molrep question - how get our ducks in a row?

From: Gloria Borgstahl
Date: 24 February 2012 00:07
Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each other.
Then we read this into molrep as the "fixed" model and solved for the
second part.
The solution was found but the 6 for the second model are in different
ASU's and unit cells.
What is the easiest way to get everyone together in one asu?

We can think of hard ways to do it, but any advice?
Thanks, Gloria

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From: David Shin
Hi Gloria,

It depends on if you mean hard as in thinking up a slick trick, or hard as in maybe 20-30 mins of tedious work. I had the same problem with 18 in the ASM, where the solution had scattered models, but didn't want to think about it, so just used pymol.

1) open the first model with the original 6 models

2) then make separate files with each of the other subunits (with the CRYST line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you can read easily in the gui  later for saving)

3) then open m1.pdb

4) on the left, go to the "A" or action menu for m1 .pdb > generate > symmetry mates >  within 100 Angstroms (this can be smaller or larger, just need to see them)

5) then you'll have the symmates on the screen and the list of each right listed as m1_100-1-100 etc. So you can just click them on and off to see which one you like, then save that molecule.

6) Then delete the symmates "delete m1_*"  so you can check

7) Open the saved symmate to check

8) go to step 3 for the next model, ie. m2.pdb

not a slick answer, but can be done when tired with minimal error.

--

David Shin, 

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From: Johan Turkenburg
Hi,

There is an option in the molrep interface (in the search parameters
tab) to output all models closest to the input coordinate file With a
bit of luck, that should do it.

Johan

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From: Daniel Schlieper
Hello Gloria,

I usually let Coot display the nearest symmetry molecules (as CA) and save those that fit: Option "Save Symmetry Coordinates..." and pick the molecule to save.

Best regards, Daniel

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From: Eleanor Dodson
PISA does just this - download pdb to ebi server; let iyt cluster molecules and read back the assembled fcoordinates - plus lots gf useful info..

Eleanor