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Re: [ccp4bb] A babyish question on coot |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: A babyish question on coot From: Roberto Steiner roberto {- dot -} steiner {- at -} KCL {- dot -} AC {- dot -} UK Date: 2007-05-29 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 > 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 >> > -- 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 roberto.steiner@kcl.ac.uk CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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