Stuart, Empty PDB files can result from writing a file while PyMOL's global state number is set to a numerical state that does not actually contain the coordinates. Note that by default, single state objects are displayed in all states (unless static_singletons is disabled), which can cause some confusion.
If this is the cause of your problem, then make sure that [ 1/ ... is displayed in the lower-right hand corner before saving. Cheers, Warren > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Stuart Endo-Streeter > Sent: Wednesday, April 25, 2007 5:57 AM > To: PYMOLBB > Subject: [PyMOL] failure to save coordinates adjusted with edit tool > > Hi all, > > I am trying to fit part of my search model into my > experimental density using pymol. I got initial model > fitting to the experimental map using molrep, but want to > make some changes to certain helices and strands before I pop > the model into a rigid body and simulated annealing run, > since they're obviously off by eye and a correction here > would make the subsequent runs that much better. I've done > the following: > > Loaded molrep fit model > Loaded experimental maps > Created selection of residues to move > Turned selection into an object > Moved object using "3-button Editing" mode Save object.pdb, > object name > > However, when I look at the saved file that should contain > the coordinates of the adjusted model, it is empty except for > an END statement. As a control I loaded another model, > rotated it in editing mode, then saved it as a new pdb file > (so no selection creation or change from selection to > object). It also wrote an empty but for END file. I googled > around and look through some of the mailing list, but have > not found any clues. > > I also used File-> Save molecule from the pull-down menu, same result. > > Does anyone have an idea what is going on or how to correct? > Pymol version 0.99rc6 running on Linux (CentOS 4.4) > > > Stuart Endo-Streeter > > > > > > > > > > ______________________________________ > Stuart T. Endo-Streeter > Structural Biology and Biophysics > Dept. Biochemistry > LSRC C266 > Duke University > 919-681-1668 > stuart.endostree...@duke.edu > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by DB2 Express Download DB2 > Express C - the FREE version of DB2 express and take control > of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
