Dear Phenix.BB, I wrote a mail earlier about some problems I had with phenix.elbow but it didn't seem to get through. I've solved two of the problems now but also found a new one so I'll try posting again. When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn't happen with --tripos. Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds). For an example try phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles='C=CCN.C1C(O1)CCl' The period is supposed to designate two seperate molecules. Remember to use elbow.become_expert before running that line. I hope someone can help me. Sincerely, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 52 61 Fax: +45 86 12 31 78 www.bioxray.dk
Hi Morten, Nigel is out of town for the next two weeks. I hope you can work around the issues until he is back. Ralf
Morten Thanks for your patience while I was away. I have answered your questions below.
When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn't happen with --tripos. Sure, I put this in to quickly delete so files. I think its better to use --no-output which doesn't write most of the files to disk. I'll look into --clean and may remove it. Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds). For an example try phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles='C=CCN.C1C(O1)CCl' The period is supposed to designate two seperate molecules. You are correct that a period means two separate molecules. If you are using eLBOW to generate restraints for a protein refinement, you should never pass two molecules (via SMILES) because of the nature of the lookup that is required for a ligand and its restraints. That is, a single molecule such have a single three character code. Also, the quantum code does not rely on explicit bond definitions to calculate the molecule energy.
Having said that, eLBOW does operate on a PDB with multiple ligands in a sensible fashion so if you can provide a case for running phenix.elbow --smiles="C=CCN.C1C(O1)CCl" rather than running phenix.elbow --smiles="C=CCN" phenix.elbow --smiles="C1C(O1)CCl" and some sort of rationale I'm sure I can support it. Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
participants (3)
-
Morten Grøftehauge -
Nigel W. Moriarty -
Ralf W. Grosse-Kunstleve