[PyMOL] Label on top of molecules?
Hello PyMOL users, When I print atom names with label all, name the labels are often behind the spheres (I use balls and sticks representation). I tried moving labels around, but my system is very dence -- and labels generally get under one or another sphere. Is there a way I can print labels on top of everything? With great respect, Boris. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Label on top of molecules?
Hi Boris, set float_labels, on will do the job. But it doesn't seem to affect ray-traced images. Then you might want to manually adjust label_position. See http://www.pymolwiki.org/index.php/Label_position For example, set label_position, (0, 0, 20) will bring labels 20 angstroms in front of its original position. Best regards, Takanori Nakane -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Label on top of molecules?
Hi Boris, Takanori had some good ideas to try. I just wanted to let you know that you uncovered some bugs that we've taken note of and will fix in both on-screen rendering and in ray traced mode. Cheers, -- Jason On Wed, Oct 17, 2012 at 7:47 AM, Boris Kheyfets kheyfbo...@gmail.com wrote: Hello PyMOL users, When I print atom names with label all, name the labels are often behind the spheres (I use balls and sticks representation). I tried moving labels around, but my system is very dence -- and labels generally get under one or another sphere. Is there a way I can print labels on top of everything? With great respect, Boris. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Tab completion using object names, not filesystem files?
PyMOL-users, I'm wondering if there's a way to make the tab completion engine use the currently loaded (or visible) object names rather than (or in addition to) the files in the filesystem? I usually have sessions with very long object names that I want to include in custom selection expressions and the tab completion doesn't work because oftentimes the PDB files are not in the same directory as the session. I found the function complete() in modules/pymol/parsing.py that seems to be what figures out how to complete the command that's been entered. I think if I just added a list of the currently loaded objects to the list obtained by globbing the filesystem, it would do what I'm looking for. Any ideas on the best way to do that? Best, -Ron -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Tab completion using object names, not filesystem files?
Hi Ron,
tab completion is controlled by the cmd.auto_arg variable, which is a
list of dictionaries.
http://pymolwiki.org/index.php/auto_arg
For all arguments which do not have an entry in auto_arg, the default is
to auto-complete file names. For your purpose you need to define
something like this:
python
import glob
cmd.auto_arg[0]['save'] = [
lambda: cmd.Shortcut(cmd.get_names() + glob.glob('*')),
'filename or object name', '']
python end
Cheers,
Thomas
Ron Jacak wrote, On 10/17/12 22:25:
PyMOL-users,
I'm wondering if there's a way to make the tab completion engine use
the currently loaded (or visible) object names rather than (or in
addition to) the files in the filesystem? I usually have sessions
with very long object names that I want to include in custom selection
expressions and the tab completion doesn't work because oftentimes the
PDB files are not in the same directory as the session. I found the
function complete() in modules/pymol/parsing.py that seems to be what
figures out how to complete the command that's been entered. I think
if I just added a list of the currently loaded objects to the list
obtained by globbing the filesystem, it would do what I'm looking for.
Any ideas on the best way to do that?
Best,
-Ron
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_sfd2d_oct
___
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Re: [PyMOL] Tab completion using object names, not filesystem files?
Hi Thomas,
Thanks for the quick reply. That worked exactly the way I wanted! I
had read the auto_arg Wiki page, but it didn't click that I had to
define a new list specifically for the command I wanted the tab
completion to work for (i.e. select). I thought it applied to all
commands.
So, for anyone else who is trying to do this, the command to have tab
completion use only loaded and visible object names *during select
statements* is as follows:
cmd.auto_arg[0]['select'] = [ lambda:
cmd.Shortcut(cmd.get_names(objects, enabled_only=1)), 'visible
object name(s)', '']
If you want tab completion to pull up loaded objects (visible or not)
as well as PDB files in the current working directory, it would be:
cmd.auto_arg[0]['select'] = [ lambda: cmd.Shortcut(cmd.get_names() +
glob.glob('*.pdb')), 'PDB file and object name(s)', '']
Best,
-Ron
On Wed, Oct 17, 2012 at 2:31 PM, Thomas Holder
spel...@users.sourceforge.net wrote:
Hi Ron,
tab completion is controlled by the cmd.auto_arg variable, which is a list
of dictionaries.
http://pymolwiki.org/index.php/auto_arg
For all arguments which do not have an entry in auto_arg, the default is to
auto-complete file names. For your purpose you need to define something like
this:
python
import glob
cmd.auto_arg[0]['save'] = [
lambda: cmd.Shortcut(cmd.get_names() + glob.glob('*')),
'filename or object name', '']
python end
Cheers,
Thomas
Ron Jacak wrote, On 10/17/12 22:25:
PyMOL-users,
I'm wondering if there's a way to make the tab completion engine use
the currently loaded (or visible) object names rather than (or in
addition to) the files in the filesystem? I usually have sessions
with very long object names that I want to include in custom selection
expressions and the tab completion doesn't work because oftentimes the
PDB files are not in the same directory as the session. I found the
function complete() in modules/pymol/parsing.py that seems to be what
figures out how to complete the command that's been entered. I think
if I just added a list of the currently loaded objects to the list
obtained by globbing the filesystem, it would do what I'm looking for.
Any ideas on the best way to do that?
Best,
-Ron
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_sfd2d_oct
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
