Dear Sabine and Ed,
The masking option does the trick!
Many thanks,
Dave
PS. the Arg side-chains do have their own density, it's just not as strong as that for the DNA.
-------------------------------
Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [log in to unmask]
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm
-----Original Message-----
From: Sabine Schneider [mailto:[log in to unmask]]
Sent: 20 April 2011 14:05
To: david lawson (JIC)
Subject: Re: problems building low resolution protein-DNA complex
Hello Dave,
you could try masking the map by the DNA Extensions-> Maps -> Mask map
by atom selection and use the masked map for RSR.
Alternatively one could put the 'head' of the Arg where it should be and
fix the NH1 NH2 or CZ at the position, followed by RSR of thr rest.
Sabine
----------
-----Original Message-----
From: Ed Pozharski [mailto:[log in to unmask]]
Sent: 20 April 2011 14:33
To: david lawson (JIC)
Cc: [log in to unmask]
Subject: Re: problems building low resolution protein-DNA complex
On Wed, 2011-04-20 at 13:57 +0100, david lawson (JIC) wrote:
> I am building and refining a protein-DNA complex at 3 Ang resolution
> and having a bit of trouble with side-chains that interact with DNA.
> In particular Arg side-chains that H-bond to the phosphate backbone
> tend to get dragged into the phosphate density when I do real space
> refinement. I have tried playing about with the weight matrix in the
> R/RC menu, but this doesn't seem to help much. I am running version
> 0.6 for Mac (Miramar revision 2540).
Look at Extensions->Maps->Mask map by atom selection. This should
exclude phosphates from the map.
But if these arginines do not have "their own" density to latch on, some
people would say you should not model them at all.
Good luck,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
david lawson (JIC) wrote:
>
> Dear All,
>
> I am building and refining a protein-DNA complex at 3 Ang resolution
> and having a bit of trouble with side-chains that interact with DNA.
> In particular Arg side-chains that H-bond to the phosphate backbone
> tend to get dragged into the phosphate density when I do real space
> refinement. I have tried playing about with the weight matrix in the
> R/RC menu, but this doesn't seem to help much. I am running version
> 0.6 for Mac (Miramar revision 2540).
>
> Any help much appreciated.
>
> Thanks
>
> Dave
>
> -------------------------------
>
> Dr. David M. Lawson
> Biological Chemistry Dept.,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Fax: +44-(0)1603-450018
> Email: [log in to unmask] <mailto:[log in to unmask]>
> Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm
>
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