• With protein with water molecules or/and ligand (1PAX for example with both), when i select water molecules or the ligand and delete them/it, previous secondary structures are deleted too (not the surfaces).

• Why if i delete a protein, in the document view, secondary structures are deleted but not surfaces (i've to delete them manually !)

After loading a PDB structure, i create a secondary structure. In the document viewer, i click on the Secondary structure node then click to create a surface. A new node is created but empty ! Should not happen, right ? A surface node should appear only if atoms or groups of atoms are selected ?

With a PDB structure with water (1PAX for example), in the biology menu, the water icon is selecting only water oxygen atom. If you add hydrogens then click on water icon, delete water, hydrogens from water are still there !

Hello,
i open a structure with a ligand (for example: 4DFR or 1PAX), in Selection filter i choose 'residues'. With the mouse i select all the protein then in 'Biology' menu, i click on 'Secondary structure' => SAMSON is crashing (using Win10).

OK. That's the point. It's working if the Selection filter is set to Residues.
It is confusing. If i select Ramachandran Plot, is it possible to switch automatically to Residues instead of Atoms and bond by default ?

No. It's not working.
If i select a residue or a set of residues and then click Update in the Ramachandran plot i see ALL residues.

If i change the hydrophobic scale for the whole residues, i expect to see residues be recolored but nothing append. I didn't find an update button in the inspector

Thanks. But if 1CRN is already loaded, i expect to see the ramachandran plot when i open it the first time ! This is not the case. I have to click update even the first time to see it.
If i select a residue and click update, i see all protein residues not only the one selected. Is it correct ?

After loading a structure, if i choose to colore it by secondary structure (ss), the whole protein is green. I've to select Secondary structure representation then ss color to see amino acids color by ss. And colors are not the same between ss representation and ss residues colors...not good !
If i choose a surface representation, it take previously selected colors. If i want to change the color, i have to create another surface, correct ?
In the surface properties, if i change the Opacity from 100% to 99% (or less), the surface disappear.
For a selected residue with hydrophobic color, if i change the hydrophobic scale, nothing change with the color of the residue....

After loading a PDB file (1CRN for example) and selecting Ramachandran Plot (Menu Biology and More), i can't see any residues on the map ! Selecting a single residue or the whole protein is not changing anything.
Any idea ?