JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for COOT Archives


COOT Archives

COOT Archives


COOT@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

COOT Home

COOT Home

COOT  July 2009

COOT July 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Refine zone set-matrix

From:

Stephen Graham <[log in to unmask]>

Reply-To:

Stephen Graham <[log in to unmask]>

Date:

Thu, 16 Jul 2009 10:38:03 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (59 lines)

Incidentally, would it be possible to condense all of these options
into the one place?  In the regularisation/refinement dialog box that
is linked off the model/fit/refine toolbar???  At the moment these
controls seem to be scattered all over the place (and thus easy to
miss if you're a 'newbie').

Cheers,

Stephen

2009/7/16 Bernhard Lohkamp <[log in to unmask]>:
>> I'm working on a low resolution structure with less than ideal
>> maps. In an attempt to restrain the Refine Zone command to take
>> into account the geometry more I've tried playing with the
>> 'set_matrix' keyword through the Python Scripting window. I've
>> varied the value from 10-100, but the results of real space
>> refinement are always the same (ie more often than not the residues
>> are distorted beyond recognition in an attempt to fit them into the
>> density).
>
> I doubt the refinements are the same. What kind of Chi2 do you get for
> the different settings?
>
>> Combining Regularise Zone with Refine Zone doesn't help.
>> It may improve the geometry, but it often undoes any previous
>> fitting to the maps.
>> Any suggestions?
>
> Have you tried torsion angle restraints? And secondary structure
> restraints, Ramachandran restraints? Are planar peptide restraints
> switched on?
>
> B
>
> ***************************************************
>
> Dr. Bernhard Lohkamp
> Assistant Professor
> 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: [log in to unmask]
>



-- 
Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager