[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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