Superpose problem

From: SUBSCRIBE CCP4BB Huo tong
Date: 29 December 2011 06:06


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!

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From: Antony Oliver


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

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From: herohonan

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

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From: Antony Oliver

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