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Oh dear, I refined some similar discontinuously-numbered structures in refmac and got the automatically generated gap links, and like Bernhard, I presumed these were intended to set peptide link restraints. Unfortunately I did not notice by eye any deviation from normal peptide bond distances, but now that I go back and check, I see that the gap link distances are in the range of 1.35-1.38A, while the properly restrained peptide links are 1.32-1.33A. Ah well, thanks for the information, and I will know better next time. Regards, Evette Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-2857 (lab) -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ulrich Englich Sent: Wednesday, August 09, 2006 9:37 AM To: [EMAIL PROTECTED] Cc: [email protected] Subject: Re: [ccp4bb]: gap links *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Dear Bernhard: just came across the same problem yesterday. There is a message way back in ccp4bb, but the problem still seems to exist: http://www.ysbl.york.ac.uk/ccp4bb/2003/msg00678.html After moving TRANS to the right position I got peptide bonds of a more reasonable distance...the word "gap" is slightly misplaced! Best, ulrich http://www.ysbl.york.ac.uk/ccp4bb/2003/msg00678.html >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >Dear Refmacers, > >I run refmac 5.2.0019 on a structure with sequence gaps. >Refmac finds those and enters the proper gap links >LINK ASN A 34 SER A 37 gap >LINK LEU A 67 GLY A 69 gap >LINK THR A 125 SER A 127 gap >LINK SER A 130 ALA A 132 gap >LINK GLY A 189 LYS A 192 gap >LINK LYS A 208 LEU A 213 gap >LINK SER A 221 GLY A 223 gap >LINK ALA A 225 GLN A 227 gap > >but does not seem to use them, the link distances are all over the place. > >The log also says the links were created, without the '(not to be used)' >statement it >usually gives when it does detect links but does not use them. > >If I renumber the residues consecutively, it restrains the links >properly and all is fine. > >???? > >Thx, br > >-------------------------------------------- >Bernhard Rupp >www.ruppweb.org >-------------------------------------------- -- -- \|/ (o o) --------------------------oOO--(_)--OOo------------------------- www.macchess.cornell.edu Dr. Ulrich Englich Tel: 607-255 9386 209 Biotechnology Building Fax: 607-255 6249 Ithaca, New York 14853 E-mail: [EMAIL PROTECTED] ---------------------------------------------------------------- *** This message was written entirely with recycled electrons ***
