I have a question related to the hot-key question. I have defined a list of aliases in a python script. I would like to advance through the list by hitting the space bar, return key, or the scroll wheel on the mouse. Set_key does not work on the spacebar or the return key.
Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Director of the Laboratory of Biomolecular Structure and Function Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-moo...@ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d- Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0 X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory ________________________________________ From: pymol-users-requ...@lists.sourceforge.net [pymol-users-requ...@lists.sourceforge.net] Sent: Wednesday, September 09, 2015 12:02 AM To: pymol-users@lists.sourceforge.net Subject: PyMOL-users Digest, Vol 112, Issue 2 Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_pymol-2Dusers&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=-3Qc66gQ6PDJ4rToLpdVN5OLBKghvsWj9UZAaBwKJdg&e= or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: any hotkey? (Osvaldo Martin) 2. Unable to import fragment (Pablo Garay) 3. Re: XYZ format - max size of the name field (Thomas Holder) 4. Re: any hotkey? (Thomas Holder) 5. Stereoscopic 3D with DLP Projector (Laurin Stahl) 6. PyMOLWiki: Quick Update (Jason Vertrees) ---------------------------------------------------------------------- Message: 1 Date: Thu, 3 Sep 2015 07:48:25 -0300 From: Osvaldo Martin <aloctavo...@gmail.com> Subject: Re: [PyMOL] any hotkey? To: Albert <mailmd2...@gmail.com> Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net> Message-ID: <CAGMH68XG5E5bW4Cq-ChAqO5fuMo4=kfs5ksr0c8rtnsxaxh...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Albert, You can use Set_Key <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.pymolwiki.org_index.php_Set-5FKey&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=ieWRi-48KhehuRFi2YVUx6lq84mM3CvmqZyWOOuk47I&e= >, to bind any function (predefined or defined by you) to any ?hotkey/shorcut? Cheers, Osvaldo. On Thu, Sep 3, 2015 at 5:57 AM, Albert <mailmd2...@gmail.com> wrote: Hello: > > I am just wondering is there any hotkey in Pymol so that we can center > in the Ligand automatically? For instance: > > If I press keyboard "L", Pymol zoom to ligand binding pocket > automatically.... > > Thanks a lot > > Albert > > > ------------------------------------------------------------------------------ > Monitor Your Dynamic Infrastructure at Any Scale With Datadog! > Get real-time metrics from all of your servers, apps and tools > in one place. > SourceForge users - Click here to start your Free Trial of Datadog now! > https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D241902991-26iu-3D_4140&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=xns6j0cfWFvaFg4cacBvy30Th9uFDj_G4Z5qX1WqkSY&e= > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_pymol-2Dusers&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=-3Qc66gQ6PDJ4rToLpdVN5OLBKghvsWj9UZAaBwKJdg&e= > Archives: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=7wKMLPGx-O20_KyoOEnR5JYq0N4rwizg4sEO3HoL0cQ&e= > ? -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Thu, 3 Sep 2015 10:06:23 -0300 From: Pablo Garay <garaypabl...@gmail.com> Subject: [PyMOL] Unable to import fragment To: pymol-users@lists.sourceforge.net Message-ID: <CAE5=q0-kg8sfxq8hdnceleoofi5d+3qmfjjjg0vdtocynty...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" The problem is solved changing the path of chempy from this file : /usr/lib/python2.7/dist-packages/chempy/fragments/__init__.py In that file I change the line: path = chempy.path + 'fragments/' for this line: path = '/usr/share/pymol/data/chempy/fragments/' And that works, cheers. -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 3 Date: Thu, 3 Sep 2015 09:20:08 -0400 From: Thomas Holder <thomas.hol...@schrodinger.com> Subject: Re: [PyMOL] XYZ format - max size of the name field To: Pawe? Gniewek <gniewko.pa...@gmail.com> Cc: pymol-users@lists.sourceforge.net Message-ID: <c505c0e1-cc49-4385-982e-aa4aa82b9...@schrodinger.com> Content-Type: text/plain; charset=iso-8859-1 Hi Pawel, The 4 character limit is currently a hard limit. As a workaround I suggest you reformat your file into PDB format and split the atom name into the name and segi columns for example. Your selection expression will become: For H1: name H1 and segi "" For H1000: name H100 and segi "0" To properly handle atom names with more than 4 characters we would have to refactor the internal data representation, just like we did for multi-letter chain identifiers in PyMOL 1.7.4. Cheers, Thomas On 02 Sep 2015, at 20:03, Pawe? Gniewek <gniewko.pa...@gmail.com> wrote: > Hi, > > I'm trying to read a large file in XYZ format. > > By default the first line is the number of atoms in the file. > The other lines are giving the name and the coordinates for each atom: > <NAME> <X> <Y> <Z> > > I've noticed that when the name of the atom is longer than 4 characters, I > cannot select that atom - or it's not even read. For example I have a file > like that: > 1000 > H1 0.0 0.0 0.0 > ... > H1000 1000.0 1000.0 1000.0 > > then the command: > select H_1000, name H1000 > gives me: > selection "H1000" defined with 0 atoms > > However, at the same time if I do: > select H_100, name H100 > I get: > selection "H100" defined with 2 atoms > what means that the last character has been omitted. > > Of course I can work it out by naming atoms like: HH01 instead of H1000, but > I wonder if there is more elegant way of doing it. Any tricks off top of your > heads ? > > Thanks. > Pawel -- Thomas Holder PyMOL Principal Developer Schr?dinger, Inc. ------------------------------ Message: 4 Date: Thu, 3 Sep 2015 09:07:40 -0400 From: Thomas Holder <thomas.hol...@schrodinger.com> Subject: Re: [PyMOL] any hotkey? To: Osvaldo Martin <aloctavo...@gmail.com>, Albert <mailmd2...@gmail.com> Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net> Message-ID: <0069f332-fc95-427f-9be8-ef40d6bf0...@schrodinger.com> Content-Type: text/plain; charset=windows-1252 Hi Albert & Osvaldo, This should work in PyMOL 1.7+ to bind the F1 key to zoom on the first "organic" residue: set_key F1, zoom byres first organic, animate=1 Cheers, Thomas On 03 Sep 2015, at 06:48, Osvaldo Martin <aloctavo...@gmail.com> wrote: > Hi Albert, > > You can use Set_Key, to bind any function (predefined or defined by you) to > any ?hotkey/shorcut? > > Cheers, > Osvaldo. > > On Thu, Sep 3, 2015 at 5:57 AM, Albert <mailmd2...@gmail.com> wrote: > > Hello: > > I am just wondering is there any hotkey in Pymol so that we can center > in the Ligand automatically? For instance: > > If I press keyboard "L", Pymol zoom to ligand binding pocket > automatically.... > > Thanks a lot > > Albert -- Thomas Holder PyMOL Principal Developer Schr?dinger, Inc. ------------------------------ Message: 5 Date: Fri, 4 Sep 2015 12:24:06 +0200 From: Laurin Stahl <laurinst...@gmail.com> Subject: [PyMOL] Stereoscopic 3D with DLP Projector To: pymol-users@lists.sourceforge.net Message-ID: <CAEzaZSrTTzo6RUwvToedTtK3ZW=FB+6WJMRPoYxJMoD=wwg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hey guys, I am having some trouble getting stereoscopic 3D to work with PyMOL. As a disclaimer, I have no idea or experience about stereoscopy, 3D or DLP Link, so the solution might be super obvious and I am just oblivious to it. I am trying to get 3D to work with the following setup: Graphics: Geforce GT240 Beamer: SHARP PG-D45X3D,stereoscopy manual <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sharp-2Dcee.com_cps_rde_xbcr_documents_documents_om_15-5Flcd-2Dprojector_PGD3510X-2DD3010X-2DD2710X-5FOM-5F3D-2DProjection-5FGB.pdf&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=EQNki7csFyPltyTf-Vi5M-7Qiiiu6spdh39sYRGHDsI&e= > 3D glasses: Acer E4W *What I want to do* I work in a biotechnology lab and I am responsible for the computer room. In this room, we have the SHARP PG-D45X3D beamer connected to a computer with the Geforce GT240. We want to use this setup to be able to use the software PyMOL to watch molecules in 3D. Pymol has so many different ways to do 3D and even with the wiki entry, I am not seeing any progress in this. Any help would be greatly appreciated. Thanks a lot in advance! -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 6 Date: Wed, 09 Sep 2015 05:02:21 +0000 From: Jason Vertrees <jason.vertr...@gmail.com> Subject: [PyMOL] PyMOLWiki: Quick Update To: pymol-users <pymol-users@lists.sourceforge.net> Message-ID: <canuv1tzacmfq8sfqoqhbo71u7t+secfmpfydp-+_sokbs3f...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Greetings, It's been a while, I hope this message finds everyone well. I'm writing to briefly let you know that I recently moved, upgraded, and reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast and more useful. Feel free to report any bugs. Back to the startup-life. Cheers, -- Jason -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D241902991-26iu-3D_4140&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=xns6j0cfWFvaFg4cacBvy30Th9uFDj_G4Z5qX1WqkSY&e= ------------------------------ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_pymol-2Dusers&d=AwICAg&c=qRnFByZajCb3ogDwk-HidsbrxD-31vTsTBEIa6TCCEk&r=39ovrj_9gtbpqLqHj52qObHez22uGBx1oHrj21rIdII&m=AqQFolqhEjPXTBL5CieZKi_Dxssj-rbGOhGpPG3Zj2o&s=-3Qc66gQ6PDJ4rToLpdVN5OLBKghvsWj9UZAaBwKJdg&e= End of PyMOL-users Digest, Vol 112, Issue 2 ******************************************* ------------------------------------------------------------------------------ Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/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
