MERRIFIELD RESIN

ChemAxon 587f88acea

23-02-2005 13:16:18

ISIS software represents resin as 'Pol' in the sketch. How does JCHEM handle resin ? here is the smiles generated by JCHEM with an SDF export from ISIS for the MERRIFIELD RESIN : the resin has just disappeared !





[]C1=CC=C(C=C1)C([H])([H])Cl





Thanks for your help





Pierre-Olivier

ChemAxon 43e6884a7a

23-02-2005 15:05:33

Please attach a Molfile causing problem.


Ferenc

ChemAxon a3d59b832c

23-02-2005 16:01:53

POJ2 wrote:
ISIS software represents resin as 'Pol' in the sketch. How does JCHEM handle resin ? here is the smiles generated by JCHEM with an SDF export from ISIS for the MERRIFIELD RESIN : the resin has just disappeared !





[]C1=CC=C(C=C1)C([H])([H])Cl





Thanks for your help





Pierre-Olivier
`





JChem/Marvin can handle these so-called pseudo atom types, and they can be saved in mol and mrv formats. They are drawn using the "More..." window of marvin and can searched for in JChem.





In the current release there is an exception during smiles export for these structures indicating that they cannot be described in that format. However, we plan to add pseudo atom support into the cxsmiles format:





http://www.chemaxon.com/marvin/doc/user/cxsmiles-doc.html





Until then I suggest for you to use the mol or mrv formats for those structures.

ChemAxon 587f88acea

23-02-2005 16:08:47

please Ferenc, find the ISIS sdf export

ChemAxon 587f88acea

25-02-2005 08:56:18

Hi Szabolcs


I was not able to locate 'Pol' atoms type in Marvin. Could tou tell me more about it.





Moreover I have loaded the resin as a mol file into Marvin and got the same result : the source code given by Marvin is :








Marvin 02250509482D





11 11 0 0 0 0 999 V2000


4.9887 -2.0845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


5.7086 -1.6643 0.0000 0 0 0 0 0 0 0 0 0 0 0 0 0


4.2803 -1.6692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.5651 -2.0804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.5620 -2.9055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.2801 -3.3177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.9923 -2.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.8436 -3.3286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.1227 -3.7475 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


3.2623 -4.0483 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0


2.4239 -2.6073 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


5 6 1 0 0 0 0


2 1 1 0 0 0 0


6 7 2 0 0 0 0


7 1 1 0 0 0 0


3 4 1 0 0 0 0


5 8 1 0 0 0 0


8 9 1 0 0 0 0


4 5 2 0 0 0 0


8 10 1 0 0 0 0


1 3 2 0 0 0 0


8 11 1 0 0 0 0


M END


$$$$





instead of :








-ISIS- 02250509182D





11 11 0 0 0 0 0 0 0 0999 V2000


3.4791 0.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.1959 1.1125 0.0000 Pol 0 0 0 0 0 0 0 0 0 0 0 0


2.7739 1.1076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.0619 0.6958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.0588 -0.1263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.7737 -0.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.4827 -0.1291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.3435 -0.5458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.6215 -0.9653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


1.7587 -1.2666 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0


0.9232 0.1723 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


5 6 1 0 0 0 0


2 1 1 0 0 0 0


6 7 2 0 0 0 0


7 1 1 0 0 0 0


3 4 1 0 0 0 0


5 8 1 0 0 0 0


8 9 1 0 0 0 0


4 5 2 0 0 0 0


8 10 1 0 0 0 0


1 3 2 0 0 0 0


8 11 1 0 0 0 0


M END





Thanks for helping me

ChemAxon a3d59b832c

25-02-2005 09:29:14

POJ2 wrote:
Hi Szabolcs


I was not able to locate 'Pol' atoms type in Marvin. Could tou tell me more about it.


In the "More..." window type Pol in the text box (or any other name you prefer), click the Pseudo button (second after the textfield), and click on the canvas to draw atom Pol.
POJ2 wrote:



Moreover I have loaded the resin as a mol file into Marvin and got the same result : the source code given by Marvin is :


Oh, I see. Then you won't find the Pseudo button in that version. Please download the latest Marvin from here:





http://www.chemaxon.com/marvin/download.html

ChemAxon a3d59b832c

25-02-2005 11:16:03

Szabolcs wrote:
Please download the latest Marvin from here:





http://www.chemaxon.com/marvin/download.html
Oh, sorry. You are using JChem, aren't you? Then you should upgrade JChem:





http://www.jchem.com/licensefrset.html