Re: [Jmol-users] Secondary structure does not match DSSP

[Nicholas Newell]

Understood. Thanks for your replies and for a great program.

Nicholas

From: Eric Martz 
Sent: Sunday, April 23, 2017 11:18 AM
To: jmol-users@lists.sourceforge.net 
Subject: Re: [Jmol-users] Secondary structure does not match DSSP

Dear Nicholas,


Angel is correct. By default, Jmol shows the secondary structure that the 
authors specified in the PDB file with HELIX, SHEET and TURN records. You will 
notice that often, authors do not specify TURN records so there are no blue 
turns initially. After you calculate structure, and color structure, turns are 
colored blue, and the ends of strands and helices may be different than before. 


Also, Jmol distinguishes three kinds of helices, and gives them distinct colors:

  a.. Alpha 3.6(13) 
  b.. 3.0(10) 
  c.. Pi 4.4(16) 
Each kind is illustrated here in JSmol:
http://proteopedia.org/w/Helices_in_Proteins

See also http://proteopedia.org/w/Secondary_structure

-Eric



On 4/23/17 4:56 AM, Angel Herráez wrote:

Hi Nicholas 

However, if I issue the command $calculate structure and then redisplay, the 
structure 
is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can 
anyone 
tell me why Jmol doesn't display this stretch according to DSSP in the first 
place? 
I am not certain, but it is likely that when you load a file Jmol will use the 
secondary structure declared in the PDB file, and not the DSSP result unless 
you invoke this later (using calculate).

As far as I can interpret, the pdb file says beta strands for
Tyr350---Trp356
Cys370---Pro373

so  365-368  are not a beta strand








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[Jmol-users] Secondary structure does not match DSSP

[Nicholas Newell]

Hello,

I'm using Jmol 14.13, which should use the DSSP v2.0 algorithm to compute 
secondary structure. The command $show defaultStructureDSSP returns true, so 
this
should indeed be the case. However, Jmol displays residues 365-368 from 
7odc.pdb as loop-type, not ribbon, while DSSP 2.0 computes this stretch as type 
E, part of a strand that strectches from residue 365 to residue 373. To 
complicate matters, at residue 369 Jmol does not not start the ribbon at the 
residue's nitrogen but instead at its alpha carbon.

However, if I issue the command $calculate structure and then redisplay, the 
structure is then shown with a ribbon consistent with DSSP, running from 365 to 
373. Can anyone tell me why Jmol doesn't display this stretch according to DSSP 
in the first place? It's true that a ramachandran angle calculation does show 
the stretch 365 to 368 as loop-type with no ribbon, so perhaps for some reason 
Jmol is doing a ramachandran calculation instead of DSSP for these residues, 
but then still doesn't explain why the ribbon starts at residue 369's alpha 
carbon instead of its nitrogen.

It's worth noting that this stretch is somewhat ambiguous in secondary 
structure. Although it shows strand-like H-bonding with an adjacent strand, the 
chain bends tightly enough at these residues to fit the definition of a beta 
turn. Does Jmol override DSSP in such cases?

Any insight is appreciated.

Nicholas Newell--
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