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

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@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

CCP4BB Home

CCP4BB Home

CCP4BB  December 2007

CCP4BB December 2007

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

From:

Edward Berry <[log in to unmask]>

Reply-To:

Edward Berry <[log in to unmask]>

Date:

Tue, 18 Dec 2007 22:22:02 -0800

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (134 lines)

Zheng Zhou wrote:
> Hi, Ed
> 
> I am dealing the similar problem. I checked CNS qindividual.inp. But how 
> do I refine one compound with two or more possible conformations (mainly 
> due to one bond rotation), each of wihich has a different occupancy? 
> Thanks in advance.
> 
Hi Zheng,
Others can answer better than I, but for what it's worth:
You have basically two methods for refining alternate,
possibly overlapping, models.
One is the "alternate conformations" formalism which I have
not used but is documented in the CNS FAQ
http://cns.csb.yale.edu/v1.2/faq/text.html#xtal_refine
(search for:
Q. How do I deal with alternate conformations in my refinement? )

The other way is by modeling both structures (with different chain
letter or range of residues or something) and turn off vdw
interactions between the two entities which never occur
simultaneously in the same unit cell using the igroup statement.
Some hints can be gleaned from the answer to this different question
(in the same FAQ):

Q. My structure contains a molecule which lies across a symmetry operation. This means that some parts of the molecule are mapped onto each other by symmetry. It is not a 
special position case, because no one atom lies on the symmetry operation exactly. How can I tell CNS to refine the molecule while allowing the overlap to occur?
A. You can use the igroup statement to turn the pvdw (Packing-Van-der-Waals) interactions off by setting the weight to zero:
   -------------------

Syntax for the statement is something like: interaction (selection1 selection2)
    means for it to check interaction between each atom in selection1 with
    each atom in selection2. What I am using (with CNS 1.1) is:

  igroup
    interaction ( &atom_select and not (segid "M" or segid "Z" or attr store9 > 0))
                ( &atom_select and not (segid "M" or segid "Z" or attr store9 > 0))

    interaction ( &atom_select and not (segid "E" or attr store9 > 0))
                ( segid "M")
    interaction ( &atom_select and not (segid "R" or attr store9 > 0))
                ( segid "Z")
{
    interaction ( segid "E   ") ( segid "M   ") weights * 1.0 pvdw 0.0 end
    interaction ( segid "R   ") ( segid "Z   ") weights * 1.0 pvdw 0.0 end
}	

    evaluate ($alt=1)
    while ( $alt <= $nalt ) loop alcs
      interaction ( &atom_select and ( attr store9 = $alt or attr store9 = 0 ))
                  ( &atom_select and ( attr store9 = $alt ))
      evaluate ($alt=$alt+1)
    end loop alcs
  end

Here segid M and Z are the same subunits as E and R, but in alternate conformations.
Store9 has to do with the formally declared alternate conformations (see "atom selection").

The first interaction statement ignores M and Z and checks interaction of everything
else with everything else. The second checks interaction of everything in M with
everything except its alternate self E; the third checks Z with everything except R.
I see I have {commented out} the section that sets pvdw weights to zero between
alternate conformations of the same thing, but I'm not sure if this is right.
It may be this is not needed since we avoid checking those interactions, but I think
at one point we were turning off the NBONDS messages but not the vdw interaction,
so there may be two separate things needed here. I would be glad for any clarification.
Ed
> 
> On Dec 17, 2007 2:24 PM, Edward Berry <[log in to unmask] 
> <mailto:[log in to unmask]>> wrote:
> 
>     I think the correlation between occupancy and B-factor depends
>     also on the size of the ligand (relative to resolution).
>     Bob Stroud, I think, has estimated occupancy by comparing
>     the integrated electron density of the ligand with that of
>     a well-defined, isolated water (assumed to be at unit occuancy?).
> 
>     In principle the integrated electron density is not affected
>     by applying a B-factor, it is just spread out over a wider
>     area. In the case of a single atom at 3 A resolution, it
>     is spread out under the neighboring atoms and effectively
>     lost, so it is hard to distinguish high B-factor from low
>     occupancy.
>     In a large ligand most of the atoms are inside the ligand,
>     so their spread-out density remains inside the ligand
>     and gets counted in the integrated density. In that case
>     high B-factor has a very different effect than low occupancy,
>     as only the latter reduces the total electron density of
>     the ligand.
> 
>     During a previous reincarnation of this thread I did the
>     simple test of refining occupancy and B-factor for a
>     stretch of the protein (holding the rest of the protein
>     at unit occupancy) in CNS 1.1, and I felt the results
>     were quite satisfactory (don't have the specifics now).
> 
>     Ed
> 
>     Anastassis Perrakis wrote:
>      >> I have already changed occupancies as Eleanor mentioned, and got
>      >> approximate values. But my hope is to try to get much precise
>     ones if
>      >> possible.
>      >>
>      > I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
>      > but in this case what you need is more accurate answers, not more
>      > precise ones
>      > (or better both, but precision alone can be a problem, and you can
>      > easily get
>      > 'precise' but inaccurate data easily by making the wrong assumptions
>      > in your experiment)
>      >
>      > http://en.wikipedia.org/wiki/Accuracy
>     <http://en.wikipedia.org/wiki/Accuracy>
>      >
>      >> I have heard from my colleague SHELX can refine occupancies, and
>      >> got its license. I'll next try SHELX.
>      >
>      > I think that phenix.refine can also do occupancies ?
>      > The problem is not  if the program can do it, but if at your
>     specific case
>      > you have enough information to do that in a meaningful way.
>      >
>      > For a soaking experiment and 1.5 A data, I would say that Eleanor's
>      > suggestion
>      > of tuning Occ based on B, is as close as you would get, accurate
>     enough
>      > given the data,
>      > although not necessarily too precise.
>      >
>      > Tassos
> 
> 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
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