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CCP4bbers, I am trying to do a restrained refinement in refmac using a rhenium tricarbonyl (RTC) fragment similar to the one in PDB 1I53. My understanding of how to proceed is to take the PDB description of the file, read it into sketcher, and then run libcheck to create the various cif and lib files in my local directory. Assuming I can get this to work (see below), then refmac should recognize the monomer files in the local directory from the residue name and use the proper restraints? Or do I need to explicitly read in the lib file(s) (e.g., libcheck_RTC.cif) in the LibIn field in CCP4i? I can read in the RTC PDB file below into sketcher and change the CO bonds to triple (they come up double on read-in), but then running libcheck dutifully makes the carbons sp2 and adds riding hydrogens. Arrrrgh. Running libcheck at the command line does the same thing with or without the HFLAG set. I would be grateful for any assistance/suggestions. I thought this would be an easy task... :) I must be missing something obvious. BTW, the RTC monomer in the HIC-UP server is incorrect: it is meridional instead of (the correct) facial geometry. THe PDB file below is correct. ATOM 1976 RE RTC B 905 39.199 36.612 61.900 1.00 20.26 RE ATOM 1977 O1 RTC B 905 41.664 36.504 60.063 1.00 20.75 O ATOM 1978 O2 RTC B 905 40.911 37.753 64.220 1.00 20.54 O ATOM 1979 O3 RTC B 905 39.925 33.794 62.879 1.00 20.49 O ATOM 1980 C1 RTC B 905 40.757 36.541 60.750 1.00 20.06 C ATOM 1981 C2 RTC B 905 40.269 37.327 63.349 1.00 20.00 C ATOM 1982 C3 RTC B 905 39.667 34.827 62.518 1.00 20.04 C Cheers, --
Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu |
