Hello did anybody see the below email or was there an error? Just checking as
I've not posted to this forum before.
Thanks
Mark
Thanks,
Mark Lewis
em...@ej73.com
> On 20 Oct 2017, at 18:25, mark <em...@ej73.com> wrote:
>
> Hello
>
> I ran obabel on macOS installed with cairo through homebrew on a structure I
> downloaded in SDF format from PubChem.
> On PubChem, the 2D structure displayed is
> <PastedGraphic-1.png>
> also visible on wikipedia as
>
> <PastedGraphic-2.png>
>
> when I converted the SDF to PNG with obabel using
>
> $ obabel Structure2D_CID_5761.sdf -O Structure2D_CID_5761.png -d -xp 1025
> -xu -xU -xb none -xd -xm
>
> I get this
>
> <PastedGraphic-3.png>
>
> which I have annotated to show the hydrogen which is plotted over the C-C
> bond 'below it'. --gen3D also didn't work - plus I really need to use -xt
> for thick bonds:
>
> $ obabel Structure2D_CID_5761.sdf -O Structure2D_CID_5761.png -d --gen3D -xp
> 1025 -xu -xU -xb none -xd -xm -xt
>
> <PastedGraphic-6.png>
>
> I've hunted through the manual and tried out a load of different option
> combinations, but I cannot work out how to get obabel to display the hydrogen
> attachment so it doesn't overlay other bonds in the image (like the two other
> images above). Can anyone tell me how to plot this hydrogen so that it looks
> like either of the pubchem or wikipedia images please?
>
> BTW, I love obabel.
>
> Thanks!
>
> Mark Lewis
> em...@ej73.com <mailto:em...@ej73.com>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org!
> http://sdm.link/slashdot_______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
