Re: [PyMOL] auto_show_cartoon or similar
Hi all, The "auto_show_classified" feature is now available from the open-source SVN code repository. I've also uploaded pre-compiled builds to http://pymol.org/download (alpha release, not intended for production use). The setting has 3 modes: 0 (off, default), 1 (like Adam suggested), 2 (including the default lines), and 3 (simplified version with ribbon instead of cartoon). See also: http://pymolwiki.org/index.php/auto_show_classified Any feedback will be appreciated. Cheers, Thomas On 08 Feb 2016, at 15:16, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote: > Every application has to satisfy it's users. > > Thinking out loud… > If you show all lines the new users find it confusing and overwhelming but > they do get to see every atom. Experienced users generally know what atoms > are in a PDB or know how to find them if they are looking for them and > therefore do not need to see all lines. > > The current proposal is to show more structure (cartoon, sticks, spheres) but > leave on all lines behind this structure. My first thought is what would that > look like. So I open a current structure and show both options (attached). If > I leave all lines on it’s still a bit of a mess. I think it looks better with > all lines off. > > > > PM.pdf> > > > >> On Feb 8, 2016, at 1:29 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >> >> Adam, Abhinav, Dave, >> thanks for the very useful feedback. >> >> To keep it simple, I propose a "auto_show_classified" setting (will depend >> on "auto_classify_atoms", on by default) which will be equivalent to: >> >> show cartoon, polymer >> show sticks, organic >> show spheres, inorganic >> >> Question: should this automatically hide lines for classified atoms? >> >> By the way, you may also like the "nice" preset (with "x" alias) from psico: >> https://github.com/speleo3/pymol-psico/blob/master/psico/viewing.py >> >> Cheers, >> Thomas >> >> On 08 Feb 2016, at 13:50, Bourgaize David <dbourga...@whittier.edu> wrote: >> >>> My thoughts exactly! >>> >>> Dave Bourgaize >>> >>> On 2/8/16, 9:54 AM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com> wrote: >>> >>>> Every year I teach students PyMOL, and the look on their faces when they >>>> first open a pdb in PyMOL and get a cluster of green sticksŠ yikes! >>>> >>>> YES!!! to the default being secondary structure, ligands as sticks, and >>>> metal ions as spheres! Add - nucleic acids as cartoon. >>>> >>>>> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav <aku...@intrexon.com> wrote: >>>>> >>>>> Showing metal ions (and FES clusters etc) as spheres would also be >>>>> useful. >>>>> >>>>> Thanks, >>>>> Abhinav >>>>> >>>>> Abhinav Kumar, PhD >>>>> Senior Scientist, Bioinformatics >>>>> Intrexon, Inc. >>>>> 329 Oyster Point Blvd., South San Francisco, CA 94080 >>>>> (650) 597-4072 | aku...@intrexon.com >>>>> >>>>> >>>>> >>>>> From: Thomas Holder [thomas.hol...@schrodinger.com] >>>>> Sent: Monday, February 08, 2016 8:51 AM >>>>> To: Ivan Vulovic; Schubert, Carsten [JRDUS] >>>>> Cc: pymol-users@lists.sourceforge.net >>>>> Subject: Re: [PyMOL] auto_show_cartoon or similar >>>>> >>>>> Hi Ivan and Carsten, >>>>> >>>>> I can take "auto_show_cartoon" as a feature request. It's trivial to >>>>> implement. >>>>> >>>>> What also would be nice: automatically showing sticks for ligands. e.g. >>>>> corresponding to the "not polymer" or the "organic" selection. Thoughts? >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] >>>>> <cschu...@its.jnj.com> wrote: >>>>> >>>>>> Hi Ivan, >>>>>> >>>>>> you could either try to overload the ³load² function in Pymol (not >>>>>> sure this is supported) or write your own custom load function under a >>>>>> different name, which loads the protein, assigns the name of the >>>>>>
Re: [PyMOL] auto_show_cartoon or similar
Hi Ivan and Carsten, I can take "auto_show_cartoon" as a feature request. It's trivial to implement. What also would be nice: automatically showing sticks for ligands. e.g. corresponding to the "not polymer" or the "organic" selection. Thoughts? Cheers, Thomas On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Ivan, > > you could either try to overload the “load” function in Pymol (not sure this > is supported) or write your own custom load function under a different name, > which loads the protein, assigns the name of the object, hides lines and > shows the cartoon. > > Sorry, this is a rather generic answer but should point you in the right > direction. > > Cheers, > > Carsten > > From: Ivan Vulovic [mailto:i...@uw.edu] > Sent: Saturday, February 06, 2016 8:18 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] auto_show_cartoon or similar > > Hello > > Is there a way to make cartoon the default representation, something akin to > "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 > (link below) but I haven't found anything more recent that does what I'd like. > > http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html > > Thanks > Ivan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] auto_show_cartoon or similar
Hi Ivan, you could either try to overload the “load” function in Pymol (not sure this is supported) or write your own custom load function under a different name, which loads the protein, assigns the name of the object, hides lines and shows the cartoon. Sorry, this is a rather generic answer but should point you in the right direction. Cheers, Carsten From: Ivan Vulovic [mailto:i...@uw.edu] Sent: Saturday, February 06, 2016 8:18 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] auto_show_cartoon or similar Hello Is there a way to make cartoon the default representation, something akin to "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 (link below) but I haven't found anything more recent that does what I'd like. http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html Thanks Ivan -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ 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] auto_show_cartoon or similar
Hello Is there a way to make cartoon the default representation, something akin to "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 (link below) but I haven't found anything more recent that does what I'd like. http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html Thanks Ivan -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___ 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] auto_show_cartoon or similar
Showing metal ions (and FES clusters etc) as spheres would also be useful. Thanks, Abhinav Abhinav Kumar, PhD Senior Scientist, Bioinformatics Intrexon, Inc. 329 Oyster Point Blvd., South San Francisco, CA 94080 (650) 597-4072 | aku...@intrexon.com From: Thomas Holder [thomas.hol...@schrodinger.com] Sent: Monday, February 08, 2016 8:51 AM To: Ivan Vulovic; Schubert, Carsten [JRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] auto_show_cartoon or similar Hi Ivan and Carsten, I can take "auto_show_cartoon" as a feature request. It's trivial to implement. What also would be nice: automatically showing sticks for ligands. e.g. corresponding to the "not polymer" or the "organic" selection. Thoughts? Cheers, Thomas On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Ivan, > > you could either try to overload the “load” function in Pymol (not sure this > is supported) or write your own custom load function under a different name, > which loads the protein, assigns the name of the object, hides lines and > shows the cartoon. > > Sorry, this is a rather generic answer but should point you in the right > direction. > > Cheers, > > Carsten > > From: Ivan Vulovic [mailto:i...@uw.edu] > Sent: Saturday, February 06, 2016 8:18 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] auto_show_cartoon or similar > > Hello > > Is there a way to make cartoon the default representation, something akin to > "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 > (link below) but I haven't found anything more recent that does what I'd like. > > http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html > > Thanks > Ivan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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 CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] auto_show_cartoon or similar
Every year I teach students PyMOL, and the look on their faces when they first open a pdb in PyMOL and get a cluster of green sticks… yikes! YES!!! to the default being secondary structure, ligands as sticks, and metal ions as spheres! Add - nucleic acids as cartoon. > On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav <aku...@intrexon.com> wrote: > > Showing metal ions (and FES clusters etc) as spheres would also be useful. > > Thanks, > Abhinav > > Abhinav Kumar, PhD > Senior Scientist, Bioinformatics > Intrexon, Inc. > 329 Oyster Point Blvd., South San Francisco, CA 94080 > (650) 597-4072 | aku...@intrexon.com > > > > From: Thomas Holder [thomas.hol...@schrodinger.com] > Sent: Monday, February 08, 2016 8:51 AM > To: Ivan Vulovic; Schubert, Carsten [JRDUS] > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] auto_show_cartoon or similar > > Hi Ivan and Carsten, > > I can take "auto_show_cartoon" as a feature request. It's trivial to > implement. > > What also would be nice: automatically showing sticks for ligands. e.g. > corresponding to the "not polymer" or the "organic" selection. Thoughts? > > Cheers, > Thomas > > On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> > wrote: > >> Hi Ivan, >> >> you could either try to overload the “load” function in Pymol (not sure this >> is supported) or write your own custom load function under a different name, >> which loads the protein, assigns the name of the object, hides lines and >> shows the cartoon. >> >> Sorry, this is a rather generic answer but should point you in the right >> direction. >> >> Cheers, >> >>Carsten >> >> From: Ivan Vulovic [mailto:i...@uw.edu] >> Sent: Saturday, February 06, 2016 8:18 PM >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] auto_show_cartoon or similar >> >> Hello >> >> Is there a way to make cartoon the default representation, something akin to >> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 >> (link below) but I haven't found anything more recent that does what I'd >> like. >> >> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html >> >> Thanks >> Ivan > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 > ___ > 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 > > > > CONFIDENTIAL TRANSMISSION - This message, including any attachments, is > confidential and may be privileged. If you are not the intended recipient, > please delete it without further distribution and reply to the sender that > you have received the message in error. > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 > ___ > 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 H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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] auto_show_cartoon or similar
My thoughts exactly! Dave Bourgaize On 2/8/16, 9:54 AM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com> wrote: >Every year I teach students PyMOL, and the look on their faces when they >first open a pdb in PyMOL and get a cluster of green sticksŠ yikes! > >YES!!! to the default being secondary structure, ligands as sticks, and >metal ions as spheres! Add - nucleic acids as cartoon. > >> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav <aku...@intrexon.com> wrote: >> >> Showing metal ions (and FES clusters etc) as spheres would also be >>useful. >> >> Thanks, >> Abhinav >> >> Abhinav Kumar, PhD >> Senior Scientist, Bioinformatics >> Intrexon, Inc. >> 329 Oyster Point Blvd., South San Francisco, CA 94080 >> (650) 597-4072 | aku...@intrexon.com >> >> >> >> From: Thomas Holder [thomas.hol...@schrodinger.com] >> Sent: Monday, February 08, 2016 8:51 AM >> To: Ivan Vulovic; Schubert, Carsten [JRDUS] >> Cc: pymol-users@lists.sourceforge.net >> Subject: Re: [PyMOL] auto_show_cartoon or similar >> >> Hi Ivan and Carsten, >> >> I can take "auto_show_cartoon" as a feature request. It's trivial to >>implement. >> >> What also would be nice: automatically showing sticks for ligands. e.g. >>corresponding to the "not polymer" or the "organic" selection. Thoughts? >> >> Cheers, >> Thomas >> >> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] >><cschu...@its.jnj.com> wrote: >> >>> Hi Ivan, >>> >>> you could either try to overload the ³load² function in Pymol (not >>>sure this is supported) or write your own custom load function under a >>>different name, which loads the protein, assigns the name of the >>>object, hides lines and shows the cartoon. >>> >>> Sorry, this is a rather generic answer but should point you in the >>>right direction. >>> >>> Cheers, >>> >>>Carsten >>> >>> From: Ivan Vulovic [mailto:i...@uw.edu] >>> Sent: Saturday, February 06, 2016 8:18 PM >>> To: pymol-users@lists.sourceforge.net >>> Subject: [PyMOL] auto_show_cartoon or similar >>> >>> Hello >>> >>> Is there a way to make cartoon the default representation, something >>>akin to "auto_show_lines", but for cartoon? There was some dicussion of >>>this in 2010 (link below) but I haven't found anything more recent that >>>does what I'd like. >>> >>> >>>http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734 >>>.html >>> >>> Thanks >>> Ivan >> >> -- >> Thomas Holder >> PyMOL Principal Developer >> Schrödinger, Inc. >> >> >> >>- >>- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 >> ___ >> 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 >> >> >> >> CONFIDENTIAL TRANSMISSION - This message, including any attachments, is >>confidential and may be privileged. If you are not the intended >>recipient, please delete it without further distribution and reply to >>the sender that you have received the message in error. >> >> >>- >>- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] auto_show_cartoon or similar
That would be great, my standard is open file, cartoon, ligand sticks Great idea -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Tuesday, 9 February 2016 5:52 AM To: Ivan Vulovic <i...@uw.edu>; Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] auto_show_cartoon or similar Hi Ivan and Carsten, I can take "auto_show_cartoon" as a feature request. It's trivial to implement. What also would be nice: automatically showing sticks for ligands. e.g. corresponding to the "not polymer" or the "organic" selection. Thoughts? Cheers, Thomas On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: > Hi Ivan, > > you could either try to overload the "load" function in Pymol (not sure this > is supported) or write your own custom load function under a different name, > which loads the protein, assigns the name of the object, hides lines and > shows the cartoon. > > Sorry, this is a rather generic answer but should point you in the right > direction. > > Cheers, > > Carsten > > From: Ivan Vulovic [mailto:i...@uw.edu] > Sent: Saturday, February 06, 2016 8:18 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] auto_show_cartoon or similar > > Hello > > Is there a way to make cartoon the default representation, something akin to > "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 > (link below) but I haven't found anything more recent that does what I'd like. > > http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html > > Thanks > Ivan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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 -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140 ___ 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
