Re: [ccp4bb] A babyish question on coot

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: A babyish question on coot
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-05-29

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Subject: Re: How to determine ligand binding from diffraction pattern?
From: "Gerhardt, Stefan" Stefan {- dot -} Gerhardt {- at -} ASTRAZENECA {- dot -} COM
Date: 2007-05-29

Subject: Re: A babyish question on coot
From: Yanming Zhang yzhang {- at -} MAILER {- dot -} SB {- dot -} FSU {- dot -} EDU
Date: 2007-05-29

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 )
>
> There's also a coot-bb, btw.
>
> JED
>
>
>
>
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On 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
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: A babyish question on coot
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-05-29

Next message:
Subject: Re: How to determine ligand binding from diffraction pattern?
From: "Gerhardt, Stefan" Stefan {- dot -} Gerhardt {- at -} ASTRAZENECA {- dot -} COM
Date: 2007-05-29