Kevin Thanks for the email :) On Aug 15, 2011, at 12:42 PM, Kevin Keating wrote:
> Francis, do you have CCP4 installed on this machine as well? What > version is it? CCP4 v 6.2.0 > Also, what's the naming on the newly created ideal RNA. Is it using * or ' > for prime? Here's a G when built with the Ideal RNA tool: ATOM 1 P G A 1 32.529 19.364 22.942 1.00 76.88 P ATOM 2 OP1 G A 1 32.785 18.497 24.119 1.00 78.59 O ATOM 3 OP2 G A 1 31.557 20.470 22.989 1.00 75.20 O ATOM 4 O5' G A 1 33.922 20.007 22.502 1.00 78.76 O It seems to be using the PDB3-style for naming the P's and sugar atoms. It also seems to have reverted from ' Gr' to ' G' for the residue name. Smells like CNS style naming. > > If your installation of CCP4 isn't the newest version (6.2), that may be > causing your problem. Starting with rev 3489, Coot switched from PDB2-style > naming of RNA (O1P, O2P, C1*, C2*, etc) to PDB3-style naming (OP1, OP2, C1', > C2', etc). However, if Coot finds CCP4 installed on the computer, it > defaults to using CCP4's monomer libraries. If CCP4 is 6.1 (or older), than > the monomer libraries will contain the old-style names and Coot will have > problems. > > When Coot launches, you should see a bunch of messages along the lines of: > There are 125 data in > C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/list/mon_lib_list.cif > There are 2 data in > C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/a/ALA.cif > There are 2 data in > C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/a/ASP.cif > If those messages point to Coot's directory, then your problem is different > from what I'm describing and you can safely ignore the rest of the e-mail. > If those messages point to CCP4 6.1's directory, then this is probably > causing your issues. > There are 2 data in /sw64/share/coot/lib/data/monomers/u/UR.cif Must be reading its own internal monomer library. The built RNA residues with the tool are inconsistent with the internal monomer library. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
