Clean 3D using amino acid templates doesn't work any more

Hi, now there is a new problem in Marvin 5.4.0.0.

In a direct email to the Marvin developers I mentioned the following procedure as a nice tool:

We made the following (MarvinSketch 5.3.8):

1) Inserting the amino acid from the templates.

2) Clean 3D with hydrogenize (I like it ...)

3) Replacing the formyl-H by OH.

4) Once more Clean 3D with hydrogenize.

And we had fine 3D structures of the amino acids, we could mirror these and do other fine things.

Testing this with the new 5.4.0.0 there is nothing, see screenshot.

What is wrong ?

Regards, Hans-Ulrich

Hi Hans-Ulrich,

The short answer is that you have to ungrop the aminoacid between point 1 and 2, and then it will work on the same way.

The long answer:

In 5.3.x versions there was a side effect of adding explcit hydrogens to an Sgroup: It automatically expanded the Sgroup. Actually, if a bond was added to any atom of the Sgroup that had no attachment point, the Sgroup was automatically ungrouped, because then the Sgroup was not the same structure anymore. But there were claims that if only explicit hydrogens are added, then the Sgroup chemically still remains the same, which is true, so we fixed this issue in 5.4.0.0 and therefore now the action of adding explicit hydrogens does not result in the automatic ungrouping of the Sgroup. As a consequense, the attachment point is not removed from the carbonyl, and therefore no explicit H is added there. If you ungroup the aminoacid before the first 3D clean with hydrogenize, the problem is solved.

Best regards,

Akos

Hi Hans-Ulrich,

In version 5.4.1 (coming at the end of this month) the 3D Clean with "Fine with hydrogenize" option will ungroup abbreviated groups automatically again.

Best regards,

Akos

Dear Akos,

thank you for the positive information. So we can avoid the "workaround".

And we will install the new version immediately when it is coming!

Best regards, Hans-Ulrich