Re: [PyMOL] apbs plugin
hi, good idea, it runs from the command line after adding /pymol/ext/lib to my library path but the plugin still crashes. something is odd about my APBS plugin setup. if i even just click to change the file locations it crashes. the other plugins seem fine. thanks jpd From: "Schubert, Carsten [JRDUS]" To: jp d ; "pymol-users@lists.sourceforge.net" Sent: Tuesday, February 11, 2014 12:14 PM Subject: RE: [PyMOL] apbs plugin Hi jpd, try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. HTH Carsten From:jp d [mailto:yo...@yahoo.com] Sent: Tuesday, February 11, 2014 2:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] apbs plugin hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2c29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd-- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk___ 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] apbs plugin
Hi jpd, try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. HTH Carsten From: jp d [mailto:yo...@yahoo.com] Sent: Tuesday, February 11, 2014 2:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] apbs plugin hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2c29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk___ 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] apbs plugin
hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2c29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk___ 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] RNA stick depiction with filled-out rings
Hi Thomas, thinks work like a charm! Thanks a lot. Claus On Feb 11, 2014, at 10:50 AM, Thomas Holder wrote: > Hi Claus, > > this works for me: > > set cartoon_ring_mode, 1 > set cartoon_ring_finder, 4 > show cartoon > hide cartoon, elem P > > Cheers, > Thomas > > On 10 Feb 2014, at 15:03, Kuhn, Claus-Dieter wrote: > >> Hi Pymol users, >> >> I am trying to depict RNA as sticks, however with filled-out rings (bases >> and ribose). >> I have been going about doing this by combining cartoon view for the >> filled-out bases, using set_cartoon_radius=0 and stick view for the backbone. >> >> When doing this I am always left with a fine line of cartoon_tube, which I >> would love to be invisible. >> >> How can I make this line invisible? >> >> Thanks a lot. >> >> Claus > > -- > Thomas Holder > PyMOL Developer > Schrödinger, Inc. > -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk ___ 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] RNA stick depiction with filled-out rings
Hi Claus, this works for me: set cartoon_ring_mode, 1 set cartoon_ring_finder, 4 show cartoon hide cartoon, elem P Cheers, Thomas On 10 Feb 2014, at 15:03, Kuhn, Claus-Dieter wrote: > Hi Pymol users, > > I am trying to depict RNA as sticks, however with filled-out rings (bases and > ribose). > I have been going about doing this by combining cartoon view for the > filled-out bases, using set_cartoon_radius=0 and stick view for the backbone. > > When doing this I am always left with a fine line of cartoon_tube, which I > would love to be invisible. > > How can I make this line invisible? > > Thanks a lot. > > Claus -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk ___ 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] RNA stick depiction with filled-out rings
Hi Claus, Maybe this: fetch 1rna, async=0 as sticks show cartoon set cartoon_side_chain_helper, 1 set cartoon_ring_mode, 1 Cheers, -- Jason On Mon, Feb 10, 2014 at 2:03 PM, Kuhn, Claus-Dieter wrote: > Hi Pymol users, > > I am trying to depict RNA as sticks, however with filled-out rings (bases and > ribose). > I have been going about doing this by combining cartoon view for the > filled-out bases, using set_cartoon_radius=0 and stick view for the backbone. > > When doing this I am always left with a fine line of cartoon_tube, which I > would love to be invisible. > > How can I make this line invisible? > > Thanks a lot. > > Claus > -- > Androi apps run on BlackBerry 10 > Introducing the new BlackBerry 10.2.1 Runtime for Android apps. > Now with support for Jelly Bean, Bluetooth, Mapview and more. > Get your Android app in front of a whole new audience. Start now. > http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk > ___ > 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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk ___ 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
