For my homology model protein, I have done energy minimization through YASARA energy minimization server (http://www.yasara.org/minimizationserver.htm). I got energy minimized model as Yasara scence, which can be viewed in Yasara viewer.
I have doubt , how to save the energy minimized model as pdb file?. When I did file->save as->pdb->select all->file.pdb, it says object "command failed".
1.How to save the energy minimized Yasara scene as single pdf file? 2. Can I go for Protein structure quality check with the energy minimized model?