Dear Tong, I actually raised this point with the developers of Phaser a while back, at a CCP4 meeting, as the wording and nomenclature can be a little confusing at times.
Molecular replacement in Phaser can be done with a single structure, or an ensemble or "group" of structures (all of which should be superimposed onto each other). You can also search with more than one ensemble — e.g if your protein comprises a number of different domains, say an FHA domain and a kinase domain. So… Add superimposed PDB to the ensemble: adds another structure to an exisiting group or ensemble, say "FHA domains". Add ensemble, makes a completely new group, to which you can add another set of superimposed structures, say "kinase domains". You can then specify a search in Phaser for 2 FHA domains and 1 kinase domain; both of which are separate ensembles or groups of structures. Hopefully this makes some kind of sense?! Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: [email protected]<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 From: herohonan <[email protected]<mailto:[email protected]>> Reply-To: herohonan <[email protected]<mailto:[email protected]>> Date: Wed, 4 Jan 2012 21:16:41 +0800 To: <[email protected]<mailto:[email protected]>> Subject: Re: [ccp4bb] Superpose problem Thank you for your reply! But I still wonder the differences between "Add superimposed PDB file to the ensemble" and "Add ensemble" in Phaser program and when to use the former. If I want to search for a complex model, I often just click the "Add ensemble" till completing the search model. -- Tong Huo Ph.D candidate College of Life Sciences Nankai University Tianjin, China At 2011-12-29 16:56:03,"Antony Oliver" <[email protected]<mailto:[email protected]>> wrote: >You could use the Superpose program to generate >superpositioned/superposed/superimposed models - i.e. to put your structures >on top of each other. There are also a host of other programs available to do >the same thing (!) > >In Phaser, you would then load each of these superimposed models, to generate >your search "ensemble". > >The words superposition, superimposition, and superpose, to all intents and >purposes mean the same thing (ducks behind flame-resistant wall). > >With regards, Tony. > >Sent from my iPhone > >On 29 Dec 2011, at 06:16, "SUBSCRIBE CCP4BB Huo tong" ><[email protected]<mailto:[email protected]>> wrote: > >> Hello everyone: >> I am just learning how to use the CCP4 Program suite. When I use the MR >> approach --Phaser, there is a column say >> "Add superimposed PDB file to the ensemble". And there is another CCP4 >> supported program called "Superpose". >> I am afraid if my question is professional, but I wonder >> 1)if there is any differences between "Superpose" and "Superimpose"; >> 2)when to use the Superpose or Superimposed function >> >> Any answer is welcomed!
