SAMSON Extensions

Hi Andrea, sorry for the delay. Typization is normally performed automatically (this is a benefit of this SAMSON Element, as described in the paper Artemova, S., Jaillet, L., & Redon, S. (2016). Automatic molecular structure perception for the universal force field. Journal of computational chemistry, 37(13), 1191-1205.). The typization functions are there when you know for sure that you would like to use a different typization, but even then you should refer to the original UFF paper to make sure this is what you want.

wonderful! Thanks

Great! Diana, thank you very much for providing good descriptions of your problem and solution - it might help others experiencing the same problem. Sorry for the issue. Yes, the Python version is important since the Python Scripting Element is linked to a particular version of the Python library.

Dear Dimitriy, Thank you very much. Best Regards, Surendra

Sorry for the issue!

Hi Arnaud, thanks for your interest in SAMSON and sorry about this crash. We are not able to reproduce it here. Could you please try to remove the GROMACS element and add it again as follows: Sign in on SAMSON Connect, you will arrive in My SAMSON / My Elements On the SAMSON Element called "GROMACS interaction models", you should see an "Installed" button. When you hover the mouse over it, the button turns to "Remove". Click on it. Restart SAMSON, this will uninstall the GROMACS element. Quit SAMSON. On SAMSON Connect, the button mentioned above should turn to "Add again" (this might take a minute). Click on it. It should turn to "Pending". Restart SAMSON, this will install the GROMACS element. Please let me know if this helps. Academic accounts are the ones with academic email addresses. Is it possible for you to sign up with one?

Thank you so much sir....It really helped.

Dear Patrice, yes, it is planned in a very near future, I didn't have time for the update yet... Regards, Sergei

Gaussian surfaces may be slow to recompute sometimes (e.g. for large molecules), so there is an "Update" button to recompute the surface. You need to use it when you change the color. About the transparency: it depends on the order of visual models. Since order-independent transparency is not yet implemented, you will see the secondary structure only if it comes before the gaussian surface (when you traverse the document in depth-first order). Here is an example with the Gaussian surface first: [image: 0_1512040615642_GSS.png] And here is an example with the Gaussian surface after the secondary structure: [image: 0_1512040385013_SSG.png]