screen3d not converging

User b4f15198ac

19-08-2014 03:41:09


I have recently started using screen3d to preform structure comparisons, and have been getting the message:

Aug 18, 2014 8:27:45 PM chemaxon.marvin.alignment.AlignmentBase optimization

INFO: Optimization was not converged.

How can I avoid this? It is only happening for about half the structures I am screening, but it has me stumped! can I increase the time allowed, or would this help?

I am using screen3d as follows:

screen3d s -t ncidiv.ser -q Abacavir.ser frq 

Where ncidiv.ser is a list of ~1600 structures. Would it be possible to view which structure is throwing the errors so that it may be examined or removed?


OS: 64 bit linux


Thank you in advance! Your tools have been indispensable. 

User b4f15198ac

19-08-2014 04:31:24

is there any significant difference from the Alignment package included in marvin beans? I am trying to do rigid-rigid alignment.

ChemAxon d51151248d

19-08-2014 11:34:52

Hi ajaceves,

the problem you encountered is due to the internal optimizer in the alignment module. This means that some

optimization runs do not meet the convergence criteria. In this case that info message is given, and the run

continues. This issue does not influence the similarity result for a query-target pair. 

The alignment module is also built in MarvinSketch as a plugin (3D Flexible Alignment Plugin), but that is only able

to superimpose 1 ensemble (or pair) of molecules.


Best regards,


User b4f15198ac

19-08-2014 15:50:24

Hello Daniel,

Thank you for your prompt and informative reply! 

If I may ask one other question... Is the default method rigid-flexible? I am aware of the switch for force the query to be rigid, but how does one control the rigid/flex state of the target? Thank you again for your support.


ChemAxon d51151248d

27-08-2014 15:03:07

Hi Aiden, 

yes, there is an option for this. So to keep the target rigid, omit the -F option that forces the target to be flexible during the first phase of the screening. This is the default, by the way. So for example

screen3d g ada_ligands.mol2 -match

uses the Match screening method, but keeps the target molecules in the file rigid during the preparation phase.

In the Alignment Plugin you just have to select the molecule on the canvas that you want to treat rigid.

You can reach the manual of the screen3d tool by typing

screen3d -h 

I hope this helps.