secondary structure

HI, Is there any way to selectively turns on Secondary structure in MarvinSpace?

I've opened a PDB file that have protein + carbohdyrate, (e.g. PDB:1L6X), and turned on the secondary structure drawing. And MarvinSpace somehow tries to draw the secondary structure for sugars, and it does not look good.

Hi,

Use the selection panel on the right side, click the yellow rectangles associated with the sugar molecules (they get deselected, rectangle is greyed). Then click secondary structure drawing, you get it for the protein only. After that you can turn the display of the sugars on again by clicking the yellow rectangles again.

 

Does this help?

Miklos

Thanks Miklos,

The problem was I'm using javascript, and chain selection seems to be impossible in javascript. Further, I just realized that MarvinSpace has various problems reading carbohydrate in general.

1. Carbohydrates are in HETATM section in regular PDB format, and MarvinSpace does not recognize those residue names for carbohydrates. The workaround that I found is changing the residue name of carbohydrates into UNK.

2. If the carbohydrates are placed in ATOM section, as I'm reading the PDB in CHARMM and generated CHARMM format PDB, now, MarvinSpace think it is a part of macromolecule and tries to draw secondary structure, though there is no problem with residue name in this case. 

Currently, I've implemented to generate a modified version of PDB, which detects carbohydrate chains and change the ATOM to HETATM and change residue name to UNK. But it would be appreciable if there is more easier way to deal with this in general. Also, it should be able to read regular PDB with no problem, for example, PDB:1L6X.

 

Thanks,
Sunhwan 

It seems OK with 6.3 .