PyMOL(TM) 2.3.2 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 2.1. Shaders available.
Detected GLSL version 1.20.
OpenGL graphics engine:
GL_VENDOR: Intel Inc.
GL_RENDERER: Intel HD Graphics 3000 OpenGL Engine
GL_VERSION: 2.1 INTEL-10.4.14
License Expiry date: 01-mar-2020
License expired
Detected 4 CPU cores. Enabled multithreaded rendering.
ObjectMolecule: Read crystal symmetry information.
CmdLoad: PDB-string loaded into object "T0911", state 1.
CmdLoad: PDB-string loaded into object "QUARK_TS1", state 1.
Match: read scoring matrix.
Match: assigning 408 x 445 pairwise scores.
MatchAlign: aligning residues (408 vs 445)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
ExecutiveRMS: 24 atoms rejected during cycle 1 (RMSD=3.68).
ExecutiveRMS: 10 atoms rejected during cycle 2 (RMSD=2.76).
ExecutiveRMS: 6 atoms rejected during cycle 3 (RMSD=2.57).
ExecutiveRMS: 3 atoms rejected during cycle 4 (RMSD=2.50).
ExecutiveRMS: 1 atoms rejected during cycle 5 (RMSD=2.47).
Executive: RMSD = 2.458 (364 to 364 atoms)
Executive: object "aln_T0911_to_QUARK_TS1" created.
CmdLoad: PDB-string loaded into object "BAKER-ROSETTASERVER_TS3", state 1.
Match: read scoring matrix.
Match: assigning 408 x 445 pairwise scores.
MatchAlign: aligning residues (408 vs 445)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
ExecutiveRMS: 24 atoms rejected during cycle 1 (RMSD=5.95).
ExecutiveRMS: 13 atoms rejected during cycle 2 (RMSD=3.22).
ExecutiveRMS: 12 atoms rejected during cycle 3 (RMSD=2.89).
ExecutiveRMS: 11 atoms rejected during cycle 4 (RMSD=2.70).
ExecutiveRMS: 8 atoms rejected during cycle 5 (RMSD=2.52).
Executive: RMSD = 2.410 (340 to 340 atoms)
Executive: object "aln_T0911_to_BAKER-ROSETTASERVER_TS3" created.
CmdLoad: PDB-string appended into object "QUARK_TS1", state 2.
CmdLoad: PDB-string loaded into object "QUARK_TS1", state 1.
Executive: Colored 6397 atoms and 1 object.
Executive: Colored 3450 atoms and 1 object.
Executive: Colored 6397 atoms and 1 object.
ObjectMolecule: Read crystal symmetry information.
CmdLoad: PDB-string loaded into object "T0911", state 1.
Setting: bg_rgb set to white.
PyMOL>show QUARK_TS1
Error: unknown representation: 'QUARK_TS1'. Choices:
angles cgo ellipsoids licorice nonbonded sticks
callback dashes everything lines ribbon surface
cartoon dihedrals extent mesh slice volume
cell dots labels nb_spheres spheres wire
PyMOL>show cartoon,QUARK_TS1
Match: read scoring matrix.
Match: assigning 408 x 445 pairwise scores.
MatchAlign: aligning residues (408 vs 445)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
ExecutiveRMS: 24 atoms rejected during cycle 1 (RMSD=3.68).
ExecutiveRMS: 10 atoms rejected during cycle 2 (RMSD=2.76).
ExecutiveRMS: 6 atoms rejected during cycle 3 (RMSD=2.57).
ExecutiveRMS: 3 atoms rejected during cycle 4 (RMSD=2.50).
ExecutiveRMS: 1 atoms rejected during cycle 5 (RMSD=2.47).
Executive: RMSD = 2.458 (364 to 364 atoms)
Executive: object "aln_T0911_to_QUARK_TS1" created.
Executive: Colored 6397 atoms and 1 object.
Match: read scoring matrix.
Match: assigning 445 x 408 pairwise scores.
MatchAlign: aligning residues (445 vs 408)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
ExecutiveRMS: 24 atoms rejected during cycle 1 (RMSD=5.95).
ExecutiveRMS: 13 atoms rejected during cycle 2 (RMSD=3.22).
ExecutiveRMS: 12 atoms rejected during cycle 3 (RMSD=2.89).
ExecutiveRMS: 11 atoms rejected during cycle 4 (RMSD=2.70).
ExecutiveRMS: 8 atoms rejected during cycle 5 (RMSD=2.52).
Executive: RMSD = 2.410 (340 to 340 atoms)
Executive: object "aln_BAKER-ROSETTASERVER_TS3_to_T0911" created.
Executive: Colored 3451 atoms and 1 object.
Executive: Colored 6397 atoms and 1 object.
PyMOL>png /Users/mingai/Documents/T0911_BAKER.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Users/mingai/Documents/T0911_BAKER.png".
PyMOL>png /Users/mingai/Documents/T0911_QUARK.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Users/mingai/Documents/T0911_QUARK.png".
Executive: Colored 3451 atoms and 1 object.
PyMOL>png /Users/mingai/Documents/T0911total.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Users/mingai/Documents/T0911total.png".
PyMOL>png /Volumes/Untitled/T0911_best_cmp.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Volumes/Untitled/T0911_best_cmp.png".
CmdLoad: PDB-string loaded into object "chuo-u-server_TS2", state 1.
Match: read scoring matrix.
Match: assigning 408 x 445 pairwise scores.
MatchAlign: aligning residues (408 vs 445)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
Executive: RMSD = 23.683 (408 to 408 atoms)
Executive: object "aln_T0911_to_chuo-u-server_TS2" created.
Executive: Colored 3451 atoms and 1 object.
PyMOL>png /Volumes/Untitled/T0911_QDeep_loss.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Volumes/Untitled/T0911_QDeep_loss.png".
CmdLoad: PDB-string loaded into object "chuo-u2_TS4", state 1.
Match: read scoring matrix.
Match: assigning 408 x 445 pairwise scores.
MatchAlign: aligning residues (408 vs 445)...
MatchAlign: score 2121.000
ExecutiveAlign: 408 atoms aligned.
ExecutiveRMS: 3 atoms rejected during cycle 1 (RMSD=21.01).
Executive: RMSD = 20.766 (405 to 405 atoms)
Executive: object "aln_T0911_to_chuo-u2_TS4" created.
Executive: Colored 3451 atoms and 1 object.
PyMOL>png /Users/mingai/Downloads/draw/T0911_QA-RESE_loss.png, 0, 0, -1, ray=0
ScenePNG: wrote 640x476 pixel image to file "/Users/mingai/Downloads/draw/T0911_QA-RESE_loss.png".
