Re: [PyMOL] PyMOL MOPAC format

[Thomas H. <sp...@us...>]

Hi Martin,

I don't know the MOPAC format and couldn't find a specification ad hoc.
But the attached script will produce output which is equivalent to your
example. Use the "zero" argument to specify the selection of "+0" 
flagged atoms.

Cheers,
    Thomas

On 06/21/2012 11:27 PM, Martin Hediger wrote:
> Dear PyMOL users
> I'm using MOPAC to do quantum chemical calculations of enzymes.
> I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
> An example of this format is here:
>
>      C(     1 LEU  24)   9.04500000 +0   4.94400000 +0  19.45600000 +0                     0.4527
>      O(     2 LEU  24)   8.05600000 +1   5.59200000 +1  19.15100000 +1                    -0.5188
>      H(     3 LEU  24)  10.04000000 +1   5.40500000 +1  19.57200000 +1                     0.1090
>      N(     4 ASP  25)   9.08100000 +1   3.59500000 +1  19.71600000 +1                    -0.4910
>      C(     5 ASP  25)   7.89300000 +1   2.76600000 +1  19.57800000 +1                    -0.0307
>      C(     6 ASP  25)   7.70800000 +0   1.88300000 +0  20.81000000 +0                     0.3465
>      O(     7 ASP  25)   8.44900000 +1   0.95600000 +1  21.12200000 +1                    -0.4321
>      C(     8 ASP  25)   7.97500000 +1   1.90500000 +1  18.33900000 +1                    -0.4663
>      C(     9 ASP  25)   6.66900000 +1   1.15400000 +1  18.28400000 +1                     0.7179
>      O(    10 ASP  25)   5.64600000 +1   1.70700000 +1  18.79700000 +1                    -0.7657
>      O(    11 ASP  25)   6.69700000 +1   0.02300000 +1  17.72800000 +1                    -0.6565
>      H(    12 ASP  25)   7.03100000 +1   3.43800000 +1  19.54700000 +1                     0.1841
>      H(    13 ASP  25)   8.81500000 +1   1.20200000 +1  18.39200000 +1                     0.1979
>      H(    14 ASP  25)   8.10000000 +1   2.50700000 +1  17.43400000 +1                     0.1919
>      H(    15 ASP  25)   9.95700000 +1   3.14300000 +1  19.95300000 +1                     0.2791
>      H(    16 ASP  25)   6.98200000 +1   2.29500000 +1  21.52500000 +1                     0.1043
>
> What I'm especially interested in is the "+0" and "+1" flags, which
> sometimes are required but are quite inconvenient to find for single
> atoms in a large file, it's also very error prone. The parenthesis after
> the atom type can be omitted, also the very last column (0.4527, ...)
> Would it be possible to write a PyMOL plugin, where single atoms could
> be added to a selection (using point-and-click) and when saving to the
> MOPAC file, the selected atoms would be written with the "+0" flags?
> Any hints on what part of the API to look at are very appreciated.
>
> Best regards
> Martin

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen