I don't think should be an "option". I don't think there is any case
for SSM in NCS detection: it _must_ in register, or it's not NCS
Phil
On 8 Dec 2008, at 09:42, Bernhard Lohkamp wrote:
Currently there is the option to use the manual_ncs_ghosts function
Paul
mentioned in the last email.
I have already made an LSQ option for NCS detection which sits on my
hard drive and will be included in due time (next few hrs/days),
certainly for 0.5.1!
Bernhard
***************************************************
Dr. Bernhard Lohkamp
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487673
fax: (+46) 08-327626
email: [EMAIL PROTECTED]
----- Original Message -----
From: Phil Evans <[EMAIL PROTECTED]>
Date: Monday, December 8, 2008 10:36 am
Subject: Re: [COOT] defining NCS-related chains
To: [email protected]
On the subject of NCS chains, Paul, I note that you are still using
SSM superposition in determining NCS operators (unless it's been
changed _very_ recently), rather than the LSQ algorithm which would
preserve the sequence register. SSM gets the wrong answer in some
cases, eg in some coiled-coil proteins such as BAR domains, where
an
out-of-register SSM superposition can give a lower score than the
in-
register one, and of course the correct NCS must be in register.
You did say quite a long time ago that you going to change this :-)
Best wishes
Phil
