Hi Ahmad - thanks for posting such an interesting question 
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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On 21/08/2019 16:28, Ahmad Khalifa wrote: