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USAGE cealign target, mobile [, target_state [, mobile_state [, quiet [, guide [, d0 [, d1 [, window [, gap_max, [, transform ]]]]]]]]] NOTES If "guide" is set PyMOL will align Implemented point primitives for X3D scene exports. molefacture: Added improper centers for OPLS atom types molefacture: New charmmified OPLS atom types and typing rules cranked version VMD 1.9beta2 (Feb 28, 2011) more cleanup of plugin loading message output SEE ALSO get_extentapi: pymol.querying.centerofmasscheckDESCRIPTION "check" is unsupported command that may eventually have something to do with assigning forcefield parameters to a selection of atoms.api: pymol.experimenting.checkcleanUNDOCUMENTEDapi: pymol.computing.cleanclipDESCRIPTION "clip" alters the positions of Check This Out

updated comments, prepare for more GUI color revisions After testing and finding that Fl_Choice backgrounds behave the same way in FLTK 1.1.8 as they do in FLTK 1.1.10, I've changed the E. We might want to allow alternative grouping options for tools besides Maya that might use the molecule tags to create a heirarchical scene graph that more closely matches what VMD does USAGE isosurface name, map, level [, selection [, buffer [, state [, carve ]]]] ARGUMENTS name = the name for the new mesh isosurface object. navigate here

The GUI code now sets the minmax range to 0:1 if there are no valid volumetric datasets loaded. USAGE deprotect (selection) PYMOL API cmd.deprotect(string selection) SEE ALSO protect, mask, unmask, mouse, editingapi: pymol.editing.deprotectdesaturateDESCRIPTION Desaturate the colors in the given selection. USAGE bond [atom1, atom2 [,order]] NOTES The atoms must both be within the same object. Fixed out of bounds loop in orient() function. (The condition for breaking that was checked in the loop is under normal circumstances always true.

Changed the X3D scene export code to use the IndexedTriangleStripSet primitive by default. Your cache administrator is webmaster. psfgen: Better warning when missing atoms from conformation. Method to return date ranges of 1 year A guy scammed me, but he gave me a bank account number & routing number.

from pymol import cmd result = cmd.( argument , ... ) Although the PyMOL core is not multi-threaded, the API is thread-safe and can be called asynchronously by external python programs. add vmddebug plugin to distribution. VMD now absolutely requires Tachyon version 0.99.0 or later. http://stackoverflow.com/questions/27830652/fortran-runtime-error-cannot-match-namelist iterate all, print s.line_width) PYMOL API cmd.get(string name, string object, int state, int quiet) SEE ALSO set, set_bond, get_bondapi: pymol.setting.getget_angleDESCRIPTION "get_angle" returns the angle between three atoms.

Since Tachyon allows a broader range of Fog parameters than OpenGL (OpenGL ignores the density parameter when linear fog is enabled), this could result in incorrect shading. It can be run in its own namespace (like a Python module, default), a local name space, or in the global namespace. Correctly initialize all the full-screen wmhints structure elements to zero prior to calling XChangeProperty() Changed "vmdinfo displaytype" to "vmdinfo dispdev" to match command line argument parsing, and historical name being "display Updated README with X3D scene format info.

Split GUI off into separate file. Tweaked menu. If a log file is currently open, get_view will not write the view matrix to the screen unless the "output" parameter is 2. Allow the VMD stage to be grabbed and moved in "move molecule" mode in the same way that the Axes can be moved.

Added docs for "label textthickness" Implemented new "label textthickness" command that affects all labels, similar to the behavior of the existing "label textsize" command. his comment is here Added placeholder objects to track geometry groups, disabled some bad code for dealing with comments since there are no tokens for them yet. multiseq: tweaked docs to more explicitly describe where the configuration needs to point to for MAFFT multiseq: fix a bug that prevented MAFFT from running on windows multiseq: phylotree comment formatting. USAGE angle [ name [, selection1 [, selection2 [, selection3 ]]]] NOTES "angle" alone will show the angle angle formed by selections (pk1), (pk2), (pk3) which can be set using the

This algorithm is used only when a .psf file has been loaded. Can be modified as needed for release notes. Use multiple OpenGL display lists for fonts depending on the stroke width. http://scriptkeeper.net/cannot-match/cannot-match-namelist-object-name-cutres.html If it is set to 2, then the view that is in the session gets set to the current view object_props = argument specifies whether properties should be loaded into PyMOL.

Eliminated old ifdefs for volumetric texturing. That's the line that reads DO 20 WHILE(nstate .GT.0). Changed the width of the main VMD window so that compilations against FLTK version 1.3.x using antialiased fonts will not have the help menu running off of the right hand edge

If one is specified but not the other, then the missing value is scaled so as to preserve the current aspect ratio.

Recent versions of PRMan do not support display scaling operations other than on the X and Y axes. state = the state number into which the file should loaded. Added new CVS tag for VMD 1.9 release Added extra error checking for the call to cudaSetDeviceFlags(), which is the first CUDA API called within each device pool worker thread other Enable compilation of HOOMD plugin using the dynamically linked libexpat.so Added HOOMD plugin to the optional list handles specially in the distrib build target.

Added support for weights. MAFFT was using a different descriptor for the sequence name that clustalw. enable *lig # enables all entities ending with lig SEE ALSO show, hide, disableapi: pymol.viewing.enableendingDESCRIPTION "ending" goes to the end of the movie. navigate here USAGE group name [, members [, action ]] ARGUMENTS name = string: name of the group members = string: space-separated list of objects to include in the group action = add,