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Generating rigid bodies from CIF
csmalley97 #1
Member for 2 weeks · 1 post · Location: Cardiff University
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Subject: Generating rigid bodies from CIF
Hi all,

Currently I am trying to refine a tetrapeptide using Topas and would like to be able to do this with the use of rigid bodies instead of a massive number of restraints. However, after looking through the recently published Topas book as well as countless bits and pieces online (including Durham tutorials) I'm pretty stuck.

Is there any way of generating rigid bodies from a trial structure following structure solution (similar to how DASH generates them)? I would do this using DASH but we have an in-house structure solution program and we only get a .cif file as output.

Could anyone help?

Chris
johnsoevans (Administrator) #2
User title: John Evans
Member since Aug 2009 · 224 posts
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Chris,

It's not clear whether your issue is how to create a z-matrix description or how to map a z-matrix description onto your cif format solution.

Have you looked at: https://github.com/mspillman/zmatrix-to-inp?

My recollection is that it uses dash to create the rigid bodies from a dash-output cif, but you could do the same with your cif.

There's a z-matrix thread on using topas' rigid body editor to create the z-matrix at: http://topas.dur.ac.uk/unb/forum.php?req=thread&id=362

The book has some hints on how to map the z-matrix rigid body onto your cif coordinates, or there's an outline on the wiki at: http://topas.dur.ac.uk/topaswiki/doku.…?id=matching_a_ri…

Hope that's some help.

John
btrump1 #3
Member since Feb 2015 · 12 posts
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Chris,

Another open that I've found works well is using Avogadro. It can load a *.cif file and output it as a *.gzmat (z-matrix). I often using this as well for creating/drawing rigid bodies, optimizing their structure, and then writing them out as a z-matrix.

Once you have that z-matrix you can load it into the Topas rigid body editor to make sure it is done correctly, as they don't always use dihedral angles in the same way.

Enjoy!
-Ben
AlanCoelho #4
Member since Aug 2011 · 294 posts
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Another way is to describe the  CIF coordinates using point_for_site within a rigid body. Place the atoms in the Rigid Body Editor  and then use the "First guess z-matrix". I'm not sure how good the "First guess z-matrix" would be but it may be as good as any other guess.
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