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

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


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"


or more complex but scalable CIF links


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

Usage: phenix.metal_coordination [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 model.pdb

    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 merge1 merge2 ... target

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


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

More information about the phenixbb mailing list