Re: [PyMOL] (no subject)

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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] PyMOL 1.6 final release

I missed it! Sorry cheers, Gianluigi Da: Thomas Holder thomas.hol...@schrodinger.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users pymol-users@lists.sourceforge.net Inviato: Giovedì 13 Giugno 2013 10:10 Oggetto: Re: [PyMOL] PyMOL 1.6 final

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 jmsstarli...@gmail.com A: pymol-users pymol-users@lists.sourceforge.net

[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 tlin...@gmail.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users

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

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

,   Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano chimic...@yahoo.it 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

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

[PyMOL] APBS-electrostatics

,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 '_self' Thank you for your help Gianluigi Caltabiano

Re: [PyMOL] APBS surface

Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS

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 - Messaggio originale - Da

[PyMOL] APBS surface

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, BioStatistic Dept. UAB, Universitat Autonoma de