From: grid b. <gri...@gm...> - 2012-12-20 16:49:11
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Hi all, I am trying to use PyMol version 1.2r1 to do one test but I always failed to label my selection. the command line I used is the following: /usr/bin/pymol 1D5R.pdb 'show_as cartoon; spectrum b; sele t0, (resi 30); color red, selection=t0; show spheres, selection=t0; label t0, "test message"; save t0.pse;' I always got the error message as the following. Actually , I just want to label my selection t0 with one string message. Any ideas ? thank you. Spectrum: range ( 9.77000 to 117.74000). Selector: selection "t0" defined with 7 atoms. Executive: Colored 7 atoms. File "<string>", line 1 label="test message"; save t0.pse; ^ SyntaxError: invalid syntax Label: labelled 0 atoms. |
From: Thomas H. <tho...@sc...> - 2012-12-21 09:45:43
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Hi grid bird, the label command is parsed in "literal" mode, which means the semicolon is not recognized as command separator. Try this instead: /usr/bin/pymol -d 'fetch 1D5R, async=0; show_as cartoon; spectrum b; select t0, (resi 30); color red, selection=t0; show spheres, selection=t0; label t0, "test message"' -d 'save t0.pse' Cheers, Thomas grid bird wrote, On 12/20/12 17:49: > Hi all, > > I am trying to use PyMol version 1.2r1 to do one test but I always > failed to label my selection. > the command line I used is the following: > > /usr/bin/pymol 1D5R.pdb 'show_as cartoon; spectrum b; sele t0, (resi > 30); color red, selection=t0; show spheres, selection=t0; label t0, > "test message"; save t0.pse;' > > I always got the error message as the following. Actually , I just want > to label my selection t0 with one string message. Any ideas ? thank you. > > Spectrum: range ( 9.77000 to 117.74000). > Selector: selection "t0" defined with 7 atoms. > Executive: Colored 7 atoms. > File "<string>", line 1 > label="test message"; save t0.pse; > ^ > SyntaxError: invalid syntax > Label: labelled 0 atoms. -- Thomas Holder PyMOL Developer Schrödinger Contractor |