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: [email protected] Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm -----Original Message----- From: Sabine Schneider [mailto:[email protected]] 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:[email protected]] Sent: 20 April 2011 14:33 To: david lawson (JIC) Cc: [email protected] 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: [email protected] <mailto:[email protected]> > Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm >
