James, The "stars" are atoms in a residue that are no longer within recognizable bonding distances of other atoms. Somewhere along the way these residues were mangled to the point that some atoms are no longer within bonding distance of each other. (In Refmac, for example, this can happen if the X-ray weighting term is too high for the resolution of the data,and atoms start "wandering off" during refinement.)
I'm not terribly familiar with Molrep, but most MR programs do rigid body searches, and do not normally alter the geometry of the search model. Is the original search model geometrically correct? Whatever the cause, you can at least snap residues back into line by doing a "regularize zone" in Coot. That should round up all the wayward atoms. 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: [EMAIL PROTECTED] -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of James Pauff Sent: Thursday, May 24, 2007 9:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] another quick question... Good day all, In COOT, when I view my coordinate pdb file with my ccp4 map file (using "Auto-open mtz"), I have a couple residues for which only a part of the peptide chain is visible. E.g. for a Lys, only the terminal nitrogens at the end of the R-group chain are visible as bonds. The other parts of the residue (and even parts of adjacent residues) are visible only as stars/stellate points that may or may not be within my blue electron density. If I click on the stars, the atom names that appear are consistent with the missing peptide chain, and correspond to the "missing" amino acid that has the occassional visible R group. Just wondering what this means, that I am seeing stellate points that seem to be acting as place holders for my residues in a couple locations in my structure. The structure was obtained using molrep. Thank you, James Pauff ________________________________________________________________________ ____________Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC
