How to prepare high-resolution protein secondary structures diagrams?

Question

[sunyeping]

Dear everyone,

I would like to prepare some protein secondary structures diagrams. I know that I can do this by uploading my pdb file to the pdbsum server (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.plpdbcode=index.html) which produces the econdary structure diagrams like the following:

https://drive.google.com/file/d/18bZmOosiA0UpWxcoG8KeYgWR53l3XxQd/view?usp=sharing

However, this image produced by pdbsum is low-resolution gif file. Do you know which online server or program can produce high-resolution secondary structures diagrams like what produced by pdbsum?

Thank you in advance.

[Ram]

Please read How to add images to a Biostars post to understand how to upload images properly. Switch to imgbb instead of Google Drive.

Answer 1

[jgreener]

The PSIPRED web server at http://bioinf.cs.ucl.ac.uk/psipred gives you a nice diagram available in SVG format.

[sunyeping]

PSIPRED predict secondary structures from sequence. What I need is to plot secondary structures diagrams from pdb file.

Answer 2

[Mensur Dlakic]

I think Procheck or its online server have some of the properties you need, but the plot is spread out over several pages. You may want to check out the residue property plot in online version, and scroll down until you find the cartoon. It shows residue solvent accessibility as well. In the stand-alone version the plots are in PostScript, so you can convert them to high-res images afterwards.

[sunyeping]

Among the outputs of Procheck, the "residue properties plot" contains the secondary structure information and that is useful. Thank you.