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.holder@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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