From: Thomas H. <tho...@sc...> - 2013-09-19 17:03:22
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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 > @<TRIPOS>MOLECULE > untitled > 57 57 0 0 0 > PROTEIN > USER_CHARGES > @<TRIPOS>ATOM > 1 N 0.394 -2.167 -1.142 ?? 1.000 > 2 CA 0.891 -0.794 -1.142 ?? 1.000 > 3 C 2.400 -0.765 -1.142 ?? 1.000 > 4 O 3.074 -1.654 -0.600 ?? 1.000 > 5 CB 0.286 0.038 0.061 ?? 1.000 > 6 CG1 -1.272 -0.010 0.168 ?? 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 |