinement.
I did not turn the Jelly-body refinement on.
Thanks
Ros
On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote:
Hi Uma,
Which sigma do you mean? The one for Jelly-body
