Subject: | | Re: run of Refmac5 (latest version of CCP4) |
From: | | [log in to unmask][log in to unmask], 14 Oct 2009 19:24:19 +0100382_us-ascii Dear Yaun,
On Thu, Oct 15, 2009 at 01:44:31AM +0800, SHANG Yuan wrote: > Then,how can I activate this? (PS,sharp is also disable...)
To have the autoSHARP module enabled: just get the latest version of SHARP/autoSHARP from our site. Once you have installed and configured it, the autoSHARP button should switch from 'greyed out' to 'active'. [...]48_14Oct200919:24:[log in to unmask] |
Reply-To: | | [log in to unmask][log in to unmask], 12 Oct 2009 14:14:30 -0400823_ISO-8859-1 Paul,
I just looked at the source code for "reduce." It seems there is a global variable that gets returned from main(), ReturnCodeGlobal, which is set to 0 by default. However, further down in the code is this (in the "processPDBfile" function):
// adjust cliques
std::list< std::list<MoverPtr> > cc_list = clst.cliques(); //cerr << "start: " << cc_list.size() << endl; for (std::list< std::list<MoverPtr> >::iterator cc = cc_list.begin(); cc != cc_list.end(); ++cc) { //cerr << "start2" << endl; int nscnt = xyz.orientClique(*cc, ExhaustiveLimit); if (nscnt > 0) { Tally._num_adj += nscnt; } else { // too many permutations, make note ReturnCodeGlobal = [...]48_12Oct200914:14:[log in to unmask] |
Date: | | Wed, 14 Oct 2009 16:17:16 +0100 |
Content-Type: | | text/plain |
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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:[log in to unmask]] On Behalf Of
Vellieux Frederic
Sent: 14 October 2009 14:27
To: [log in to unmask]
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.
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