[Chimera-users] reading .sd files

Conrad Huang conrad at cgl.ucsf.edu
Tue Sep 16 10:59:35 PDT 2014

FYI.  I responded privately asking for an example .sd file.  It might be 
easy.  I didn't promise to do it.


On 9/16/2014 9:50 AM, Elaine Meng wrote:
> Hi Fabian, The ViewDock tool doesn't read SD format, sorry… there is
> a list of the formats it knows about here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
>  You could try converting to one of those formats (pdb, mol2, pdbqt,
> mae …) with some other tool like Babel, or maybe even in Chimera:
> I didn't know anything about .sd but some Googling has led me to
> believe it is the same as SDF or multi-MOL format.  Chimera can read
> SDF files, but they aren't recognized specifically as docking
> results; it would just show all the structures at once.  Only
> filename extensions .sdf and .mol are automatically recognized as SDF
> (not .sd) so you would have to specify the "MDL MOL/SDF" type
> directly or change the filename to open it  in Chimera.  Then you
> could save as a single multimodel PDB file or Mol2 file using the
> respective choices in the Chimera File menu.
> I don't know what program created your .sd file and I haven't tried
> this process myself, so I don't know how well the resulting PDB or
> Mol2 file would work with ViewDock.
> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF
> Computer Graphics Lab (Chimera team) and Babbitt Lab Department of
> Pharmaceutical Chemistry University of California, San Francisco
> On Sep 14, 2014, at 5:13 AM, Fabian Glaser <fglaser at technion.ac.il>
> wrote:
>> Hi,
>> I have tried to read .sd files with docking ligands, without
>> success.
>> Is there a way to ready results of docking in .sd format in
>> Chimera?
>> Thanks a lot,
>> Fabian
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