[PyMOL] strange behavior when using create
Hi, I have attached two pdb files and one pymol script. For some reason the atom ID's in the first state of test are not properly copied from test-1. The ID's of the second state of test are on the other hand. Am I doing something wrong here? Thanks already, nick test.pml Description: Binary data test-1.pdb Description: Protein Databank data test-2.pdb Description: Protein Databank data -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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] pymol within VNC session
Hello list, I find that running pymol within a VNC session looks horrible. The molecule in the main window flickers, disappears at times, comes back, making pymol basically unusable. Avogadro on the other hand works just fine, and looks just like running it on the local desktop. What could I do to fix this? Is there a compile time option? A runtime option? Thanks already, nick -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] store/recall stick_transparency in scene?
Thanks. On 05/20/11 11:13, Jason Vertrees wrote: > Hi Nick, > > This is something Robert Campbell alluded to a few days ago. To get > what you want, the "python block" and "mdo" are you friends: > > # create an ala fragment and setup the view > > frag ala > as sticks > orient > > # 60-frame movie > > mset 1x60 > > # start a Python block that fades out the fragment > > python > for x in range(60): > cmd.mdo(x, "set_bond stick_transparency, %f, ala" % (x/60.)) > python end > > # play the movie > > mplay > > See: > * -- http://www.pymolwiki.org/index.php/Mdo > * -- http://www.pymolwiki.org/index.php/Python > > Cheers, > > -- Jason > > > On Fri, May 20, 2011 at 12:54 PM, Nicolas Bock wrote: >> When I do the following >> >> hide all >> show sticks, all >> scene 001, store >> >> set_bond stick_transparency, 0.5, all >> scene 002, store >> >> scene 001 >> >> the stick_transparency setting is not restored. I was hoping I could use >> scenes to slowly fade out a part of a molecule by adding several scenes >> with increasing stick_transparency values. >> >> Thanks, nick >> >> >> -- >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> ___ >> 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 >> > > > signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] mdo command
I realized that the "mdo" command can be used to change the stick_transparency setting. mdo 1: set_bond stick_transparency, 0, all mdo 100: set_bond stick_transparency, 0.8, all and so on. I noticed that the example section in the help text for the mdo command is incorrect. It states: > EXAMPLE > > // Creates a single frame movie involving a rotation about X and Y > > load test.pdb > mset 1 > mdo 1, turn x,5; turn y,5; > mplay however, it should read: mdo 1: turn x,5; turn y,5; nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] store/recall stick_transparency in scene?
When I do the following hide all show sticks, all scene 001, store set_bond stick_transparency, 0.5, all scene 002, store scene 001 the stick_transparency setting is not restored. I was hoping I could use scenes to slowly fade out a part of a molecule by adding several scenes with increasing stick_transparency values. Thanks, nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] change atom coordiates?
Hello, can I selectively change coordinates of particular atoms in a state? It seems that "alter_state" is not able to do that, since the expression (at least according to the help text) seems to apply to the x-coordinate of all atoms in the state for instance. The result of cmd.get_model() might be useful here, but I can't figure out how to access individual coordinates and then store them back into the state. Any hints are greatly appreciated. Thanks, nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] movie: interpolate between different states
Hi Jason, I have the incentive version, but how do I use rigimol? I can't find documentation for it on the documentation webpage. The link from http://pymol.org/dsc/dokuwiki/doku.php?id=ip&s=rigimol seems to be dead. Thanks, nick On 05/18/11 15:20, Jason Vertrees wrote: > Hi Nick, > > You can use the "smooth" command > (http://www.pymolwiki.org/index.php/Smooth) on the structure of > choice. Incentive PyMOL comes with a molecular morpher called > "rigimol" that morphs a starting structure into an ending structure. > I suggest trying the "smooth" command first if you already have the > states. > > Cheers, > > -- Jason > > On Wed, May 18, 2011 at 3:39 PM, Nicolas Bock wrote: >> Hi, >> >> can pymol interpolate between states in a movie? Suppose I have >> coordinates of a docking process with several states, and I would like >> to animate that process, but smoothly. I would >> >> madd 1 x15 >> madd 2 x15 >> . >> . >> . >> >> but would like pymol to interpolate in those 15 frames between state 1 >> and 2, then 2 and 3, and so on. >> >> Thanks, nick >> >> >> -- >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> ___ >> 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 >> > > > signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] movie: interpolate between different states
Hi, can pymol interpolate between states in a movie? Suppose I have coordinates of a docking process with several states, and I would like to animate that process, but smoothly. I would madd 1 x15 madd 2 x15 . . . but would like pymol to interpolate in those 15 frames between state 1 and 2, then 2 and 3, and so on. Thanks, nick signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] change transparency for only a selection
Hi Jason, thanks, that works! nick On 05/18/11 12:08, Jason Vertrees wrote: > Hi Nick, > > Sticks are bonds. For that we use "set_bond" not set. > > Try: > > set_bond stick_transparency, 0.8, rest > set_bond stick_transparency, 0.0, sel_01 > > Cheers, > > -- Jason > > On Wed, May 18, 2011 at 1:39 PM, Nicolas Bock wrote: >> Hello list, >> >> I would like to change the stick_transparency for a selection but it >> doesn't seem to work. I am using the xyz file from the wiki: >> >> http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example >> >> and the attached script. What am I doing wrong? >> >> Thanks already, nick >> >> -- >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> ___ >> 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 >> > > > signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] change transparency for only a selection
Hello list, I would like to change the stick_transparency for a selection but it doesn't seem to work. I am using the xyz file from the wiki: http://www.pymolwiki.org/index.php/Visualizing_a_computed_structure_-_a_commented_example and the attached script. What am I doing wrong? Thanks already, nick example.xyz Description: Xmol XYZ data example.pml Description: application/vnd.ctc-posml signature.asc Description: OpenPGP digital signature -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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] drawing of objects for illustration
Hi Jason,
nice. I didn't know about the pseudoatoms, very cool.
nick
On Wed, May 19, 2010 at 10:39, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Nicolas,
>
> Cool idea. First the "witihin" operator works on more than just
> single atoms. So, how about something like this:
>
> # fetch a protein
> fetch 1oky, async=0
>
> # let's target _all_ atoms within 8 Angs of _all_ of
> # residue 55, not just one atom
> select target, all within 8 of i. 55
> color red, target
>
> cmd.center("i. 55")
> vPos = cmd.get_position()
>
> cmd.pseudoatom("identifier",pos= vPos);
> show_as spheres, identifier
> cmd.set("sphere_transparency", 0.5, "identifier")
> cmd.set("sphere_scale", 8, "identifier")
>
> In sum, use pseudoatom for and position it at vPos.
>
> Cheers,
>
> -- Jason
>
> On Wed, May 19, 2010 at 12:22 AM, Nicolas Bock
> wrote:
> > Hello,
> >
> > I would like to do the following: I have a large protein loaded in pymol.
> I
> > would like to select all atoms within a radius around a point. I know
> about
> > "select within", however, this command requires the second selection to
> be
> > an atom. I would prefer if the center of the sphere is not necessarily
> > centered on an atom. Is this possible? In addition I would like to draw
> the
> > spherical selection region somewhat transparently, so that I can
> illustrate
> > what I have selected. Is that possible?
> >
> > Thanks already,
> >
> > nick
> >
> >
> >
> --
> >
> >
> > ___
> > 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
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
___
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Re: [PyMOL] drawing of objects for illustration
Hi Michael, thanks! nick On Tue, 2010-05-18 at 23:55 -0500, Michael Zimmermann wrote: > Dear Nicolas, > > As for the semi-transparent sphere, there are a number of ways to do > that. One option: You could create a new object named new_obj with an > atom at the center point and use "alter new_obj, vdw=radius" to make > the sphere. Then use "set sphere_transparency, 0.5, new_obj" > > Alternatively, you could make a cgo object: > http://pymolwiki.org/index.php/Ellipsoid > > Now, on to your first question: If you use the first approach I > mention for making your sphere, then this problem is also solved > because now you have an atom to select around. > > Cheers, > > Mike Z > > > On Tue, May 18, 2010 at 11:22 PM, Nicolas Bock > wrote: > > Hello, > > I would like to do the following: I have a large protein > loaded in pymol. I would like to select all atoms within a > radius around a point. I know about "select within", however, > this command requires the second selection to be an atom. I > would prefer if the center of the sphere is not necessarily > centered on an atom. Is this possible? In addition I would > like to draw the spherical selection region somewhat > transparently, so that I can illustrate what I have selected. > Is that possible? > > Thanks already, > > nick > > > > > > -- > > > ___ > 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 > > > > > -- > Michael Zimmermann > Ph.D. student in Bioinformatics and Computational Biology > Department of Biochemistry, Biophysics and Molecular Biology > Iowa State University signature.asc Description: This is a digitally signed message part -- ___ 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] drawing of objects for illustration
Hello, I would like to do the following: I have a large protein loaded in pymol. I would like to select all atoms within a radius around a point. I know about "select within", however, this command requires the second selection to be an atom. I would prefer if the center of the sphere is not necessarily centered on an atom. Is this possible? In addition I would like to draw the spherical selection region somewhat transparently, so that I can illustrate what I have selected. Is that possible? Thanks already, nick signature.asc Description: This is a digitally signed message part -- ___ 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] Fwd: feature request: supercell construction
forgot to also send to the list. -- Forwarded message -- From: Nicolas Bock Date: Thu, Apr 15, 2010 at 15:46 Subject: Re: [PyMOL] feature request: supercell construction To: Thomas Holder Hi Thomas, On Thu, Apr 15, 2010 at 03:42, Thomas Holder wrote: > Hi Nick, > > > I noticed a few things: > > > > - when I run "supercell 2, 1, 1" I get another cell outline along the > > a axis, but no atoms are shown in the second cell. Do I have to run > > another command for them to show up? > > the script does not create symmetry mates. The "symexp" command can > create symmetry mates within a given radius (it will not just fill up > the cell). > Maybe I just don't understand the symexp command, but how would it help me in constructing a 2x2x2 supercell from a unit cell with atom positions? Isn't the radius meaningless in this context since it implies a radial cutoff, whereas a simple cubic unit cell has a cubic cutoff? When I look at a crystal I would want the supercell construction to get a better idea of how the bulk crystal looks like. With small unit cells this is sometimes tricky without explicitly constructing a supercell. Also, in the case of a triclinic unit cell, for example, finding the correct symmetry operation for the "symexp" command might be rather tricky. > > > - when I run the command again with other values for a, b, or c, > > nothing changes. I would expect that running the sequence "supercell > > 2, 1, 1" and then "supercell 2, 2, 1" would show me a 2x2x1 supercell > > at the end, but I see only the 2x1x1 supercell. > > the second call will create a new state for the same object. This is not > convenient, so I changed it to replace the first state again. I put the > modified script to the PyMOLWiki: > > http://www.pymolwiki.org/index.php/Supercell > > Thanks! > Cheers, > Thomas > > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request: supercell construction
Hi Thomas, thanks! I noticed a few things: - when I run "supercell 2, 1, 1" I get another cell outline along the a axis, but no atoms are shown in the second cell. Do I have to run another command for them to show up? - when I run the command again with other values for a, b, or c, nothing changes. I would expect that running the sequence "supercell 2, 1, 1" and then "supercell 2, 2, 1" would show me a 2x2x1 supercell at the end, but I see only the 2x1x1 supercell. Thanks again, nick On Wed, Apr 14, 2010 at 03:24, Thomas Holder wrote: > Hi Nick, > > I recently was playing with (aka learning) the crystallographic symmetry > information in PDB files and now took your feature request as an > exercise. See attached file, hope it does what you had in mind. > > Cheers, > Thomas > > On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote: > > It would be great if pymol had support for constructing and displaying > > a supercell: > > > > For data files that support crystallographic information, e.g. pdb, > > pymol can already display the unit cell (show cell). It would be great > > if one could easily display multiple copies of the unit cell, along > > the lines of > > > > supercell 1,1,2 > > > > where pymol would then copy the unit cell along the c-axis and display > > 2 unit cells. > > > > supercell 2,2,2 > > > > would display 2 copies along the a, b, and c axes, and display 8 unit > > cells in total. > > > > As a related request it would be great if pymol could construct a unit > > cell in case the crystallographic information in the input file does > > not exist. This could come in handy for instance when reading from > > xyz. Maybe a command such as > > > > construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90, > > gamma=90 > > > > would construct a cubic cell with dimensions axbxc. > > > > Thanks, > > > > nick > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request: supercell construction
It would be great if pymol had support for constructing and displaying a supercell: For data files that support crystallographic information, e.g. pdb, pymol can already display the unit cell (show cell). It would be great if one could easily display multiple copies of the unit cell, along the lines of supercell 1,1,2 where pymol would then copy the unit cell along the c-axis and display 2 unit cells. supercell 2,2,2 would display 2 copies along the a, b, and c axes, and display 8 unit cells in total. As a related request it would be great if pymol could construct a unit cell in case the crystallographic information in the input file does not exist. This could come in handy for instance when reading from xyz. Maybe a command such as construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90, gamma=90 would construct a cubic cell with dimensions axbxc. Thanks, nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] supercell?
Hello, I load a pdb file with crystal cell information and I would like to display a 2x2x2 supercell. I can't figure out how to do that. Is this possible in pymol? nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
Could the connect_mode setting be better documented? The current documentation doesn't say much about what that setting does. nick On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > 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 > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
Great, that works! On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > 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 > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
I should mention that the first 3 columns are the cartesian coordinates in Angstroms, and the last 3 columes the forces in eV/A. On Fri, Mar 12, 2010 at 11:50, Nicolas Bock wrote: > Please find attached an example xyz file. > > nick > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > >> When I load an xyz file with several frames (for example the result of an >> MD simulation) I find that pymol calculates and sets the bonds only using >> the initial frame. For frames > 1 the bonds are not recalculated. The only >> "work around" I found is to load(..., multiplex=1) which loads the frames >> into separate objects. But now I can not play the MD trajectory as a movie. >> >> I would like to suggest that this feature be added to pymol so that MD >> trajectories can be played with proper bonding for all frames. >> >> Thanks >> >> nick >> >> > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
Please find attached an example xyz file. nick On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > When I load an xyz file with several frames (for example the result of an > MD simulation) I find that pymol calculates and sets the bonds only using > the initial frame. For frames > 1 the bonds are not recalculated. The only > "work around" I found is to load(..., multiplex=1) which loads the frames > into separate objects. But now I can not play the MD trajectory as a movie. > > I would like to suggest that this feature be added to pymol so that MD > trajectories can be played with proper bonding for all frames. > > Thanks > > nick > > HCN_to_CHN.xyz Description: Protein Databank data -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
After editing a molecule it can happen that the bonds that used to be there don't all make sense anymore, for example, because I moved an atom pretty far away from its original place. It would be nice if one could call a function to force pymol at some point to recalculate the bonds in the molecule. Unfortunately there is currently no "rebond" function. I would like to suggest that it be added. Thanks nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request
When I load an xyz file with several frames (for example the result of an MD simulation) I find that pymol calculates and sets the bonds only using the initial frame. For frames > 1 the bonds are not recalculated. The only "work around" I found is to load(..., multiplex=1) which loads the frames into separate objects. But now I can not play the MD trajectory as a movie. I would like to suggest that this feature be added to pymol so that MD trajectories can be played with proper bonding for all frames. Thanks nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] feature request?
Hello list, what's the mechanism for submitting feature requests or bug reports? To this list? nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] what function creates the bonds?
Hi Jason, thanks for the reply. I was assuming that the load function works something like this: def load(): load_xyz() create_bonds() I take it from your comments that what I called "create_bonds()" is not directly accessible? Or possibly not all contained in one function call? nick On Wed, Mar 10, 2010 at 21:43, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nick, > > You can manually create/delete bonds using PyMOL builder (click the > "builder" button in the upper control window). The command to create > a bond is "bond," but you really don't want to poke around the > internal code for bonds. Feel free, but consider yourself warned. > :-) > > Cheers, > > -- Jason > > On Wed, Mar 10, 2010 at 11:21 AM, Nicolas Bock > wrote: > > Hello list, > > > > when I load an xyz file, pymol somehow manages to add bonds to the atoms. > > What function does that? Can I directly call that function to recalculate > > the bonds? > > > > nick > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > 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 > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] what function creates the bonds?
Hello list, when I load an xyz file, pymol somehow manages to add bonds to the atoms. What function does that? Can I directly call that function to recalculate the bonds? nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] dynamic bonding
Hi Jason, thanks for the hint. That works just fine. nick On Mon, Dec 14, 2009 at 11:12, Jason Vertrees wrote: > Nick, > > Interesting question. My best guess at this point is that PyMOL can't > do what you want. You can load the XYZ file into multiple distinct > objects: > >load myXYZ.xyz, multiplex=1 > > and each object will be shown with proper bonding. However, the > moment you try to combine those into one structure they retain the > bonding topology of the first structure. If you change any > intermediate state, then they all change. > > Anyone else? > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock > wrote: > > Hello list, > > > > I have a bunch of xyz files that are along a transition path in a > molecule. > > When I load all of them into pymol and step through the individual > frames, > > pymol calculates the bonds only for the initial frame. This leads to > wrong > > bonding in subsequent frames since some atoms move quite a bit during the > > transition. How can I get "dynamic" bonding so that bonding is > recalculated > > for each frame? > > > > nick > > > > > > > -- > > Return on Information: > > Google Enterprise Search pays you back > > Get the facts. > > http://p.sf.net/sfu/google-dev2dev > > > > ___ > > 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 > > > -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ 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] dynamic bonding
Hi Jason, sure, I have attached the xyz file to this email. We print out forces in columns 4-6 in the xyz. I run PyMOL(TM) Molecular Graphics System, Version 1.2r1. on linux, 64-bit. Let me know if you need any additional information. Thanks, nick On Mon, Dec 14, 2009 at 10:20, Jason Vertrees wrote: > Nick, > > Can I have a copy of that xyz file? I just tried loading a multi-xyz > file here and it worked fine. What system (OS) and version of PyMOL > are you using? > > Thanks, > > -- Jason > > -- > Jason Vertrees, PhD > > PyMOLWiki -- http://www.pymolwiki.org > > > > On Mon, Dec 14, 2009 at 11:30 AM, Nicolas Bock > wrote: > > Hello list, > > > > I have a bunch of xyz files that are along a transition path in a > molecule. > > When I load all of them into pymol and step through the individual > frames, > > pymol calculates the bonds only for the initial frame. This leads to > wrong > > bonding in subsequent frames since some atoms move quite a bit during the > > transition. How can I get "dynamic" bonding so that bonding is > recalculated > > for each frame? > > > > nick > > > > > > > -- > > Return on Information: > > Google Enterprise Search pays you back > > Get the facts. > > http://p.sf.net/sfu/google-dev2dev > > > > ___ > > 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 > > > TS.xyz Description: Protein Databank data -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ 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] dynamic bonding
Hello list, I have a bunch of xyz files that are along a transition path in a molecule. When I load all of them into pymol and step through the individual frames, pymol calculates the bonds only for the initial frame. This leads to wrong bonding in subsequent frames since some atoms move quite a bit during the transition. How can I get "dynamic" bonding so that bonding is recalculated for each frame? nick -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ 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
