Re: [PyMOL] (no subject)

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Re: [PyMOL] PyMOL 1.6 final release

I missed it! Sorry cheers, Gianluigi Da: Thomas Holder A: Gianluigi Caltabiano Cc: pymol-users Inviato: Giovedì 13 Giugno 2013 10:10 Oggetto: Re: [PyMOL] PyMOL 1.6 final release Hi Gianluigi, since 1.5.0.6 PyMOL has an integrated Plugin Manager which

Re: [PyMOL] PyMOL 1.6 final release

Hi all, I am experiencing a problem with the X11 version of 1.6 (MAC user). The new version is not auto loading the plugins in the repository directory, which worked fine to me until yesterday, (pymol 1.5.3) When opening HybridPymol  no error messages are displayed, but if I manually give the

Re: [PyMOL] Cartoon transparency

You need to create a new object of the part you want transparent and then set that cartoon as transparent (and hide the "original" cartoon for the selection).  G. Da: James Starlight A: pymol-users Inviato: Giovedì 6 Giugno 2013 12:36 Oggetto: [PyMOL] Carto

[PyMOL] Transparency of VASCo surfaces

Hi all, I often use  VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not "respond" to: set transparency, value, object  Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding

Re: [PyMOL] PyMOL to 3D PDF

Hi Troels, yes I did try  many save name.idtf, selection / object / all / *  and no output in the command window did appear... thanks anyway, Gianluigi Da: Troels Emtekær Linnet A: Gianluigi Caltabiano Cc: "pymol-users@lists.sourceforge.net"

Re: [PyMOL] PyMOL to 3D PDF

Very interesting features! I have never tried and was trying to do it, following the tutorial in pymolwiki but at : * Save your molecule to an IDTF file in PyMOL: save pymol.idtf, * PyMOL will print a line that looks like: 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.4

Re: [PyMOL] Memory not released after load and delete of structure

mas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano wrote: > I have the same problem since pymol 1.5, mainly with the hybrid (I can reach > 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and > pymol version 1.5.0.3. > I had to renounce working with

Re: [PyMOL] Memory not released after load and delete of structure

I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in.  Gianluigi ___

[PyMOL] Info graphical cards

Dear PyMOLers, I am going to buy a new PC and want to make sure no issues come with the graphical card and PyMOL.  The PC will run on Ubuntu 11.10 on a Intel Core i5 2400  vPro. The card will be NVIDIAGeForceGTX 560 Ti   Does anybody had any issues with this card? cheers Gianluigi

Re: [PyMOL] problems cloring sticks

With Ubuntu 10.04 LTS - Lucid Lynx and Pymol 1.4.1 it seems to solve the problem. thanks, Gianluigi Da: Jason Vertrees A: "pymol-users@lists.sourceforge.net" Inviato: Mer 8 giugno 2011, 20:34:46 Oggetto: Re: [PyMOL] problems cloring sticks For those using

[PyMOL] APBS-electrostatics

pymol\wizarding.py", line 86, in wizard r = _wizard(name,arg,kwd,0) File "C:\Archivos de programa\DeLano Scientific\PyMOL/modules\pymol\wizarding.py", line 45, in _wizard wiz = apply(getattr(mod_obj,oname),arg,kwd) TypeError: __init__() got an unexpected keyword argument 

Re: [PyMOL] Are there any feature requests for the PyMOL-APBS plugin?

What about the possibility to show the surfaces of just a selection of residues? Thank You, Gianluigi Caltabiano, Ph.D. Lab of Computational Medicine Autonomic University of Barcelona Spain - Messaggio originale - Da: Michael Lerner A: pymol-users@lists.sourceforge.net Inviato: Giovedì

Re: [PyMOL] APBS surface

OK...it's as I thought. That is uploading the "wrong structure" it shows me the map from the "ligand" but on receptors VdW surface. Thanks all, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Mes

Re: [PyMOL] APBS surface

luigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers A: Gianluigi Caltabiano Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to "create&q

[PyMOL] APBS surface

teractions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine,