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CCP4BB  February 2012

CCP4BB February 2012

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Subject:

Re: molrep question - how get our ducks in a row?

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Wed, 29 Feb 2012 22:49:38 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (66 lines)

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

On Feb 24 2012, David Shin wrote:

>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.
>
> On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl
> <[log in to unmask]>wrote:
>
>> 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
>>
>
>
>
>

--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266

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