Re: [PyMOL] using morph where only one state contains a small molecule
Hi Claus, going from the example on the PyMOLWiki, which uses also one structure with ligand and one without: fetch 1akeA 4akeA, async=0 align 1akeA, 4akeA morph mout, 1akeA, 4akeA extract ligand, 1akeA and organic hide everything show cartoon, mout show sticks, ligand The ligand can't be part of the morphed multi-state object (mout), because there are no target coordinates for it. But if you just extract it to a separate object (with one state), it still can be part of a movie and even move around independently. Try this: mset 1-30 unset movie_auto_store mview store, 1, object=ligand translate [10,0,0], object=ligand mview store, 30, object=ligand (this might move in a silly direction, but you get the idea...) Cheers, Thomas On Oct 11, 2013, at 9:59 AM, "Kuhn, Claus-Dieter" wrote: > Hi everyone, > > I am trying to use the new morph command with incentive Pymol 1.6. The 2 > states I am morphing between show an enzyme, which closes its active site > over an incoming small molecule, meaning, the small molecule is only present > in the second structure. > How can I get Pymol to display the small molecule during morphing? > I always receive an error message where Pymol tells me that it couldnt > recognize the small molecule. Is there a way I can load a library into Pymol > as can be easily done in Coot? > > Thanks for any advice, > > Claus > > Cold Spring Harbor Laboratory > Cold Spring Harbor, NY, USA -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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] neutral aminoacids
Thanks for the tip! On Fri, Oct 11, 2013 at 8:53 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Osvaldo, > > To make PyMOL pick fragments from another location just edit the path > at the top of pymol/modules/chempy/fragments/__init__.py. > > The fab command is in pymol/modules/pymol/editor.py. > > Cheers, > > -- Jason > > > > On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin > wrote: > > BTW, there is an easy option to make cmd.fab() to pick the fragments > from an > > alternative location? (just to avoid modifying the original fragments > files) > > > > thanks, > > > > Osvaldo. > > > > On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin > > wrote: > >> > >> Ok, I will try editing those files. > >> > >> Cheers, > >> > >> Osvaldo. > >> > >> > >> > >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees > >> wrote: > >>> > >>> Hi Osvaldo, > >>> > >>> This isn't built in yet. But, if you need to do that, you can edit the > >>> Python picked files found here: > >>> > >>> pymol/data/chempy/fragments > >>> > >>> Cheers > >>> > >>> -- Jason > >>> > >>> On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin > > >>> wrote: > >>> > > >>> > I am using the comand cmd.fab() to create small peptides. There is an > >>> > easy > >>> > option to add neutral aminoacids? The default behaviour is to add > >>> > charged > >>> > amino acids with the charge of the free amino acid in solution at pH > = > >>> > 7 > >>> > i.e. Lys and Arg protonated and Glu, Asp and His unprotonated. > >>> > > >>> > Thanks in advance. > >>> > > >>> > > >>> > > -- > >>> > October Webinars: Code for Performance > >>> > Free Intel webinars can help you accelerate application performance. > >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the > >>> > most > >>> > from > >>> > the latest Intel processors and coprocessors. See abstracts and > >>> > register > > >>> > > >>> > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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 > >> > >> > > > > > > -- > Jason Vertrees, PhD > Director of Core Modeling Products > Schrödinger, Inc. > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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] using morph where only one state contains a small molecule
Hi everyone, I am trying to use the new morph command with incentive Pymol 1.6. The 2 states I am morphing between show an enzyme, which closes its active site over an incoming small molecule, meaning, the small molecule is only present in the second structure. How can I get Pymol to display the small molecule during morphing? I always receive an error message where Pymol tells me that it couldnt recognize the small molecule. Is there a way I can load a library into Pymol as can be easily done in Coot? Thanks for any advice, Claus Cold Spring Harbor Laboratory Cold Spring Harbor, NY, USA -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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] neutral aminoacids
Osvaldo, To make PyMOL pick fragments from another location just edit the path at the top of pymol/modules/chempy/fragments/__init__.py. The fab command is in pymol/modules/pymol/editor.py. Cheers, -- Jason On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin wrote: > BTW, there is an easy option to make cmd.fab() to pick the fragments from an > alternative location? (just to avoid modifying the original fragments files) > > thanks, > > Osvaldo. > > On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin > wrote: >> >> Ok, I will try editing those files. >> >> Cheers, >> >> Osvaldo. >> >> >> >> On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees >> wrote: >>> >>> Hi Osvaldo, >>> >>> This isn't built in yet. But, if you need to do that, you can edit the >>> Python picked files found here: >>> >>> pymol/data/chempy/fragments >>> >>> Cheers >>> >>> -- Jason >>> >>> On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin >>> wrote: >>> > >>> > I am using the comand cmd.fab() to create small peptides. There is an >>> > easy >>> > option to add neutral aminoacids? The default behaviour is to add >>> > charged >>> > amino acids with the charge of the free amino acid in solution at pH = >>> > 7 >>> > i.e. Lys and Arg protonated and Glu, Asp and His unprotonated. >>> > >>> > Thanks in advance. >>> > >>> > >>> > -- >>> > October Webinars: Code for Performance >>> > Free Intel webinars can help you accelerate application performance. >>> > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the >>> > most >>> > from >>> > the latest Intel processors and coprocessors. See abstracts and >>> > register > >>> > >>> > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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 >> >> > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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] Residue selection problem in PyMOL 1.6
I found a previous report on the same issue and it is fixed in the svn: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11581.html I guess I will try the updated version. Hongbo -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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] Residue selection problem in PyMOL 1.6
Hi, I have downloaded PyMOL v1.6.0.0 from sourceforge and installed it on my Ubuntu 12.04. It works very well. Recently I noticed there is a problem when selecting residues from the sequence panel (Display -> Sequence). If I select multiple residues using mouse in the sequence panel, only the first selected residue is highlighted in the corresponding structure. Then rest selected residues are not highlighted. But if I disable my selection and enable it again (e.g. by clicking on the selection name in the control panel), all the selected residues will be highlighted. This is different from PyMOL 1.5 or older version, and I don't think it is a feature (I read what's new for 1.6 :). There is no any warning or error message output on the terminal. Has anyone had similar problem? Hongbo -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&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
