Hi, Yes, zero origin is a sure sign that it hasn't identified the atoms in the TLS group.
There is presumably some problem matching atom names, but am not sure what. If you send me the files, I can have a play. However, you might have problems with the group definitions anyway. I seem to remember that TLS is not stable for 3 atoms. In any case, you have more TLS parameters (20) than anisotropic parameters (3*6). It does sound like that's what they did in the Nat. Struct. Biol. but they seem to have deposited the pre-TLS coordinates from CNS, so hard to tell. Cheers Martyn On Thu, 2010-07-15 at 15:54 +0100, Huw Jenkins wrote: > Hi, > > I am currently refining some reasonably high (1.4-1.6 Å) resolution > protein:RNA complex structures and was trying the approach described > in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they > divided each nucleotide into three TLS groups – the ribose, the > phosphorus atom plus both nonesterified oxygens and the base. > > When I define a tlsin file that does this with the ribose, P OP1 and > OP2, and base from 3 successive nucleotides everything seems to work > fine so the groups are defined correctly. However when I divide a > single nucleotide into 3 TLS groups only the first group has its > origin calculated and actually has TLS parameters refined: > > > TLS origin for group 1 -3.1622999 -6.9280601 -9.6330261 > > TLS origin for group 2 0.0000000 0.0000000 0.0000000 > > TLS origin for group 3 0.0000000 0.0000000 0.0000000 > > > TLS group 1: > > T tensor ( 1) = 0.046 0.115 0.103 -0.003 -0.008 0.087 > L tensor ( 1) = 1.341 1.887 5.684 0.509 -2.040 -0.436 > S tensor ( 1) = 0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 > 0.060 > > TLS group 2: > > T tensor ( 2) = 0.031 0.031 0.031 0.000 0.000 0.000 > L tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000 > S tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > TLS group 3: > > T tensor ( 3) = 0.031 0.031 0.031 0.000 0.000 0.000 > L tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000 > S tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > > An excerpt from my tlsin is below: > > TLS > RANGE 'B 3.' 'B 3.' P > RANGE 'B 3.' 'B 3.' O1P > RANGE 'B 3.' 'B 3.' O2P > > TLS > RANGE 'B 3.' 'B 3.' C1* > RANGE 'B 3.' 'B 3.' C2* > RANGE 'B 3.' 'B 3.' C3* > RANGE 'B 3.' 'B 3.' C4* > RANGE 'B 3.' 'B 3.' C5* > RANGE 'B 3.' 'B 3.' O2* > RANGE 'B 3.' 'B 3.' O3* > RANGE 'B 3.' 'B 3.' O4* > > > TLS > RANGE 'B 3.' 'B 3.' N1 > RANGE 'B 3.' 'B 3.' C2 > RANGE 'B 3.' 'B 3.' O2 > RANGE 'B 3.' 'B 3.' N3 > RANGE 'B 3.' 'B 3.' C4 > RANGE 'B 3.' 'B 3.' O4 > RANGE 'B 3.' 'B 3.' C5 > RANGE 'B 3.' 'B 3.' C6 > > I guess I've got the syntax of the tlsin file wrong? Any suggestions for > what's wrong would be much appreciated! > > Thanks, > > > Huw > > > > -- > Dr Huw Jenkins > Astbury Centre for Structural Molecular Biology > University of Leeds -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603634 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
