A blog posting last night discussed the fact that we had not yet implemented a 3D optimization engine under Jmol and that the structures displayed are 2D FLAT molecules. Well I’m happy to report that less than 24 hours later (actually it was done before I woke up this morning) the optimization of 3D structures under JMol is incorporated.

Rajarshi Guha pointed us to smi23d and we have embedded this under JMol now. This is of course, beta (we stay in constant beta) and there are a couple of bugs…we’re not sure whether these are on our side or in the Optimizer and are awaiting feedback. In the previous posting on Diazonamide A I commented on the six hits. The top two do NOT optimize while the bottom 4 do. I think it’s about the fact that the structure might be TOO far away from a starting point for optimization. I’ve opened an email dialog with Rajarshi to discuss.

Please note that the 3D coordinates are calculated in real time and the JMol screen might stay empty for a while during the optimization process. Here’s what it looks like for Diazonamide A.

Diazonamide A 3D in Jmol

Stumble it!

3 Responses to “3D Optimization Now Embedded Underneath JMol on ChemSpider”

  1. ChemSpiderMan says:

    A couple of Email exchanges with Rajarshi on the USefulChem Group and we have identified the problem. Thanks Rajarshi…active team that UsefulChem Group…we’re proud to be on it!

    “Aah, it looks like there is some van der Waal clash going on in the 2D SDF.

    In general, you should not provide a 2D SDF to mengine – you should provide some form of 3D. Otherwise it’s possible that the optimization routine (BFGS IIRC) will barf on stuff such as everything being in a plane and so on.

    Is there a reason that you have to feed 2D SDF’s? The role of smi23d is to get a rough set of 3D very fast (< 1 sec for this case) and mengine will work fine with that.

    If nothing you could try converting your 2D SDF to a randomized 3D SDF
    - but then you can’t guarantee absence of van der Waals clashes.

    I’d still suggest going from SMILES via smi23d

    “Aargh! My eyes! :)

    No, this SDF has no chance of working with mengine – everything seems to be overlapping.

    If this is what you’re doing for the other 4 structures, I can see why they might work – I assume you’re just transferring the 2D coordinates to SD format. And the 2D depictions seem to indicate that they’re relatively well laid out – so no clashes etc. Which is why the lower 4 work.”

  2. ChemSpiderMan says:

    It appears that in SOME cases the optimizer is not working. The reason for this is as follows….smi23d consists of two programs. Smi2sdf and mengine.

    The first program generates the raw 3d coordinates from SMILES. The second minimizes the energy. At present we are feeding our 2D sdfs to the mengine and it gives problems for highly symmetrical configurations and ugly configurations, etc.

    We need to modify our implementation by feeding the associated SMILES to smi2sdf (rather than SDF directly) and then apply mengine.

    We will get to this work shortly as we have a series of higher priorities right now. This is just a public declaration of a known issue and intention to resolve.

  3. ChemSpider Blog » Blog Archive » Millions of Pre-optimized 3D Structures now Deposited on ChemSpider says:

    [...] I previously blogged about the fact that we had embedded a 3D optimizer under Jmol so that that 3D molecules could be displayed. There were two problems with the approach we took. 1) It was very time-consuming to wait for real-time 3D optimization for molecules 2) The 3D optimizer would sometimes fail to optimize a structure based on the starting geometry. [...]

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