tangram 0.0.8 Nothing happens

[JeanDidier]

Hi,

I have no messages of error but when applying the 3d-snfg nothing happens. the id of the pdb is 1b3z

thanks

[jaimergp]

Yep, sorry, this extension is not documented.

The GUI only allows to change the default values for the configuration, the actual usage is done through the command line, using snfg.

There are some optional values:

• method: icon, full, fullred, fullshown (following some of the original implementation depictions
• size: base size for all polyhedra. Default is 4.0

I will update the docs during the weekend.

[IngaJamrozek]

Hi,

where can I find the documentation? The problem is that I read my pdb info Chimera, use snfg in command line as in previous comment and in lots of cases the snfg representation is applied only partially.

Thanks!

[jaimergp]

That weekend was not very productive, I guess :) No documentation yet.

Can you attach the PDF file or its ID? The current implementation relies on residue names, so there's a chance that the missing saccharydes are incorrectly named and that's why they are not being recognized. A better implementation would rely on carefully crafted SMARTS queries but nobody has the time :) PRs welcome though!

[IngaJamrozek]

Weekends never are productive :)

I tried it for 5DK3, 3SGJ and also for glycan written in pdb format generated using http://glycam.org/ (this one was made by me, so there is a huge chance that something is incorrect).
I will also check the names in the pdb files.

Thank you for your help :)

[jaimergp]

The 3D view at RCSB does display them correctly:

• https://www.rcsb.org/3d-view/5DK3/1
• https://www.rcsb.org/3d-view/3SGJ/1

So I guess they are using something smarter or an extended definition table we don't have here... Maybe some of these files.