Thanks to all who suggested remedies. I omitted to say that the models are also (i) on different origins, and (ii) they are all helix fragments – which means SSM based superpositions are degenerate because helix look like helix look like helix…..

The CCP4i program ‘symmetry match models’ aka csymmatch in win crashed

with a normal input after reading the SGs and cells

“The program run with command: csymmatch -stdin

has failed with error message

child killed: segmentation violation”

I guess ‘child killed’ means aborted….

Phenix did not do all parts but good start – can probably be scripted too

In short, I ended up doing it by hand in coot with a ‘self-assembled’ symm + origin operator.

Thx!

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Eleanor Dodson
Sent: Thursday, July 09, 2015 1:53 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Model parts rearrangement

The CCP4 program csymmatch is what you need.

csymmatch -pdbin-ref TheGoodOne.pdb -pdbin TheFragments.pdb -origin-hand

Eleanor

On 8 July 2015 at 22:07, Andrew Purkiss-Trew <[log in to unmask]> wrote:

Having just faced this problem, I used the coot 'symm shift reference chain here' command (in Extensions / Modelling menu) to assemble the model from the scattered fragments.

This should be scriptable, but I didn't think it was worth the effort for the 20 odd fragments I had.

Hope this helps,

Andy Purkiss.

Quoting "Bernhard Rupp (Hofkristallrat a.D.)" <[log in to unmask]>:

Hi Fellows,

I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a reference model, where
the parts form a correct ASU.

Is the a program/script that can accomplish this assembly of parts onto the
correct model given the
reference model?

This is probably a common nuisance with a tool already available.

Best regards, BR
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