Dear Fred The cryptic sentence is generated in one of the CCP4 Fortran library routines (SFREAD2 in rwbrook.f), rather than in Refmac itself. It is the same message that you encountered when running Truncate.
What it means that the code has encountered an atom name of '-'. (this is the origin of the minus sign in the middle of the message; it is not a hyphen). It is trying to match this name to one of the atom names in atomsf.lib, and failing. If it cannot find a match, it removes the rightmost character from the atom name and tries again. This doesn't work for '-' as you end up with nothing, but if the atom name was say 'Cl-' and 'Cl' was in the library, but 'Cl-' was not, then it would work. Norman -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Vellieux Frederic Sent: 14 October 2009 14:27 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] run of Refmac5 (latest version of CCP4) Dear all, I have a structure (2.25 A resolution) that was refined with CNS and I'm trying to see if I can improve it ever so slightly using Refmac5. The structure has 31408 atoms in the asymmetric unit. The run of Refmac ends with the following lines: WARNING : link:SS is found dist = 2.063 ideal_dist= 2.031 ch:LL res:3872 CYS at:SG .->LL res:3873 CYS at:SG . INFO: link is found (not be used) dist= 2.142 ideal_dist= 1.990 ch:LL res:3813 ASP at:OD2 .->ch:Nv res:3995 ZN at:ZN . INFO: link is found (not be used) dist= 2.188 ideal_dist= 1.990 ch:LL res:3846 GLU at:OE2 .->ch:Nv res:3995 ZN at:ZN . INFO: link is found (not be used) dist= 2.317 ideal_dist= 2.070 ch:LL res:3947 HIS at:NE2 .->ch:Nv res:3995 ZN at:ZN . INFO: link is found (not be used) dist= 2.259 ideal_dist= 2.070 ch:LL res:3702 HIS at:NE2 .->ch:Nw res:3996 ZN at:ZN . INFO: link is found (not be used) dist= 2.180 ideal_dist= 1.990 ch:LL res:3813 ASP at:OD1 .->ch:Nw res:3996 ZN at:ZN . INFO: link is found (not be used) dist= 2.177 ideal_dist= 1.990 ch:LL res:3868 ASP at:OD1 .->ch:Nw res:3996 ZN at:ZN . <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> Refmac_5.1.24: No match for full atom ID - subtract one character Times: User: 47.5s System: 0.1s Elapsed: 0:48 </pre> <!--SUMMARY_END--></FONT></B> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> </html> <!--SUMMARY_END--></FONT></B> It ends without creating an output PDB file. I can't see one in the working directory. The last sentence is very cryptic to me (No match for full atom ID - subtract one character). Any idea? Thank you in advance, Fred. -- Scanned by iCritical.
