Thanks, I have all my answers !
Fabrice Carles - PhD student
Structural Bioinformatics & Chemoinformatics,
Institut de Chimie Organique et Analytique (ICOA)
University of Orleans - France
2018-03-16 13:41 GMT+01:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> Hi Fabrice,
>
> Interesting observation. PyMOL reads "metalc" bonds from mmCIF files and
> represents them as "zero order" bonds. Apparently this breaks double bond
> detection in your given example. This is something we need to fix.
>
> Possible workarounds:
> 1) Load .pdb files instead of .cif files
> 2) Load .mmtf files, they have full bonding information, including bond
> orders
> 3) Load .cif files, but with connect_mode=4, which looks up all bond
> orders from the chemical components dictionary
>
> Relevant settings:
> https://pymolwiki.org/index.php/Fetch_type_default
> https://pymolwiki.org/index.php/Connect_mode
>
> Cheers,
> Thomas
>
> > On Mar 15, 2018, at 5:55 PM, Fabrice Carles <carlesfabr...@gmail.com>
> wrote:
> >
> > Dear pymol users,
> >
> > I would like to know if there is a way to change pymol2 settings in
> order to fit older version.
> >
> > My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same
> results.
> >
> > I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:
> >
> > cmd.fetch('1atp')
> > cmd.select('lig','organic')
> >
> > Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of
> ATP molecule but pymol2 does not.
> > Using the command below, I compare the differences between the two
> versions in sdf file format.
> >
> > cmd.save('atp.sdf',selection='lig')
> >
> > diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf
> > 2c2
> > < PyMOL186 3D 0
> > ---
> > > PyMOL2.0 3D 0
> > 18,19c18,19
> > < 11.1000 9.8800 -1.4300 O 0 5 0 0 0 0 0 0 0 0 0 0
> > < 13.9290 9.9200 -2.7000 O 0 5 0 0 0 0 0 0 0 0 0 0
> > ---
> > > 11.1000 9.8800 -1.4300 O 0 0 0 0 0 0 0 0 0 0 0 0
> > > 13.9290 9.9200 -2.7000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 24c24
> > < 15.7480 6.8350 -0.4270 O 0 5 0 0 0 0 0 0 0 0 0 0
> > ---
> > > 15.7480 6.8350 -0.4270 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 38c38
> > < 1 18 2 0 0 0 0
> > ---
> > > 1 18 1 0 0 0 0
> > 41c41
> > < 2 19 2 0 0 0 0
> > ---
> > > 2 19 1 0 0 0 0
> > 47c47
> > < 3 24 2 0 0 0 0
> > ---
> > > 3 24 1 0 0 0 0
> >
> >
> >
> > How can I force pymol2 to write exactly the same sdf as before ?
> > Is there new defaults settings in pymol2 that I can override ?
> >
> > Thanks,
> >
> > Fabrice
> >
> > Fabrice Carles - PhD student
> > Structural Bioinformatics & Chemoinformatics,
> > Institut de Chimie Organique et Analytique (ICOA)
> >
> > University of Orleans - France
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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