Re: [ccp4bb] A babyish question on coot
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 ) 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]
Re: [ccp4bb] A babyish question on coot
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:[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
Re: [ccp4bb] A babyish question on coot
It is actually a question of 'adult-crystallographer' addressing a 'baby-coot' ;-) I also have that problem - and moreover I had it when programming real space refine in ARP/wARP ages ago. An elegant solution now is the one implemented by Serge Cohen in my group, to use a map that has the density of the part of the model that is not to be refined (and is 'claiming density') subtracted from the real map. This way atoms will not go to existing density and can not create a 'steric class'. This trick - which Alwyn uses since the dawn of crystallographic time in O rs fit as far as I know - is computationally quite cheap in our case (we know a priori what to refine and what not). In the coot case that map has to be generated every time you refine a zone, but it will be quick. A. PS If Paul wants to try our code (we use clipper anyway) I am sure your email can motivate him to get in contact ;-) ...he already owes us a visit to get going with some general plans. ;-) On 29 May 2007, at 3:54, Josiah Obiero wrote: Try alternate rotamers first, and then choose the closest to the 'right' electron density, before you do 'real space refine' Regards, Josiah. 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
Re: [ccp4bb] A babyish question on coot
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:[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
Re: [ccp4bb] A babyish question on coot
Optimize zone is also a good choice. Just drag it to the right conformation. Hold Ctrl to drag only one atom. If you include a region for real space refinement, there will be no clashes between amino acids in the region. Nian On 5/28/07, Yanming Zhang <[EMAIL PROTECTED]> wrote: 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
Re: [ccp4bb] A babyish question on coot
Try alternate rotamers first, and then choose the closest to the 'right' electron density, before you do 'real space refine' Regards, Josiah. 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] 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
