Hi Jason, I fixed ligandfit so that it should now be able to take your list of sdf files and run each file sequentially. Starting with tomorrow's build, you should be able test it out with this regression test: phenix_regression.wizards.test_command_line_ligands test_ligand_list Thanks for pointing out the problem! Let me know if that does not do it. All the best, Tom T On Jul 21, 2014, at 7:11 PM, Phan, Jason wrote:

________________________________________ From: phenixbb-bounces@phenix-online.orgmailto:phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Phan, Jason [jason.phan@vanderbilt.edu] Sent: Monday, July 21, 2014 4:32 PM To: phenixbb@phenix-online.orgmailto:phenixbb@phenix-online.org Subject: [phenixbb] phenix.ligandfit does not recognize a list of SDF file names

Hi All,

I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks. _______________________________________________ phenixbb mailing list phenixbb@phenix-online.orgmailto:phenixbb@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb