Re: [PyMOL] Background colors in PyMOL 1.6
Hi Nils, We've updated how PyMOL stores colors in sessions. You can try, cmd.get_color_tuple(cmd.get(bg_rgb)) or if you need it as a list: list(cmd.get_color_tuple(cmd.get(bg_rgb))) Cheers, -- Jason On Thu, Sep 19, 2013 at 5:17 PM, Nils NN n...@gmx.ch wrote: Hello, I recently installed PyMOL 1.6 on my Debian machine. I have noticed that the description of the background colors has somehow changed. The command get bg_color returns [R,G,B] values in all previous versions, while since 1.6 it only returns values like black (which messes up some of my plugins and scripts). I'm not sure if this some kind of bug or a new way of handling colors... When I try to set the background gradient colors (set bg_rgb_top/bottom) I get an endless output of Setting-Error: type read mismatch (color) 664 - I have to kill and restart the program to get rid of the message. Same happens with my scripts using cmd... Can someone confirm these problems? Perhaps I'm doing something wrong here. Thanks in advance, Nils -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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] Guessing bonds for a chempy model.
Hi Raul, I don't think the bond guessing routine is exposed to the python API. This would actually be very useful, so I take this as a feature request. Meanwhile, I guess you need some workaround like dumping to PDB format and loading as PDB again. Have a look at cmd.get_pdbstr and cmd.read_pdbstr. Cheers, Thomas Raúl Mera Adasme wrote, On 09/17/13 19:15: Hi all, I want to load a chempy model into PyMOL. Unfortunately, the model has all the coordinate information, but not bonds defined. I know PyMOL can guess the bonds from the distances, but it does not do it if I just use cmd.load_model, and I could not find a way of doing it. Does anyone know how can I achieve this? Thanks! Raul -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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] Trouble with saving mol2 format
Hi Jacob, saving to mol2 format is only fully supported in incentive PyMOL. It uses a proprietary library for the atom type assignment, which is not available in open-source PyMOL. Cheers, Thomas Jacob Pessin wrote, On 09/19/13 00:05: Hi, I've come across an issue saving .mol2 ( @TRIPOS ) files. MGL tools' PMV/ADT won't read them, babel/open babel issues a set of complaint and read errors. If I am reading the format correctly then ... In the atom content the columnation appears to be off after the X Y Z coordinates, the question marks under atom_type seem to throw a lot of scripts (not surprising). I'm not quite sure what the issue is, but it occurs when saving peptides and molecules built by a mouse or script as well as RCSB downloaded structures. seems the same on all builds and machines I've tried (listed at bottom) thanks for your time jacob # created with PyMOL @TRIPOSMOLECULE untitled 5757000 PROTEIN USER_CHARGES @TRIPOSATOM 1 N0.394-2.167-1.142??1.000 2 CA0.891-0.794-1.142??1.000 3 C2.400-0.765-1.142??1.000 4 O3.074-1.654-0.600??1.000 5 CB0.2860.0380.061??1.000 6 CG1-1.272-0.0100.168??1.000 ... saved from pymol 1.6 https://www.dropbox.com/s/jlpwa2lsub5ez8g/IPR.mol2 babel pipes https://www.dropbox.com/s/ruh23hcxfmbv0z8/babelmol2_mol2.txt babel out https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2 https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2 tripos mol2 format pdf http://www.tripos.com/data/support/mol2.pdf hardware dell T3600 e5-1650 w/ quadro 600 xUbuntu 13.04 pymol 1.6.0 from source w/build_seq.py and seq_convert.py 1.5.2 from package (and lots of plugins) lenovo t420 nvs 400 windows 7 1.4.? (not sitting at it while typing) pre-built many plugins also xUbuntu 12.04 1.4 from package and 1.6 from source (w/nvidia-bumblebee, and just intel graphics) -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/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
