Hi Ahmad - thanks for posting such an interesting question :)
On 21/08/2019 16:28, Ahmad Khalifa wrote:
I'm trying to create a visual 2D map of my structure and annotate its
secondary structure elements. First I need to a good visual
representation of the sequence and the ss elements that are there. Are
they going to be generated by DSSP or read from my structure header?!
Jalview automatically uses Jmol's built in DSSP to determine secondary
structure from PDB and mmCIF files. Just make sure you have 'process
secondary structure from PDB' enabled in your Jalview preferences:
http://www.jalview.org/help/html/features/preferences.html#structure
Hopefully, Jalview can actually annotate the ss elements as well in a
numerical order, like H1, S1, S1', H2,...etc. Are there guidelines
regarding how close two ss elements should be to be annotated with the
same number followed by prime?
Currently, Jalview doesn't assign numbers, but it is certainly something
that would be useful, and fairly easy to implement. I am not sure about
the use of prime - however - in the context of strands in your example,
I would normally interpret S1' as the antiparallel partner of S1. RIght
now, Jalview doesn't process any information about strand pairing - so
that might be more of a challenge, but certainly possible also.
If not I can do it manually!
Well - for one protein that might be quickest but we can certainly help
you out with a groovy script to automatically generate a numbers for
contiguous secondary structure elements (give or take bulges, etc).
I recommend you first take a look at how jalview generates secondary
structure annotation from protein structures by enabling structure
processing in your preferences, and also ticking the option so Jalview
makes secondary structure annotation visible on the alignment when PDB
data is imported (otherwise you can add these additional rows for
sequences via the sequence ID popup menu using the 'Add Reference
Annotation' option).
Let us know how you get on... and if you'd like a script !
Jim.
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