[PyMOL] disjoint surfaces

2009-12-21 Thread Raluca Mihaela ANDREI
Hi,
I imported into Blender (a 3D modelling and animation 
software) a surface created in PyMOL and I realized that there 
are some disjoint surfaces inside. Is it possible to remove 
these surfaces in PyMOL?
Thank you,
Raluca

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Re: [PyMOL] disjoint surfaces

2009-12-21 Thread Shiven Shandilya
Raluca,

Something that helps is: tabbing into edit mode, selecting all
vertices (ctrl-a) and removing doubles (Mesh Vertices Remove
Doubles).
Turning on smooth display also helps.

What exactly are you having problems with?   In what way are things
disjointed ?

Best,
Shiven


On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote:
 Hi,
 I imported into Blender (a 3D modelling and animation
 software) a surface created in PyMOL and I realized that there
 are some disjoint surfaces inside. Is it possible to remove
 these surfaces in PyMOL?
 Thank you,
 Raluca

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Re: [PyMOL] disjoint surfaces

2009-12-21 Thread Shiven Shandilya
Hi Raluca,

So I am guessing this something like the surface being in fragments,
with small vertices floating within the larger object?

Unfortunately there is no easy way to do this from within PyMOL,
unless you can separate out the residues/atoms that are contributing
the disjointed meshes into new objects and then turn them off before
export.

Right now the best thing I can think of going into edit mode in
Blender and deleting those vertices by hand.  :-(

Best,
Shiven


On Mon, Dec 21, 2009 at 12:11 PM, Raluca Mihaela ANDREI r.and...@sns.it wrote:
 Thank you Shiven,
 I know how to remove the double vertices in Blender but I would like to
 remove them directly from PyMOL. By disjoint meshes I mean non-connected
 meshes, inside my mesh I have some smaller meshes that are non connected to
 the big mesh. I would like to know how to remove these meshes before saving.
 Thank you,
 Raluca


 On Mon, 21 Dec 2009 11:24:11 -0500
  Shiven Shandilya shiven.shandi...@gmail.com wrote:

 Raluca,

 Something that helps is: tabbing into edit mode, selecting all
 vertices (ctrl-a) and removing doubles (Mesh Vertices

 Remove

 Doubles).
 Turning on smooth display also helps.

 What exactly are you having problems with?   In what way are things
 disjointed ?

 Best,
 Shiven


 On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it
 wrote:

 Hi,
 I imported into Blender (a 3D modelling and animation
 software) a surface created in PyMOL and I realized that there
 are some disjoint surfaces inside. Is it possible to remove
 these surfaces in PyMOL?
 Thank you,
 Raluca


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[PyMOL] List of Groups

2009-12-21 Thread David Hall
How would someone get the list of groups in a pymol session?  get_object_list 
doesn't have them and the only commands I can find in cmd that have the word 
group in them seems to be group and ungroup (if my quick regex search worked 
right).

Thanks,
David



  

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Re: [PyMOL] List of Groups

2009-12-21 Thread Jason Vertrees
David,

I think groups are treated like objects (see help group).  So, one can type
print cmd.get_names(objects)
and all the objects (proteins, groups, etc) will be returned.

For example:
  group a
  group b
  group c
  print cmd.get_names(objects)

The problem is that other objects will be returned, too.  So, if you
don't use special naming for your groups, they will run together with
other objects.

-- Jason

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PyMOLWiki -- http://www.pymolwiki.org



On Mon, Dec 21, 2009 at 6:45 PM, David Hall dwash59_2...@yahoo.com wrote:
 How would someone get the list of groups in a pymol session?  get_object_list 
 doesn't have them and the only commands I can find in cmd that have the word 
 group in them seems to be group and ungroup (if my quick regex search 
 worked right).

 Thanks,
 David





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[PyMOL] Linux 195.22 Nvidia binary driver + 120Hz LCD Samsung 2233RZ + Quadro FX 3700 + Nvidia 3D vision = working quad buffered stereo

2009-12-21 Thread Sabuj Pattanayek
Hi all,

Just wanted to mention that I've updated some of the info on the wiki here:

http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#LCD_Displays_.28120_Hz.29

to note that quad buffered stereo (QBS) on the 120Hz Samsung 2233RZ
LCD monitor works on Linux. It's nowhere as cheap as the Zalman
solution but will work with any other visualization apps out there
that have QBS support which don't support the Zalman.

HTH,
Sabuj Pattanayek

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