Yarrow
On Tue, Oct 4, 2011 at 9:11 AM, Yarrow Madrona
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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov