can't you feed solve with those positions or Hyss or the Sharp interface ? It's been too long ago when I faced this issue but I remember force-feeding one of the existing programs at the time with blank coordinates to figure it out - or was it mlphare ?
Too long ago probably 10 years by now. Jürgen On Dec 28, 2012, at 10:42 AM, Soisson, Stephen M wrote: 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<mailto: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<mailto:jason.vertr...@schrodinger.com> (o) +1 (603) 374-7120 On Fri, Dec 28, 2012 at 5:53 AM, Tom Oldfield <oldfi...@ebi.ac.uk<mailto: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<mailto: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<mailto: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. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
