[phenixbb] Question about restraints
nwmoriarty at lbl.gov
Fri Nov 12 12:13:51 PST 2010
I will add the buttons to the list.
On Fri, Nov 12, 2010 at 11:58 AM, Schubert, Carsten [PRDUS]
<CSCHUBER at its.jnj.com> wrote:
> thanks for the response. I'll play around with this.
> BTW at some point we were talking about having these kind of qualitative descriptors of the 'tightness' implemented in reel. AFIK currently one has to edit the restraints value by hand. A simple control using radio buttons for instance for either the whole ligand or a group of restraints might do the trick.
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
>> bounces at phenix-online.org] On Behalf Of Nigel Moriarty
>> Sent: Friday, November 12, 2010 12:20 PM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] Question about restraints
>> I'm sure you are aware of all the things I'm going to mention but I
>> mention them for completeness. Also, there will be a lot of differing
>> opinions so I state mine with the coda that its by no means an
>> absolute and others experience may suggest differing assertions. I'm
>> sure there will be some discussion.
>> Your mention of over-tightening is important. The ligand is a small
>> part of the restraints model and therefore the restraints must be
>> viewed in light of the entire set. Making the Estimated Standard
>> Deviations (ESD) smaller does have the result of tightening the
>> restraints but making them more than hundred times smaller than the
>> corresponding ESD in the protein portion is not numerically sensible.
>> Regarding the tightness of restraints, the ESD are in the units of the
>> restraint. The majority of the restraints will be within the ESD of
>> the ideal value. The variation of a restraint is dependent on the type
>> of restraint (bonds vary less than dihedrals) and on the different
>> coordinates being restrained (single bonds and double bonds).
>> Naturally, the quality of the data has an influence. You don't want
>> to restrict the geometry if the density says something different.
>> Having said all that, I would suggest that for bonds the 'loose',
>> 'medium' and 'tight' (LMT) is something like 0.05, 0.01, 0.005. For
>> angles you could use 10., 3., 1. The remaining restraints are less
>> likely to need adjusting but similar values could work for dihedrals
>> and planes.
>> On Fri, Nov 12, 2010 at 6:19 AM, Schubert, Carsten [PRDUS]
>> <CSCHUBER at its.jnj.com> wrote:
>> > Hi,
>> > I was wondering what the default values for restraints in reel/elbow
>> > represent in terms of 'tightness' for lack of a better word.
>> > I am trying to tighten up the geometry of a badly behaving ligand and
>> > to avoid over tightening. What is the consensus out there what kind
>> of ESDs
>> > represent a 'loose' 'medium' and 'tight' restraint for bond, angle,
>> > dihedral, planar and chiral restraints.
>> > Thanks
>> > Carsten
>> > _______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://phenix-online.org/mailman/listinfo/phenixbb
>> Nigel W. Moriarty
>> Building 64R0246B, Physical Biosciences Division
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
>> Fax : 510-486-5909 Web : CCI.LBL.gov
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
More information about the phenixbb