Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
Viewing sequence in pdb files (Read 6118 times)
Oct 18th, 2011 at 11:28pm

JohnR   Offline
YaBB Newbies

Posts: 17
*
 
How does one use UGene to view the amino acid sequence in a pdb file? I was working with the file 1PPI and could see a structural view as well as annotation showing secondary structure annotations for the sequence in the sequence view window. Is there a way to toggle the views so that the amino acid sequence is shown, as is seen when the sequence is displayed from Genbank format? I tried resizing the different windows but didn't see anything with the amino acid sequence shown. A screenshot of what I could see is attached. Although working with the primary sequence isn't the main purpose of using a pdb file, it would be useful to be able to view the primary sequence, as well as to select parts of the sequence to be highlighted in the structure window.

Thanks!
 
IP Logged
 
Reply #1 - Oct 19th, 2011 at 3:36am

JohnR   Offline
YaBB Newbies

Posts: 17
*
 
I found the answer to toggling the file view. There is a downward pointing green arrow on the right side of the screen that allows you to toggle views - see attached.
 
IP Logged
 
Reply #2 - Oct 19th, 2011 at 4:51am

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Some additional remarks:
  • One can hide or close 3D view using similar "green arrow" toggle menu in the upper right corner
  • Typically pdb files contain only protein sequences, so detailed view won't include the translation. However it is possible to back-translate the sequence using Export->Export sequences (region)
 
IP Logged
 
Page Index Toggle Pages: 1