One feature request, it would be nice if I open a mol2 and then save that
molecule as mol2, it would remember the atom types and charges. No need for
assignment, just remember what the user read in.
-David
On Thu, Sep 19, 2013 at 1:03 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> 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
>
>
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