I did this exact thing ages ago to place a domain using just predicted SeMet positions using O's lsq commands. Cumbersome syntax as I recall, but worked great.
Thanks, Steve On Dec 28, 2012, at 10:18 AM, "Jason Vertrees" <jason.vertr...@schrodinger.com> wrote: > Hi Dave, > > If you're still searching for a quick way to do this, check out > PyMOL's Pair Fitting Wizard (Wizard > Pair Fitting; see Page 20 > http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf). The > wizard is interactive and quick to use. > > This can also be done from the command line or scripted using the > pair_fit command (http://www.pymolwiki.org/index.php/Pair_fit). We use > the Kabsch algorithm (with the appropriate corrections for reflection) > and a faster hand-rolled technique, using if I recall correctly Jacobi > rotations, to annihilate off-diagonal values. > > Cheers, > > -- Jason > > -- > Jason Vertrees, PhD > Director of Core Modeling Product Management > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > > On Fri, Dec 28, 2012 at 5:53 AM, Tom Oldfield <oldfi...@ebi.ac.uk> wrote: >> Hi >> >> In you post you say you want to fit a small number of points. Note that >> the >> original algorithm of Kabsch has a number of maths pathalogical conditions >> where points have symmetry or lie in a plane/line - this is common for >> a small number of points (fitting residues or your example). >> >> The maths for an update to this algorithm can be found here >> Oldfield St'Fun'Gen (2002) 510-528 (appendix C) where cross terms >> are used to generate the eigen vectors. This algorithm is very stable >> for fitting a small number of points and might be more suitable for >> what you are trying to do. >> >> If you want I can email you the code in C or maybe Java, though it >> has rather a lot of other weighting schemes/masking used in the above >> paper. >> >> Regards >> Tom >> >> >>> Lsqkabsch should do the trick. >>> Herman >>> >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> Dale Tronrud >>> Sent: Thursday, December 27, 2012 9:10 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] 3D alignment of points (atoms) >>> >>> >>> If you just want the mathematics and are willing to roll your own >>> code, you can use the method of Wolfgang Kabsch. I see this has been >>> enshrined in a Wikipedia page at >>> >>> http://en.wikipedia.org/wiki/Kabsch_algorithm >>> >>> This is what I've used when I've wanted to superimpose points where the >>> mapping between the points is defined. If the points in your tetramer >>> aren't pathological, like lying in a common plane, you shouldn't have to >>> worry about SVD and can just perform the matrix inversion. >>> >>> Dale Tronrud >>> >>> >>> On 12/27/12 11:16, Waugh, David (NIH/NCI) [E] wrote: >>>> >>>> Greetings, >>>> >>>> I have what seems like a relatively simple problem to solve, but have >>> >>> not been able to do so using the software tools I know about. I have two >>> sets of 4 points in 3D space (atoms in PDB files). They represent >>> equivalent positions in two tetrameric proteins. I would like to align >>> these points in one PyMol or Coot file. I don't want a NEW set of points >>> representing the LSQ average of the two sets, which is what I get in >>> Coot's SuperPose. Instead I am looking for a way to "superimpose" one >>> atom from each set and then rotate one set for the best fit. I'm not an >>> intuitive expert on symmetry, but I think there is probably only one >>> best solution to this problem, right? I also need the atomic distances >>> to be on the same scale in the two sets of points. >>>> >>>> Thanks for any help! >>>> >>>> Dave Waugh >>>> >>>> -- >>>> David S. Waugh, Ph.D. >>>> Macromolecular Crystallography Laboratory Center for Cancer Research >>>> National Cancer Institute Bldg. 538, Room 209A Frederick, MD >>>> 21702-1201 >>>> +1 (301) 846-1842 >>>> wau...@mail.nih.gov >>>> http://mcl1.ncifcrf.gov/waugh.html >>>> -- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
