John, ????????? Thank you for your input. The residue positional database seems to be working.? I got out structures that are a little closer to what one would expect for an RNA-DNA hybrid. However, I am unable to get the NCS restraints to work. My problem seems to be this: in all the examples I have looked up, the degree of symmetry seems to be higher (e.g. near or perfect palindromes, for instance). In my case, the RNA is mostly purines, and the DNA is mostly pyrimidines. I? deselected the H2' s and a few of the O2' so that the number of atoms selected would be the same. A portion of my output from a test script I have been using is given below. How does one successfully apply the NCS restraints in this case?
test3.py(8): xplor.command(r""" ?X-PLOR> ?X-PLOR>ncs restraints ?NCS-restraints>? initialize ?NCS-restraints>?? group ?NCS-restraints-group>???????? equi (segid RNA and not name H2' and not (resid 12:20 and name O2')) ?SELRPN:??? 628 atoms have been selected out of?? 1285 ?NCS-restraints-group>???????? equi ((segid DNA) ) ?SELRPN:??? 628 atoms have been selected out of?? 1285 ?%NCS-ERR: For NCS group? 1, equivalence set? 2, atom???? 1 : ?RES = ADE , while RES from set 1 = THY ?%NCS-ERR: For NCS group? 1, equivalence set? 2, atom???? 2 : ?RES = ADE , while RES from set 1 = THY Thank you again for your help. Robert ----- Original Message ----- From: John Kuszewski <[email protected]> Date: Monday, July 2, 2007 4:43 pm Subject: Re: [Xplor-nih] RNA-DNA Hybrid To: brinson at umbi.umd.edu Cc: xplor-nih at nmr.cit.nih.gov > Hi Robert, > > A few obvious issues that eginput/dna_refi/refine_full.py would > have? > with a DNA-RNA hybrid: > > 1.? Unless you were careful with your selections, the NCS > symmetry? > term will fail during setup > because the two equivalent groups (the DNA strand and the RNA > strand)? > have different numbers > of atoms. > > The solution for this would be to select everything except the > 2' H? > or OH groups. > > 2.? Another problem would be in the setup of the residue- > residue? > position database term.? Since the > code in eginput calls the DNA version, the setup script will > fail? > (perhaps without giving any visible > warning) when it encounters a URA residue type. > > There's no perfect solution for this issue.? There are > separate? > potential surfaces for DNA and RNA, > and since the number of DNA-RNA hybrids in the PDB is rather > small,? > there's no practical way to create > one for the hybrid. > > That said, if you think that the DNA-DNA residue position > database? > would be reasonably accurate (and > it probably would be), you could trick the setup script into > running? > by temporarily changing the residue > type of your Us to Ts: > > xplor.command(""vector do (resn = "ADE") (resid 14 or > resid? > 21)"")???????? # if > resids 14 and 21 are Us > xplor.command("@dna_positional.setup") > xplor.command(""vector do (resn = "URA") (resid 14 or resid 21)"") > > > Note that the torsion angle database term is insensitive to DNA > vs? > RNA issues, so it should be OK. > > Hope this helps. > > --JK > > On Jul 2, 2007, at 2:57 PM, <brinson at umbi.umd.edu> wrote: > > > Dear users of Xplor-nih, > >????????????? I am new to python and xplor and am trying to compute? > > a 20bp RNA-DNA hybrid. I have included the standard restraints > -? > > base/backbone NOEs, hydrogen-bond NOEs, dihedrals, and one set > of? > > RDCs. I created a decent starting structure using the > anneal.py? > > protocol. When I input that structure into refine_full.py from > / > > eginput/dna_refi, the helix seems to become overwound in the > middle? > > and underwound at the ends. I have tinkered with the > force? > > constants and temperature (from 3000 down to 300). I added > some? > > "anti"-noes (~20A at various locations, generated from > InsightII)? > > to try to help, but my output structures did not improve. > There are? > > no apparent errors in the output file.? I would > appreciate advice? > > on refining the structure. > > > > Thank you, > > Robert > > _______________________________________________ > > Xplor-nih mailing list > > Xplor-nih at nmr.cit.nih.gov > > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070705/29599793/attachment.html
