Open PDB protein model

[Ivan]

SAMSON can not open tubulin model: http://www.rcsb.org/structure/5SYF

Is it possible to open such PDB structures in SAMSON?

[DmitriyMarin]

SAMSON can open 5SYF, both PDB and PDB bioassembly. You can try downloading it with the Protein Data Bank Downloader SAMSON Element.

But, beware that importing the 5SYF bioassembly consumes a lot of RAM. If you want to import the bioassembly version of 5SYF be sure to uncheck the "Create path from multiple models" in the importing options dialogue, otherwise you will get a trajectory (path).

Importer for the PDBx/mmCIF file format will be coming in the next version of SAMSON.

[DmitriyMarin]

If you have a problem loading a molecule in SAMSON, could you, please, post the logs, it would help us to determine the issue.
To see the log in the terminal, you can launch SAMSON-Core with the flag --logconsole . You can also redirect the logs into a file with the flag --logfile "filename". There is also the Log Viewer SAMSON Element, which allows redirecting the output.

[DmitriyMarin]

Meanwhile, I attach the 5SYF.sam file (archived), which you can load in SAMSON.

[Ivan]

Thank you, Dmitriy. I will try later. I just tried to open pdb file in Windows, and in status bar got the message, that it "can''t open" my file. I will try to put the log here a bit later.