denovo notes
Last login: Tue Mar 8 23:34:02 on ttys002 ~ Ryan$ cd Documents/ Documents Ryan$ git init dn_pnp Initialized empty Git repository in /Users/Ryan/Documents/dn_pnp/.git/ Documents Ryan$ cd dn_pnp/ dn_pnp Ryan$ mkdir theozyme prep runs dn_pnp Ryan$ ls README.md prep runs theozyme dn_pnp Ryan$ cd theozyme/ theozyme Ryan$ ls theozyme Ryan$ pymol PyMOL(TM) 1.7.4.5 Edu - Educational Product Copyright (C) Schrodinger, LLC
...
PyMOL>pwd /Users/Ryan/Documents/dn_pnp/theozyme PyMOL>fetch 3phb please wait ... HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-NOV-10 3PHB TITLE CRYSTAL STRUCTURE OF HUMAN PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX TITLE 2 WITH DADME-IMMG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PURINE NUCLEOSIDE PHOSPHORYLASE; COMPND 3 CHAIN: E, Q, S, T, U, Y; COMPND 4 SYNONYM: PNP, INOSINE PHOSPHORYLASE; COMPND 5 EC: 2.4.2.1; COMPND 6 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 4 symmetry operators. CmdLoad: "./3phb.pdb" loaded as "3phb". parser: no matching files. PyMOL>create chaina, chain a <--had to re-do on chain e Selector: found 0 atoms. Executive: object "chaina" created. PyMOL>create chaina, chain e Selector: found 2298 atoms. PyMOL>save crystal_chainA.pdb Save: wrote "crystal_chainA.pdb". theozyme Ryan$ ls 3phb.pdb crystal_chainA.pdb theozyme Ryan$ git add 3phb.pdb crystal_chainA.pdb
theozyme Ryan$ git commit -m 'added crystal structure and chain A' [master (root-commit) 38dc10f] added crystal structure and chain A Committer: Ryan Boyd [email protected] Your name and email address were configured automatically based on your username and hostname. Please check that they are accurate. You can suppress this message by setting them explicitly:
git config --global user.name "Your Name"
git config --global user.email [email protected]
After doing this, you may fix the identity used for this commit with:
git commit --amend --reset-author
2 files changed, 17569 insertions(+) create mode 100644 theozyme/3phb.pdb create mode 100644 theozyme/crystal_chainA.pdb
theozyme Ryan$ open crystal_chainA.pdb theozyme Ryan$ pwd /Users/Ryan/Documents/dn_pnp/theozyme theozyme Ryan$ cp ~/Downloads/LG_0001.pdb . theozyme Ryan$
<--used molfile_to_params.py script to generate params file
theozyme Ryan$ python2 /Applications/rosetta_bin_mac_2016.10.58534_bundle/main/source/scripts/python/public/molfile_to_params.py -n LG1 LG1.mol2
Centering ligands at ( -44.231, 0.280, -3.255) Atom names contain duplications -- renaming all atoms. WARNING: atom C9 has valence > 4 WARNING: atom P1 has valence > 4 Partial charges already fully assigned, no changes made; net charge -1.000 WARNING: fragment 1 has 26 total atoms including H; protein residues have 7 - 24 (DNA: 33) WARNING: fragment 1 has 25 non-H atoms; protein residues have 4 - 14 (DNA: 22) Average 26.0 atoms (25.0 non-H atoms) per fragment (Proteins average 15.5 atoms (7.8 non-H atoms) per residue) WARNING: no root atom specified, using NBR atom instead. Wrote PDB file LG1_0001.pdb Wrote params file LG1.params theozyme Ryan$
alex@lab$ ls LG.params LG_0001.pdb obj02.pdb tss.mol2
alex@lab$ mv LG.params LG1.params
alex@lab$ ls LG1.params LG_0001.pdb obj02.pdb tss.mol2
<-- redo and make to strongest H-bond. check bond valence in avogadro...make lig and phos an object in pymol and open in avogadro --> save as tss.mol2 --> run python molfile_to_params.py tss.mol2 --> see email