how to make all structures of same size?
at the moment the size of structure depend of free space in the cell - if molecule is small it increased, and conversely.
how can I make all structures (bond length) with fixed size?
The default behaviour is for each molecule to use the available area of the Marvin pane irrespetive of the size.
As you can see from this screenshot the bond lengths are essentially constant yet the smaller molecule is effectively zoomed into. I think this topic might belong in the Marvin forum as a question or "new feature request ".
We cannot see a way to configure this currently in IJC, perhaps the Marvin team can comment please.
Thanks for the answer Daniel, but maybe it possible to make all structures of same size at least when a sdf-file unloading?
Could you please expand on what you mean by "sdf unloading" ?
If you double click on any particular strucure and open Marvin, you can use view zoom in / out in order to see the details better for large molecules - this setting is permanent and will apply to any other structures you select.
A sort of half way there answer to your need !