Re: [PyMOL] Font problem
On 22/11/13 17:44, Jason Vertrees wrote: Hi Justin, We'll fix that, too. Cheers, -- Jason Hi Jason, did you find time to look into that? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- 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=119420431iu=/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=119420431iu=/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, number and label the helices
Hi guys, Thank you very much for the helps, and the Label command and the pseudoatom are very powerful, now I can add labels what I want :) Cheers, Gefei On 21 Jan 2014, at 03:37, Jason Vertrees jason.vertr...@schrodinger.com wrote: Gefei, Please read about labels (http://www.pymolwiki.org/index.php/Label; and http://www.pymolwiki.org/index.php/Category:Labeling) and pseudoatoms (http://www.pymolwiki.org/index.php/Pseudoatom). These should help you label what you need to. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:57 AM, Gefei Chen cgf-2...@hotmail.com wrote: Hi guys, I am now preparing some proteins structure figures, and I think Pymol is a good program. But now something happened to me, my protein just has 5 helices, and I want to number and label the helices as H1, H2 …and H5 in the figure with using Pymol directly (not photoshop), but I am sorry I have no idea for finishing it, however I have read the guide of Pymol. could anyone tell me something about how to number and label the helices? That will be very helpful, and thank you very much! Cheers, Gefei -- 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=119420431iu=/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=119420431iu=/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] Font problem
Justin, Yes, we put quite a bit of effort into improving the font rendering. It's still not perfect, but should be improved over the pre-release versions. Please let me know where you still have issues. (Just send me a PSE file as an example.) Cheers, -- Jason On Tue, Jan 21, 2014 at 5:27 AM, Justin Lecher j.lec...@fz-juelich.dewrote: On 22/11/13 17:44, Jason Vertrees wrote: Hi Justin, We'll fix that, too. Cheers, -- Jason Hi Jason, did you find time to look into that? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- 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=119420431iu=/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 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 matze_haf...@hotmail.com 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=119420431iu=/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
