Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Robbie Joosten
work, we may need a closer look at your input model. Cheers, Robbie Date: Thu, 27 Oct 2011 20:48:49 -0500 From: satys...@wisc.edu Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 To: CCP4BB@JISCMAIL.AC.UK Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24 A, aniso

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread LEGRAND Pierre
d'envoi : vendredi 28 octobre 2011 09:42 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Hi Kenneth, This looks like an off-by-one bug in the restraint generation. Typical sources are weird LINKs, wrong atom names and bad luck. I suggest you make sure you have the very latest

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Garib N Murshudov
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Hi Kenneth, This looks like an off-by-one bug in the restraint generation. Typical sources are weird LINKs, wrong atom names and bad luck. I suggest you make sure you have the very latest Refmac and dictionary and try setting up a new refinement

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Ed Pozharski
Just to verify, is this by any chance *unrestrained* refinement? On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kenneth A. Satyshur, what is your weight set to? If it is set to 'auto', try setting it to a specific value and lower

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread LEGRAND Pierre
Pozharski [epozh...@umaryland.edu] Date d'envoi : vendredi 28 octobre 2011 16:00 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Just to verify, is this by any chance *unrestrained* refinement? On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE

Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, If those hydrogens are in riding position, their coordinates are calculated and should not be refined at all, isn't it? Hence they should appear in the list of deviations at all. Are the hydrogens present in the PDB file? Does it work to

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Stefan Gerhardt
:00 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Just to verify, is this by any chance *unrestrained* refinement? On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kenneth A. Satyshur, what is your

[ccp4bb] Fwd: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry, should NOT appear in the list of deviations, of course! - Original Message Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Date: Fri, 28 Oct 2011 17:39:06 +0200 From: Tim Gruene t...@shelx.uni-ac.gwdg.de Reply-To: Tim Gruene t

Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread Garib N Murshudov
:00 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Just to verify, is this by any chance *unrestrained* refinement? On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kenneth A. Satyshur, what is your weight

[ccp4bb] RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-28 Thread LEGRAND Pierre
part de Garib N Murshudov [ga...@mrc-lmb.cam.ac.uk] Date d'envoi : vendredi 28 octobre 2011 17:49 À : LEGRAND Pierre Cc : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0 Dear Pierre Resolution seems to be good enough for full anisotropic refinement. Why don't you

[ccp4bb] refmac 5.6 ccp4 6.2.0

2011-10-27 Thread Kenneth A. Satyshur
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24 A, aniso with H in riding position and it just exploded! I get error in distances such as     Standard  External   All     Bonds:  3270 0  3270