Re: [PyMOL] Trouble with saving mol2 format

[David H. <li...@co...>]

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 <
tho...@sc...> 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
>
>
> ------------------------------------------------------------------------------
> 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=58041151&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>