Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-28 Thread Bosch, Juergen
oard [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 ca

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-28 Thread Soisson, Stephen M
>> 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: Th

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-28 Thread Jason Vertrees
in 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

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-28 Thread Tom Oldfield
le 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 Wikiped

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread Bernhard Rupp (Hofkristallrat a.D.)
- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of George Sheldrick Sent: Thursday, December 27, 2012 1:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D alignment of points (atoms) A computationally elegant and probably faster approach is to use quaternions, proposed

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread George Sheldrick
A computationally elegant and probably faster approach is to use quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent description of this method see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/ George On 12/27/2012 09:09 PM, Dale Tronrud wrote: If you just wan

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread Herman . Schreuder
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

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread Dale Tronrud
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

[ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread Waugh, David (NIH/NCI) [E]
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 thes