Thanks to Rajarshi for pointing us to smi23d we have now implemented this code underneath JMol and when you try and display the structures in Jmol now BEFORE they display they are optimized.
This is our beta implementation so we do not yet have a statement saying "optimizing 3D structure" so for complex structures the JMol screen stays blank while generating the 3D coordinates....so be it.
REad these blog postings from last night re. Diazonamide A...
Now, take a look at http://www.chemspider.com/Search.aspx?q=diazonamide+a Look at the bottom 4 structures out of the 6 and if you click on Jmol you will see the structures optimized. Click on the top 2 in Jmol and the optimization fails. Rajarshi...we need your assistance please!
On Sep 24, 8:22 pm, Tony at ChemSpider <tony27...@gmail.com> wrote:
> Now, take a look athttp://www.chemspider.com/Search.aspx?q=diazonamide+a > Look at the bottom 4 structures out of the 6 and if you click on Jmol > you will see the structures optimized. Click on the top 2 in Jmol and > the optimization fails. Rajarshi...we need your assistance please!
I just tried the first one locally and it seems to work fine. I took the isomeric SMILES from the Pubchem CID 395475 (as linked to from the Chemspider entry), ran it through smi23d (< 1 sec) and then mengine (< 10sec) and I was able to view the resultant SDF in Jmol locally.
I'm not sure what's going on - what SMILES are you providing to smi23d?
> -----Original Message----- > From: usefulchem@googlegroups.com [mailto:usefulchem@googlegroups.com] On > Behalf Of Rajarshi > Sent: Monday, September 24, 2007 9:13 PM > To: UsefulChem > Subject: [UsefulChem] Re: 3D optimizations using Rajarshi's optimizer now > on ChemSpider.
> On Sep 24, 8:22 pm, Tony at ChemSpider <tony27...@gmail.com> wrote: > > Now, take a look
> > Look at the bottom 4 structures out of the 6 and if you click on Jmol > > you will see the structures optimized. Click on the top 2 in Jmol and > > the optimization fails. Rajarshi...we need your assistance please!
> I just tried the first one locally and it seems to work fine. I took > the isomeric SMILES from the Pubchem CID 395475 (as linked to from the > Chemspider entry), ran it through smi23d (< 1 sec) and then mengine (< > 10sec) and I was able to view the resultant SDF in Jmol locally.
> I'm not sure what's going on - what SMILES are you providing to smi23d?
> -----Original Message----- > From: usefulchem@googlegroups.com [mailto:usefulchem@googlegroups.com] On > Behalf Of Val at ChemSpider > Sent: Monday, September 24, 2007 9:19 PM > To: usefulchem@googlegroups.com > Subject: [UsefulChem] Re: 3D optimizations using Rajarshi's optimizer now > on ChemSpider.
> Hi Rajarshi
> We don't feed SMILES, we feed 2D SDF to mengine. This is the output I > get:
> On > > Behalf Of Rajarshi > > Sent: Monday, September 24, 2007 9:13 PM > > To: UsefulChem > > Subject: [UsefulChem] Re: 3D optimizations using Rajarshi's optimizer > now > > on ChemSpider.
> > On Sep 24, 8:22 pm, Tony at ChemSpider <tony27...@gmail.com> wrote: > > > Now, take a look > athttp://www.chemspider.com/Search.aspx?q=diazonamide+a > > > Look at the bottom 4 structures out of the 6 and if you click on > Jmol > > > you will see the structures optimized. Click on the top 2 in Jmol > and > > > the optimization fails. Rajarshi...we need your assistance please!
> > I just tried the first one locally and it seems to work fine. I took > > the isomeric SMILES from the Pubchem CID 395475 (as linked to from the > > Chemspider entry), ran it through smi23d (< 1 sec) and then mengine (< > > 10sec) and I was able to view the resultant SDF in Jmol locally.
> > I'm not sure what's going on - what SMILES are you providing to > smi23d?
^^^^ 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.
On Sep 24, 9:22 pm, "Val at ChemSpider" <v...@chemspider.com> wrote:
> And here is SDF I feed, sorry...
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.
> -----Original Message----- > From: usefulchem@googlegroups.com [mailto:usefulchem@googlegroups.com] On > Behalf Of Rajarshi > Sent: Monday, September 24, 2007 9:20 PM > To: UsefulChem > Subject: [UsefulChem] Re: 3D optimizations using Rajarshi's optimizer now > on ChemSpider.
> On Sep 24, 9:19 pm, "Val at ChemSpider" <v...@chemspider.com> wrote: > > Hi Rajarshi
> > We don't feed SMILES, we feed 2D SDF to mengine. This is the output I > > get:
> 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.
On 9/25/07, Val at ChemSpider <v...@chemspider.com> wrote:
> Ok. Will try this next!
Great to see this feature online. Please correct on the ChemSpider website JMol into Jmol. Seems minor, but there is/has been another (US-based) JMol project in addition to our favorit Jmol.org project. Thanx!
Done. Typo was in just one place..but the most prominent. :)
Re great features.. we want to use some CDK capabilities at ChemSpider. Specifically to calculate some descriptors. Any recommendations what we should start from? Also, ChemSpider is ASP.NET based... to facilitate interfacing, do you have any webservice to get connected to CDK capabilities?
> -----Original Message----- > From: usefulchem@googlegroups.com [mailto:usefulchem@googlegroups.com] On > Behalf Of Egon Willighagen > Sent: Tuesday, September 25, 2007 1:02 AM > To: usefulchem@googlegroups.com > Subject: [UsefulChem] Re: 3D optimizations using Rajarshi's optimizer now > on ChemSpider.
> Hi Val,
> On 9/25/07, Val at ChemSpider <v...@chemspider.com> wrote: > > Ok. Will try this next!
> Great to see this feature online. Please correct on the ChemSpider > website JMol into Jmol. Seems minor, but there is/has been another > (US-based) JMol project in addition to our favorit Jmol.org project. > Thanx!
On 9/25/07, Val at ChemSpider <v...@chemspider.com> wrote:
> Done. Typo was in just one place..but the most prominent. :)
Thanx!
> Re great features.. we want to use some CDK capabilities at ChemSpider. > Specifically to calculate some descriptors. Any recommendations what we > should start from? Also, ChemSpider is ASP.NET based... to facilitate > interfacing, do you have any webservice to get connected to CDK > capabilities?
Rajarshi's group has a number of webservices; I'm sure he'll respond. Right now I am working on a couple of mass spectroscopy related, CDK-based SOAP web services. Maybe even BioMoby, if I get that online. Rajarshi, you are not using BioMoby, are you?
You should ignore the getDescriptors method (whose goal is to evaluate all available descriptors for a molecule) as it hasn't been updated in a while.
Any recommendations what we
> should start from? Also, ChemSpider is ASP.NET based... to facilitate > interfacing, do you have any webservice to get connected to CDK > capabilities?
We've put up a number of CDK functionality up as a webservice - some of it trivial, some of it useful (such as 2D structures - all our DB interfaces provide 2D depictions, without worrying about how I can interface CDK with PHP/Python etc, since we just call a WS with SMILES) See http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkws/cdkws....
I don't know ASP.NET, but I'd assume that you can connect via SOAP? They're all SOAP based web services
Wow - getting a realistic conformation for any molecule from ChemSpider would be awesome. It ties in nicely with the upgrade to Andrew Lang's molecule rezzer in Second Life. Andy is using Rajarshi's web services directly from InChI (and soon SMILES) to create the 3D molecules in SL.
> On 9/25/07, Egon Willighagen <egon.willigha...@gmail.com> wrote:
> > Rajarshi's group has a number of webservices;
> We do indeed and we had the CDK descriptors as a web service, but it's > not > been updated for a long time. Clearly it's time to do so :)
> Right now I am working on a couple of mass spectroscopy related, > > CDK-based SOAP web services. Maybe even BioMoby, if I get that online. > > Rajarshi, you are not using BioMoby, are you?
> No
> -- > Rajarshi Guha
-- Jean-Claude Bradley, Ph. D. E-Learning Coordinator for the College of Arts and Sciences Associate Professor of Chemistry Drexel University
<jeanclaude.brad...@gmail.com> wrote: > Wow - getting a realistic conformation for any molecule from ChemSpider > would be awesome. It ties in nicely with the upgrade to Andrew Lang's > molecule rezzer in Second Life. Andy is using Rajarshi's web services > directly from InChI (and soon SMILES) to create the 3D molecules in SL.
> On 9/25/07, Rajarshi <rajarshi.g...@gmail.com> wrote:
> > On 9/25/07, Egon Willighagen <egon.willigha...@gmail.com> wrote:
> > > Rajarshi's group has a number of webservices;
> > We do indeed and we had the CDK descriptors as a web service, but it's > > not > > been updated for a long time. Clearly it's time to do so :)
> > Right now I am working on a couple of mass spectroscopy related, > > > CDK-based SOAP web services. Maybe even BioMoby, if I get that online. > > > Rajarshi, you are not using BioMoby, are you?
> > No
> > -- > > Rajarshi Guha
> -- > Jean-Claude Bradley, Ph. D. > E-Learning Coordinator for the College of Arts and Sciences > Associate Professor of Chemistry > Drexel University
On Sep 25, 7:42 am, Tony at ChemSpider <tony27...@gmail.com> wrote:
> Rajarshi, > Can you take a look at this "locally" on your system and comment on > whether this is an algorithm issue or a "starting point" > issue...thanks
Looks like a starting point issue. I used smi23d to get rough 3D and then minimized by mengine. The resultant SDF is at http://rguha.ath.cx/~rguha/nsc2071.sdf which has the ring in the chair conformation
BTW, the latest code for mengine in trunk will, by default, not evaluate the dipole moment and various vibrational data. You can use command line params to get these values if desired
On Sep 25, 7:42 am, Tony at ChemSpider <tony27...@gmail.com> wrote:
> Rajarshi, > Can you take a look at this "locally" on your system and comment on > whether this is an algorithm issue or a "starting point" > issue...thanks
BTW, given the recent threads on web services, you might be interested in the 3D coordinate web services - send in a SMILES get back an SDF.
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