Re: [PyMOL] pymol svn

I'm also unable to checkout from that url from two separate networks and machines. Error message: svn: E210002: Unable to connect to a repository at URL 'svn://svn.code.sf.net/p/pymol/code/trunk/pymol' svn: E210002: Network connection closed unexpectedly ~Paul --

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Wed, Apr 6, 2011 at 3:07 PM, wrote: > I found the ce_types.h problem happens with autotools, but not with > setup.py method. > > -David > > On Apr 6, 2011, at 5:59 PM, Paul Rigor wrote: > > Hi all, > > So I

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

issues. I'm running python 2.6 on a CentOS 5.5 distro on a 64-bit machine. Thanks, paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Mon, Apr 4, 2011 at 6:07 AM, Tru Huynh wrote: > Hi Jason, > > On Mon, Apr 04, 2011 at 08:19:17AM -0400, Jason Vertrees wrote: > > > > A

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

Thanks for the update, looking forward to testing the new release. Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Fri, Apr 1, 2011 at 6:16 PM, Christoph Gohlke wrote: > > > On 4/1/2011 2:34 PM, Jason Vertrees wrote: > >> Greetings PyMOLers, >> >> I got ba

Re: [PyMOL] PyMOL at West Coast Meetings

I'll be at ACS! See you and the developers there. Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Tue, Mar 22, 2011 at 12:09 AM, Jason Vertrees wrote: > Hi all, > > Just a quick note to let you know that PyMOL will be represented at > the Schrodinger booths at the WCPC

Re: [PyMOL] highlighting a selection

Have you checked out the wiki? http://www.pymolwiki.org/index.php/Main_Page Cheers, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor On Fri, Feb 4, 2011 at 4:58 PM, rv...@libero.it wrote: > Hello everyone, > > when I make a selection by code: > > cmd.select(..) > >

Re: [PyMOL] Rendering issues with education version 1.3

Thanks!! -- Paul Rigor http://www.ics.uci.edu/~prigor <http://www.ics.uci.edu/%7Eprigor> On Tue, Jan 18, 2011 at 6:47 AM, Robert Campbell wrote: > Hi Paul, > > On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor wrote: > > > Hi gang, > > Just wondering if any

[PyMOL] Rendering issues with education version 1.3

al version 1.3. I've tried on linux and mac os x. The nvideo cards include both ATI and NVidia. Cheers, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor top4fix.pdbqt Description: Binary data -- Protect Your Sit

Re: [PyMOL] how to run a python script

first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.m

Re: [PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard

port installed tk tcl pymol. On a macosx 10.5.8 I get: > pymol @1.3_0 (active) > tcl @8.5.8_0+darwin (active) > tk @8.5.8_0+darwin (active) > Ultimately you could file a bug report with macports or ask on their > mailing list. > Marius > > On Sat, Jul 10, 2010 at 3:10 AM,

Re: [PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard

id you try the macports (http://www.macports.org/) version? > Marius > > On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) wrote: > >> Hi gang, >> >> Actually, I spoke too soon! I attempted this compilation to address >> another user's problems with an extern

Re: [PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard

53 PM, Paul Rigor (uci) wrote: > Hi gang, > > Just wanted to share some notes on compiling and getting Pymol 1.3.x > running on OS X Snow Leopard. Before proceeding, you'll of course need the > XCode SDK which comes supplied with the OS X cd's or downloaded through >

Re: [PyMOL] how to run a python script

first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.m

[PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard

pack; dive into the src folder and issue python setup.py build python setup.py install All should work. Cheers, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor -- This SF.net email is sponsored by Sprint What will y

Re: [PyMOL] taking snapshots from a script

>  get_view() >  and restore that view in all other proteins >  (2) PyMOL has a preset view for ligand binding sites; A > Preset > > Ligand Sites > Transparent (better) is a good one. > > Good luck, > > -- Jason > > On Thu, May 6, 2010 at 1:00 AM, Paul Rigor (uci-ics)

[PyMOL] taking snapshots from a script

Hi, Is there anyway to access the rendering engine of pymol through a command line script? I'd like to take a snapshot of a ligand-bound protein, but automate the view such that 1) The protein is shown as a surface 2) The view centers around the binding area 3) The view zooms out enough to presen

[PyMOL] odd rendering with pdbqt files containing multiple molecules

-- Paul Rigor Pre-doctoral BIT Fellow and Graduate Student Institute for Genomics and Bioinformatics Donald Bren School of Information and Computer Sciences University of California, Irvine http://www.ics.uci.edu/~prigor