Re: [ccp4bb] Problem in MAKE_U_POSITIVE
This is interesting. Would it be possible to have refmac provide some info WHICH U (i.e. atom) got negative EV ? I did not find anything and I use monitor many per default. Thx, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron Oakley Sent: Thursday, September 03, 2009 7:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problem in MAKE_U_POSITIVE If one of its eigenvalues of the ANISOU matrix is negative, the matrix is non-positive definite leading to the MAKE_U_POSITIVE problem. I understand that this could indicate that an atom is sitting on a saddle point between two minima and that the atom could be split into two conformers. I had this happen once. Cheers, a++ On Wed, 2009-09-02 at 19:26 -0700, Bernhard Rupp wrote: Hi there - a transient message appears during anisotropic refinement CCP4 6.1: Refmac_5.5.0071 Problem in MAKE_U_POSITIVE that seems to have no further consequences. I guess that means that some elements in a U tensor lead to a divergent behavior, but details evade me. Just curious BR - Bernhard Rupp b...@ruppweb.org http://www.ruppweb.org/ - Anything is possible if you don't know what you are talking about. - -- ** * * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ** * =
Re: [ccp4bb] Problem in MAKE_U_POSITIVE
This means that some U tensors are non-positive definite (i.e. no nice thermal ellipsoid). If by transient, you mean they have gone away by the last cycle of refinement, then you can maybe ignore them. But probably, you need to adjust your restraints, e.g. the SPHEricity restraint (under Geometric parameters in the gui). HTH Martyn On Wed, 2009-09-02 at 19:26 -0700, Bernhard Rupp wrote: Hi there – a transient message appears during anisotropic refinement CCP4 6.1: Refmac_5.5.0071 Problem in MAKE_U_POSITIVE that seems to have no further consequences. I guess that means that some elements in a U tensor lead to a divergent behavior, but details evade me. Just curious…. BR - Bernhard Rupp b...@ruppweb.org http://www.ruppweb.org/ - Anything is possible if you don't know what you are talking about. - -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Problem in MAKE_U_POSITIVE
If one of its eigenvalues of the ANISOU matrix is negative, the matrix is non-positive definite leading to the MAKE_U_POSITIVE problem. I understand that this could indicate that an atom is sitting on a saddle point between two minima and that the atom could be split into two conformers. I had this happen once. Cheers, a++ On Wed, 2009-09-02 at 19:26 -0700, Bernhard Rupp wrote: Hi there - a transient message appears during anisotropic refinement CCP4 6.1: Refmac_5.5.0071 Problem in MAKE_U_POSITIVE that seems to have no further consequences. I guess that means that some elements in a U tensor lead to a divergent behavior, but details evade me. Just curious BR - Bernhard Rupp b...@ruppweb.org http://www.ruppweb.org/ - Anything is possible if you don't know what you are talking about. - -- ** * * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ** *
[ccp4bb] Problem in MAKE_U_POSITIVE
Hi there - a transient message appears during anisotropic refinement CCP4 6.1: Refmac_5.5.0071 Problem in MAKE_U_POSITIVE that seems to have no further consequences. I guess that means that some elements in a U tensor lead to a divergent behavior, but details evade me. Just curious.. BR - Bernhard Rupp b...@ruppweb.org http://www.ruppweb.org/ http://www.ruppweb.org/ - Anything is possible if you don't know what you are talking about. -
