Good program for visualization of PDB data?

mhodak · Veteran Joined: 15 Nov 2003 Posts: 1218

I am looking for a good program that can read and visualize PDB files (from the Protein Databank). I know that there are several tools available in portage, but I have no experience with them so I am looking for advice from someone that know them.

It should be reasonably advanced, so that it would allow me select parts of the structure based on various criteria such as distance from given atom, plus it should be smart enough so that it would select whole residui. Also, it should be able to add hydrogens, quite a few pdb files are missing them.

So basically I want to know which of the available programs is reasonably advanced to do things like that.

I am looking at pymol at the moment, is there something better out there?

SerfurJ · l33t Joined: 10 Apr 2004 Posts: 824 Location: Texas

i think rasmol is better than pymol for visualization.

mhodak · Veteran Joined: 15 Nov 2003 Posts: 1218

Rasmol seems OK, but going through its manual I cannot find options for adding H-atoms. (The PDB files I have is missing H-atoms, they were not resolved in experiment).

>Octoploid< · n00b Joined: 27 Jun 2004 Posts: 57

IMO http://www.ks.uiuc.edu/Research/vmd/ is really nice.
There is no ebuild yet, but you can use the precompiled binaries.

SerfurJ · l33t Joined: 10 Apr 2004 Posts: 824 Location: Texas

VMD looks nice. i'll have to give it a try.