[phenixbb] combinding two CIF's and creating links in elbow

Nigel Moriarty nwmoriarty at lbl.gov
Tue Oct 4 09:28:54 PDT 2011


Yarrow

On Tue, Oct 4, 2011 at 9:11 AM, Yarrow Madrona <amadrona at uci.edu> wrote:
> Hello,
>
> 1. I have a question on creating links using elbow. I have a CIF of NO and
> I want to define a chemical link between NO and Fe of a HEME group. I need
> to input the geometry as NO is acting as a metal ligand. I really don't
> know where to begin. Any help would be greatly appreciated.

You have two choices.  The simpler "edits"

http://www.phenix-online.org/documentation/refinement.htm#anch84

or more complex but scalable CIF links

http://www.phenix-online.org/documentation/refinement.htm#anch82

I have written a couple of tools to help. If you have the NO in the
model you can try

phenix.metal_coordination
Usage: phenix.metal_coordination [options]

Options:
  --version        show program's version number and exit
  -h, --help       show this help message and exit
  --show-defaults  Display defaults

or an alpha release program

elbow.ligand_linking

  Usage:
    elbow.ligand_linking model.pdb

  Output:
    Two files containing the cif_link and selection data.

> 2. Is there a quick way of combining CIF files into one large file without
> a lot of copy and pasting?

You can use the command_line utility

elbow.join_cif_files

  usage:
    elbow.join_cif_files merge1 merge2 ... target

If you still have problems, send the files directly to me.

Nigel

NB. Any files sent to me will be held in strictest confidence.

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


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