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
If this is the cause of your problem, then make sure that [ 1/ ... is
displayed in the lower-right hand corner before saving.
> -----Original Message-----
> From: pymol-users-bounces@...
> [mailto:pymol-users-bounces@...] 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
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