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 _______________________________ Fabian Glaser, PhD Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL fglaser@technion.ac.il Tel: +972 4 8293701 Fax: +972 4 8225153
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@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
FYI. I responded privately asking for an example .sd file. It might be easy. I didn't promise to do it. Conrad 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@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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participants (3)
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Conrad Huang -
Elaine Meng -
Fabian Glaser