[ccp4bb] about RMSD bond lengths and angles
Dear All, I am wondering about the ranges of RMSD bond lengths and angles. What are the acceptable ranges for these two values? Is there some statistics for them? Thanks and best wishes.
Re: [ccp4bb] about RMSD bond lengths and angles
This has been discussed multiple times on bb, also BMC p640. The restraint target standard uncertainty provides an upper limit54 for a reasonable bond or angle r.m.s.d. from targets within the model (approximately 0.02 Å and 1.9deg, respectively), but makes no further assumption where these values de facto should be in an optimal refi nement of a protein structure.73 Assume at one extreme a low-resolution torsion angle refi nement with fixed bond lengths, where the bond length deviation from targets will be zero. At the other extreme, an unrestrained refi nement at ultra-high resolution will refl ect the bond length variation as observed in small molecules, around ~0.02 Å. In between the values will vary, depending on the properly selected overall restraint weight that minimizes R-free (or preferably LL-free).73 The notion that the r.m.s.d. from targets should be the same for all structures and that it should be close to small molecule values is not correct. br From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jiamu Du Sent: Wednesday, April 13, 2011 2:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] about RMSD bond lengths and angles Dear All, I am wondering about the ranges of RMSD bond lengths and angles. What are the acceptable ranges for these two values? Is there some statistics for them? Thanks and best wishes.
Re: [ccp4bb] about RMSD bond lengths and angles
Thank you. On Wed, Apr 13, 2011 at 6:03 PM, Bernhard Rupp (Hofkristallrat a.D.) < hofkristall...@gmail.com> wrote: > This has been discussed multiple times on bb, also BMC p640. > > > > The restraint target standard uncertainty > > provides an upper limit54 for a reasonable bond or angle r.m.s.d. from > targets > > within the model (approximately 0.02 Å and 1.9deg, respectively), but > makes no > > further assumption where these values *de facto *should be in an optimal > refi nement > > of a protein structure.73 Assume at one extreme a low-resolution torsion > > angle refi nement with fixed bond lengths, where the bond length deviation > > from targets will be zero. At the other extreme, an unrestrained refi > nement at > > ultra-high resolution will refl ect the bond length variation as observed > in small > > molecules, around ~0.02 Å. In between the values will vary, depending on > the > > properly selected overall restraint weight that minimizes *R*-free (or > preferably > > –*LL*-free).73 The notion that the r.m.s.d. from targets should be the > same for all > > structures and that it should be close to small molecule values is not > correct. > > > > br > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Jiamu > Du > *Sent:* Wednesday, April 13, 2011 2:06 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] about RMSD bond lengths and angles > > > > Dear All, > I am wondering about the ranges of RMSD bond lengths and angles. What are > the acceptable ranges for these two values? Is there some statistics for > them? > Thanks and best wishes. >
Re: [ccp4bb] about RMSD bond lengths and angles
See this thread: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A1=ind1009&L=CCP4BB#58 Cheers -- Ian On Wed, Apr 13, 2011 at 10:05 PM, Jiamu Du wrote: > Dear All, > I am wondering about the ranges of RMSD bond lengths and angles. What are > the acceptable ranges for these two values? Is there some statistics for > them? > Thanks and best wishes. > > >
