From: Yotam A. <yo...@gm...> - 2011-09-11 16:54:43
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Hi. How hard it is to write a (python?) script that will rotate the figure and color some atoms? Nothing fancy... I searched a little bit but couldn't find a quick and dirty tutorial for script writing. Thanks -- My other email account has a "professional" signature. |
From: Troels E. L. <tl...@gm...> - 2011-09-11 17:05:49
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Well, not hard. I made a script that can rotate a molecule around a line. And I made a large tutorial to take one through the available functions of this script. It is a pymol command file, ".pml". Check out: http://www.pymolwiki.org/index.php/Rotkit Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/9/11 Yotam Avital <yo...@gm...> > Hi. > > How hard it is to write a (python?) script that will rotate the figure and > color some atoms? Nothing fancy... I searched a little bit but couldn't find > a quick and dirty tutorial for script writing. > > Thanks > > -- > My other email account has a "professional" signature. > > > > ------------------------------------------------------------------------------ > Using storage to extend the benefits of virtualization and iSCSI > Virtualization increases hardware utilization and delivers a new level of > agility. Learn what those decisions are and how to modernize your storage > and backup environments for virtualization. > http://www.accelacomm.com/jaw/sfnl/114/51434361/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Yotam A. <yo...@gm...> - 2011-09-11 17:53:09
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Thanks. I'm sorry but this is too complected. Currently, I can't afford the time to learn another scripting languish. Consider gnuplot script files, which are simply a list of gnuplot commands. Sure you can do some sophisticated stuff but you don't have to. All my files will be simple atom list in xyz format (name \t x \t y \t z), and all I want to do is select all the atoms of a certain name, color them and then rotate the system. Once again, I thank you for any help. 2011/9/11 Troels Emtekær Linnet <tl...@gm...> > Well, not hard. > > I made a script that can rotate a molecule around a line. > And I made a large tutorial to take one through the available functions of > this script. > It is a pymol command file, ".pml". > > Check out: > http://www.pymolwiki.org/index.php/Rotkit > > > Troels Emtekær Linnet > Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/> > 04107 Leipzig, Tyskland > Mobil: +49 1577-8944752 > > > > 2011/9/11 Yotam Avital <yo...@gm...> > >> Hi. >> >> How hard it is to write a (python?) script that will rotate the figure and >> color some atoms? Nothing fancy... I searched a little bit but couldn't find >> a quick and dirty tutorial for script writing. >> >> Thanks >> >> -- >> My other email account has a "professional" signature. >> >> >> >> ------------------------------------------------------------------------------ >> Using storage to extend the benefits of virtualization and iSCSI >> Virtualization increases hardware utilization and delivers a new level of >> agility. Learn what those decisions are and how to modernize your storage >> and backup environments for virtualization. >> http://www.accelacomm.com/jaw/sfnl/114/51434361/ >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > -- My other email account has a "professional" signature. |
From: Thomas H. <sp...@us...> - 2011-09-12 07:05:44
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Hi Yotam, > I'm sorry but this is too complected. Currently, I can't afford the time > to learn another scripting languish. Consider gnuplot script files, > which are simply a list of gnuplot commands. PyMOL understands two languages. The "PyMOL language" is indeed similar to gnuplot commands, that's what you usually type into the PyMOL command prompt or put into .pml script files. The other language is pure python (PyMOL API) and can be used to write more complicated routines (.py script files). http://pymolwiki.org/index.php/Running_Scripts > Sure you can do > some sophisticated stuff but you don't have to. All my files will be > simple atom list in xyz format (name \t x \t y \t z), and all I want to > do is select all the atoms of a certain name, color them and then rotate > the system. by "rotate the system" do you mean a movie-like 360° rotation? Then your simple list of PyMOL commands will be something like: # color everything gray and histidines blue color gray, all color blue, resn HIS # make 100 movie frames and do full rotation about Y-axis mset 1 x100 util.mroll mplay For documentation and more examples see: http://pymolwiki.org/index.php/Color http://pymolwiki.org/index.php/Util.mroll http://pymolwiki.org/index.php/Property_Selectors http://pymolwiki.org/index.php/Selection_Algebra Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Yotam A. <yo...@gm...> - 2011-09-12 09:34:18
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Great, thank you. On Mon, Sep 12, 2011 at 10:05 AM, Thomas Holder < sp...@us...> wrote: > Hi Yotam, > > > I'm sorry but this is too complected. Currently, I can't afford the time >> to learn another scripting languish. Consider gnuplot script files, which >> are simply a list of gnuplot commands. >> > > PyMOL understands two languages. The "PyMOL language" is indeed similar to > gnuplot commands, that's what you usually type into the PyMOL command prompt > or put into .pml script files. > > The other language is pure python (PyMOL API) and can be used to write more > complicated routines (.py script files). > > http://pymolwiki.org/index.**php/Running_Scripts<http://pymolwiki.org/index.php/Running_Scripts> > > > Sure you can do some sophisticated stuff but you don't have to. All my >> files will be simple atom list in xyz format (name \t x \t y \t z), and all >> I want to do is select all the atoms of a certain name, color them and then >> rotate the system. >> > > by "rotate the system" do you mean a movie-like 360° rotation? Then your > simple list of PyMOL commands will be something like: > > # color everything gray and histidines blue > color gray, all > color blue, resn HIS > > # make 100 movie frames and do full rotation about Y-axis > mset 1 x100 > util.mroll > mplay > > For documentation and more examples see: > http://pymolwiki.org/index.**php/Color<http://pymolwiki.org/index.php/Color> > http://pymolwiki.org/index.**php/Util.mroll<http://pymolwiki.org/index.php/Util.mroll> > http://pymolwiki.org/index.**php/Property_Selectors<http://pymolwiki.org/index.php/Property_Selectors> > http://pymolwiki.org/index.**php/Selection_Algebra<http://pymolwiki.org/index.php/Selection_Algebra> > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- My other email account has a "professional" signature. |
From: Martin H. <ma...@bl...> - 2011-09-12 13:10:10
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Dear List When I try to save an object as a PDB (after editing it slightly with the PyMOL edit mode, i.e. adjusting a dihedral angle), the "Save Molecule" dialog asks to save "all", "global" or "objects current" state. When saving with the last two, I get no coordinates in the generated file only an "END" statement, thats the only thing written to the file. Only when using "all" i get the coordinates in the file, but the file is called file_state01.pdb and I need to edit it on the command line. The object I'm trying to save is the following amino acid: ATOM 1 N GLN A 189 61.015 3.522 29.377 1.00 0.00 PROT N ATOM 2 CA GLN A 189 60.796 4.359 30.552 1.00 0.00 PROT C ATOM 3 C GLN A 189 61.841 4.093 31.609 1.00 0.00 PROT C ATOM 4 O GLN A 189 62.557 5.012 32.048 1.00 0.00 PROT O ATOM 5 CB GLN A 189 59.376 4.085 31.097 1.00 0.00 PROT C ATOM 6 CG GLN A 189 59.191 4.225 32.644 1.00 0.00 PROT C ATOM 7 CD GLN A 189 59.212 5.623 33.275 1.00 0.00 PROT C ATOM 8 NE2 GLN A 189 60.166 6.464 32.970 1.00 0.00 PROT N ATOM 9 OE1 GLN A 189 58.336 5.977 34.048 1.00 0.00 PROT O ATOM 10 HA GLN A 189 60.884 5.420 30.254 1.00 0.00 PROT H ATOM 11 2HB GLN A 189 59.072 3.062 30.790 1.00 0.00 PROT H ATOM 12 3HB GLN A 189 58.662 4.765 30.594 1.00 0.00 PROT H ATOM 13 2HG GLN A 189 59.945 3.612 33.173 1.00 0.00 PROT H ATOM 14 3HG GLN A 189 58.222 3.797 32.956 1.00 0.00 PROT H ATOM 15 1HE2 GLN A 189 60.070 7.393 33.383 1.00 0.00 PROT H ATOM 16 2HE2 GLN A 189 60.828 6.131 32.266 1.00 0.00 PROT H ATOM 17 H01 GLN A 189 61.024 2.517 29.478 1.00 0.00 PROT H Any hints are welcomed, because its a bit inconvenient having to rename all the time.. Martin |
From: Jason V. <jas...@sc...> - 2011-09-12 14:16:31
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Hi Martin, > When I try to save an object as a PDB (after editing it slightly with > the PyMOL edit mode, i.e. adjusting a dihedral angle), > the "Save Molecule" dialog asks to save "all", "global" or "objects > current" state. When saving with the last two, I get no coordinates in > the generated file only an "END" statement, thats the only thing written > to the file. Only when using "all" i get the coordinates in the file, > but the file is called file_state01.pdb and I need to edit it on the > command line. First, there was a bug a few months ago we fixed that was related to this. Updating PyMOL might help. If that isn't it then let me explain "states" to clear up the issue. PyMOL has the concept of a "state". A state is any conformation of a particular set of atoms: for example, a single time-step in a trajectory or set of coordinates in an NMR ensemble. In PyMOL you can adjust the global state counter (using the right and left arrow keys on an empty command line or the movie player controls) or just type set state, 4 Instead of acting globally (on all objects), you can set an object's state individually: set state, 4, my_prot_ensemble The global state counter and an object's state counter can differ. This added bit of complexity allows you to do more powerful things: you can now take measurements from object A in state a to object B in state b even though the global state counter is in state c. (For example, if you did a docking run and have 10 conformations of the protein and 100 docked poses, you can now take measurements from state/pose 44 of the small molecule to state 5 of the protein.) So, these options are allowing you to save all states of the object, or just one state that corresponds to either the global state counter or the state you set for the object. When saving, if you get a blank file you've requested that PyMOL save a molecule beyond the number of states it has. Try this: # alanine fragment (state 1) frag ala # alanine fragment (state 2) frag ala # rotate state 2 by 45 degrees around X rotate x, 45, ala, state=2 # set global state counter to 1 set state, 1 # set/freeze ala state to 2 set state, 2, ala Now using File > Save Molecule > ... try "global" and "object's current". For the former the saved PDB should have state 1's coordinates, and the latter state 2's. Make sense? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |