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Can anyone suggest a good (free) program for viewing SDF files?

Asked by , Edited by Egon Willighagen [ Admin ]

Hi,

I’m looking for a free software package primarily for viewing structures within an SDF file (if the software makes it possible to perform basic manipulation of the content that would be even better).

I’ve seen Hyleos ChemFileBrowser recommended before and I’m going to give it a try – but it seems that this program is no longer being developed and I wondered if there are any alternatives that anyone would suggest.

Ideally, I’d like it to work in Windows 7 but I also run a Linux virtual machine so if there are any good Linux-based programs these might be of interest.

Cheers,

Dave

NN comments
baoilleach
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Do you specifically want 2D depictions, or would a 3D viewer be fine? (Please update the question to clarify)

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8 answers

2

steve wathen [ Editor ]

You could try Bioclipse.  It’s probably more than you need, but it will show the structures in sdf files.  I would suggest you drag-and-drop your sdf file into a folder in the Bioclipse Navigator panel – then click on your file in the Navigator panel to view it.


Bioclipse is a java program, so operating system shouldn’t be an issue.  However the download is quite large.
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the.chemist.ds
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Thanks for the suggestion Steve – I was always a bit scared of Bioeclipse and viewed it as much more of a proteins/large biomolecules specific package. But with your recommendation I definately think it’s time to try it out.

chem-bla-ics
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.chemist.ds Actually, it’s the bioinformatics part of Bioclipse that is underdeveloped.

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2

dmitry pavlov [ Editor ]

You can try MView (part of MarvinBeans package, free for academia, but not open-source). Also, there is ChemDiff utility (free and open-source), whose purpose is to compare two SDF/SMILES/CML files—but you can use it to view a single SDF file as well.


Both MView and ChemDiff are written in Java.
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the.chemist.ds
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Thanks for the suggestion Dmitry I’ve had a quick look at ChemDiff a few months ago. I sort of guessed that I could use it to open a single file – but thought that there might be other tools more suited to viewing SDF files. I’ll definitely take a look at the most recent version.

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1

chris.morley8_gid

OpenBabel can do 2D depiction of multi-molecule files.  It displays a contiguous range of molecules but you can choose where it is in the file and  the number of rows and columns. You can filter by SDF property or by aspects of the chemical structure and do some manipulation, like implicit/explicit hydrogen. The display currently is svg only, but in Firefox, Chrome, etc. this is zoomable, which is what you want with lots of molecules.  OpenBabel is cross-platform with a commandline and a GUI.  

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0

the.chemist.ds

Apparently, despite using the same authentication method as when I posed my question (Google) I’m not recognised as being the same account. But thank you to everyone for the suggestions.

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chem-bla-ics
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Ask on Shapado.com to have the accounts merged…

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