[phenixbb] modify the helices

19 Jul 2010


      hi everyone:
   Thanks for all the response!
   what I said last time may be chinglish and lead to some misunderstanding,
the word I said fix a helix means that the model quality of the helix is not
very good, I want to modify it manually.It is so hard to do this in  low
resolution.I modified the helix according to the electron density map, after
refinement, large red areas appear in the difference map. That made me
crazy!
  Are there any suggestions or any reviews about this point?
  I am new beginner to structural biology,  any suggestions are welcomed !

Best regards

Xinghua Qin


  Xinghua Qin
  College of Biological Sciences
  No.2, Yuan Ming Yuan West Road
  Haidian District?Beijing?China?100094
  Tel: +86-10-62732672
...
Message: 2
Date: Fri, 16 Jul 2010 22:10:32 -0700
From: Pavel Afonine 
To: PHENIX user mailing list 
Subject: Re: [phenixbb] sum(occ)<1?
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ed,
...
Reset occupancies that are outside the [0,1] range at every step of
minimization.
this simply will not work: this will invalidate the internal memory of
LBFGS minimizer that we use in phenix.refine and as result it will drive
it crazy.
Pavel.
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Message: 3
Date: Fri, 16 Jul 2010 22:24:35 -0700
From: Pavel Afonine 
To: PHENIX user mailing list 
Subject: Re: [phenixbb] how to fix a secondary structure?
Message-ID: <[email protected]>
Content-Type: text/plain; charset=UTF-8; format=flowed
Hi Xinghua,
you can use secondary structure restrains that are available in
phenix.refine. It will automatically figure out secondary structure and
apply proper restrains. This should preserve your helix geometry and
still refine it.
Example:
phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true
...
Recently I am trying to fix a helice, but found that it is so hard
for me because of the poor resolution(3.2A) and also a unvisible loop
near it, so is there any way to just fix a helice ? can I get it out
of the whole structure to refine it?
If you still prefer not refining that helix over applying
secondary-structure restrains, then you can do that too:
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A
and resseq 123:156)"
where atom selection
chain A and resseq 123:156
selects your helix, and prefix "not" means you exclude it from refinement.
Of course you can do all this from PHENIX GUI.
Let me know if you have any questions.
Pavel.
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Message: 4
Date: Fri, 16 Jul 2010 22:48:52 -0700
From: Pavel Afonine 
To: PHENIX user mailing list 
Subject: Re: [phenixbb] how to fix a secondary structure? - P.S.
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
By the way, more information about secondary structure restraints in
phenix.refine you can find in recent PHENIX Newsletter (pages 12-17):
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
Pavel.
On 7/16/10 5:52 PM, xinghua qin wrote:
...
Hi phenixers:
    Recently I am trying to fix a helice, but found that it is so hard
for me because of the poor resolution(3.2A) and also a unvisible loop
near it, so is there any way to just fix a helice ? can I get it out
of the whole structure to refine it?
Best regards
Xinghua Qin
--
Xinghua Qin
College of Biological Sciences
No.2, Yuan Ming Yuan West Road
Haidian District?Beijing?China?100094
Tel: +86-10-62732672
------------------------------