Re: [PyMOL] PyMOL v1.7 Released
Hi Matthias, yes that's all possible! Volumes can be carved around selections, no matter where the map comes from (mtz, map.ccp4, ...). In Incentive PyMOL 1.7, you can load mtz maps with the "load" or "load_mtz" commands, so just do: PyMOL> load some.pdb PyMOL> load some.mtz PyMOL> volume abc, some.2fofc, 0, organic, 4., 1, 4. This will create a volume "abc" carved around an organic ligand at a 4 Angstrom radius. Use the volume panel to adjust colors and transparency (volume scripting is coming in PyMOL 1.8). Map symmetry expansion is done based on the symmetry information of the molecule, or (new in 1.7) the map. PyMOL 1.7 reads the space group from mtz and ccp4 maps. Not all map formats have space group information, if it's missing, use set_symmetry or symmetry_copy. MTZ loading uses a proprietary Schrödinger library, so it will not make it into the open-source version. But all the volume stuff is in open-source. Unfortunately for AxPyMOL, it uses ActiveX technology, which to our knowledge is not available on OSX. If you know otherwise, we'd be happy to find a solution. Cheers, Thomas On 21 Jan 2014, at 06:53, Matthias Haffke wrote: > Nice to see how PyMOL advances over time - great job! > > Quite some time ago I posted to the list asking if it would be possible to > limit a volume (mesh, etc.) generated from a .mtz file around a selection > (residues, atoms, etc.). As far as I remember it was not possible and I had > to go "the old" way be generating a .map.ccp4 via FFT (in the CCP4 package) > to use "isomesh" to do the job. > > Are there any updates/plans on this feature? > > And I was wondering if there will be a AxPyMOL version for Mac OS X coming at > some point as well? > > Best, > > Matthias -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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] PyMOL v1.7 Released
Nice to see how PyMOL advances over time - great job! Quite some time ago I posted to the list asking if it would be possible to limit a volume (mesh, etc.) generated from a .mtz file around a selection (residues, atoms, etc.). As far as I remember it was not possible and I had to go "the old" way be generating a .map.ccp4 via FFT (in the CCP4 package) to use "isomesh" to do the job. Are there any updates/plans on this feature? And I was wondering if there will be a AxPyMOL version for Mac OS X coming at some point as well? Best, Matthias -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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] PyMOL v1.7 Released
Michael, Nice catch—we'll fix it. Thanks for letting us know. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:11 AM, Michael Banck wrote: > Hi, > > On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: > > We are happy to announce the release of PyMOL v1.7.0.0! > > Congrats! > > One thing though: the open-source splash image has not been updated for > 1.7 and still says "1.6.x". > > > Michael > > > -- > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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] PyMOL v1.7 Released
Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: > We are happy to announce the release of PyMOL v1.7.0.0! Congrats! One thing though: the open-source splash image has not been updated for 1.7 and still says "1.6.x". Michael -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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] PyMOL v1.7 Released
Greetings, We are happy to announce the release of PyMOL v1.7.0.0! Official PyMOL sponsors can download ready-to-use installers from http://pymol.org/dsc/ip . The open-source code has been pushed to sourceforge svn (revision 4060) and a downloadable bz2 source file is also available from http://sf.net/p/pymol/. A few improvements include: Incentive PyMOL (for licensed users) * Improved labels, with connectors, backgrounds, outlines, and multiline text * Callouts for general labeling * 675 documented settings in the Settings > Edit All GUI * New Find Wizard (CTRL-F) for locating objects in the object menu panel * ...and more Open Source and Incentive PyMOL * Added the focal_blur command * Added the get_renderer command to return information about the graphics renderer * Fetch command now takes SID and CID codes for PubChem * New selection keywords: metals, backbone, and sidechain * Access to settings and properties from the iterate/alter commands * Improved the PDB Loader GUI * Lots of Bugs Fixes AxPyMOL (for licensed users): * Built as a PowerPoint Add In * Option to embed data into the PowerPoint file * Supports PowerPoint PPTX files * Added support for presenting Maestro (.mae and .maegz) files * Added support for Windows 8, MS Office 2010 and 2013 (32- and 64-bit) * Support for shader-based rendering We encourage PyMOL sponsors to check out the internal documentation: * -- http://pymol.org/dsc/dokuwiki/doku.php?id=media:new17 We welcome any feedback and bug reports. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&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
