Hi Yanming,
I am glad that at least one other person has encountered this problem
so I do not feel too guilty for having asked Paul to do something about
it. Anyway, the MAN was kind enough to add a masking function under the
Extensions Menu. It is something called 'Mask map bla bla..'. (I am not
in the office so I can't read the proper name of the function). It uses
mmdb code to define Chains/atoms/.... that you want to exclude from map
calculations and produces a map masked by them. (For example if all
your metal centres are chain M something like M/* removes all of them).
Very useful imo for refining metal centers at low resolution.
Roberto
Quoting Yanming Zhang <[EMAIL PROTECTED]>:
Hi,
After JED's email I tried immediately:
case:
a metal site which has very strong density and a HIS co-ordinating
with the ion. After I click 'Real space refine zone' and then the
residue HIS, the HIS will move to the density which belongs to the
ion(clash with the ion) no matter how low the weight was set.
PS, I remember that Xfit of XtalView has the beauty to avoid this
kind of problem, but now I am a regular user of coot.
Thanks
Yanming
On Tue, 29 May 2007, Debreczeni, Judit wrote:
Unreasonable geometry can be avoided by setting the refinement
weight to a lower value -- either using Extensions->Set Matrix
(Refinement Weight) or in your .coot file:
(set-matrix <value>)
There's also a coot-bb, btw.
JED
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
Yanming Zhang
Sent: 29 May 2007 01:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] A babyish question on coot
Hi,
I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about the
'real space'(Electron density), sometimes it will bring the model to
the density no matter whether the density was already claimed by other
model atoms or not, resulting in clash and unreasonable geometry. How can
I avoid this?
Sorry for an old crystallographer to ask so babyish question. But your
help can save me lots of time.
Thanks
Yanming
--
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail [EMAIL PROTECTED]
