If you've got a nice resolution structure from PDB it is straight forward:

1) Go to http://www.pymol.org/

2) Download and install

3) Open PyMOL

4) Type 'fetch PDBID', where PDBID could be e.g. '3bqk'

5) On the right a menu will appear choose 3bqk 'H' and 'everything

6) Choose 'S' and 'surface'

7) Choose 'C' and 'Greens' and 'greens'

8) In the top menu you'll have 'File', 'Edit' and so on, choose 'Display' and 'Sequence On'

9) In the sequence, which appear, locate your amino acid residue and click it

10) '(sele)' will appear under '3bqk' on the right

11) Choose 'C' and 'Reds' and 'red'

12) Left-clik on the molecule and turn it to see if you can spot an area, which is now red instead of green

13) Compare with attachment (3BQK, D1444 in red, DOI: 10.1074/jbc.C800086200)

Enjoy! :-)

Hi Bernardo

I will recommend you Pymol or Coot. Unfortunately Pymol is no longer free, so you must apply for an academic license if you do not want to pay. Coot is more oriented to model building and refinement but still is a good tool in which you can locate sequences in the structure.

Best. Paco

Hi,

You can try PyMol, Chimera or VMD. These are freely available visualization software.

If you've got a nice resolution structure from PDB it is straight forward:

1) Go to http://www.pymol.org/

2) Download and install

3) Open PyMOL

4) Type 'fetch PDBID', where PDBID could be e.g. '3bqk'

5) On the right a menu will appear choose 3bqk 'H' and 'everything

6) Choose 'S' and 'surface'

7) Choose 'C' and 'Greens' and 'greens'

8) In the top menu you'll have 'File', 'Edit' and so on, choose 'Display' and 'Sequence On'

9) In the sequence, which appear, locate your amino acid residue and click it

10) '(sele)' will appear under '3bqk' on the right

11) Choose 'C' and 'Reds' and 'red'

12) Left-clik on the molecule and turn it to see if you can spot an area, which is now red instead of green

13) Compare with attachment (3BQK, D1444 in red, DOI: 10.1074/jbc.C800086200)

Enjoy! :-)

Just same as Leon but in command prompt

upto 4 it is the same ... install and fetch PDB

then

use these commands

"show surface

color green

color red, resid 1559

hide nonbonded"

where "resid 1559" should be replaced with your desired residue number of the amino acid

Beautiful work.

Yes, for an automated work the solvent-accessible surface area is a good idea. A similar option is to calculate Generalized-Born potential for these residues.

I prefer to use MOE software for fast visualization. Just use Sequence Editor -> Predicted solvent Accessibility. After you can mark residues using Residues Selector. For more precision calculations I use Whatif software from Prof. Vriend. They have a free web interface:

http://swift.cmbi.ru.nl/servers/html/index.html

Use Accessibility option and you can get output per atom or residue.

I still like the classic "Rasmol", very easy to use command line interface

Pymol, Chimera, MOE, BIOVIA Discovery Studio.

Good Luck.