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
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
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" <[log in to unmask]> 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" <[log in to unmask]> 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!
