Re: [Jmol-users] PubChem Load

[Robert Hanson]

There are several possible reasons for this: charge states, resonance
structures, etc. Possibly even different depositions, I'm not sure.
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Re: [Jmol-users] PubChem Load

[Angel Herráez]

Dear Otis

I have seen several files from PubChem that come with more than one 
structure, using

load :whatever

So that is the norm rather than the exception. It's easy to browse them if you 
load into the Jmol application and use the arrow buttons in the toollbar.

Sometimes, the 2nd or 3rd is more interesting than the 1st one!





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[Jmol-users] PubChem Load

[Otis Rothenberger]

Bob,

Tom Newton noticed that the PubChem sdf for :menthol is a multi molfile record. 
The sdf opens with a single molfile visible, but 3 other molfiles (all sightly 
different) appear in the data appendix of the sdf. They are loaded into Jmol 
also. I’m assuming this is all by design and part of the PubChem sdf structure.

I corrected this on my end by using Jmol’s load “" [1] as a permanent filter 
for PubChem loads. I’m not sure if you want to do this on the Jmol end, but I 
though that I’d give you a heads up.

I’ll also mention something related that I brought up before. In a conversation 
with PubChem, a staff member pointed me toward extracting data from the PubChem 
JSON files via a laborious loop. He pointed out that the structure of these 
files vary considerably from compound to compound. Indeed!

Otis

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Otis Rothenberger
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http://chemagic.org

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