From: winardi, erik (
Date: Wed Sep 07 2011 - 18:02:19 CDT

Dear Dr. Kohlmeyer,  I was mistaken on giving the information.  What I have is the .dcd format not .pdb which is also a trajectory file only.  I could upload the .dcd file but I can only draw the bonds in VMD using dynamic bonds.  But I couldn't draw the atoms using VDW or CPK. Is there anyway I can visualize the atoms ? or I need to get the .pdb or .car file ?   Thanks,  Erik ________________________________ From: Axel Kohlmeyer <> To: "winardi, erik" <> Cc: "" <> Sent: Wednesday, September 7, 2011 2:55 PM Subject: Re: vmd-l: Visualizing Trajectory file: .pdb or .xyz On Wed, Sep 7, 2011 at 2:49 PM, winardi, erik <> wrote: > Dear VMD community, > I have trajectory files which need to be visualize. They are in .pdb and > .xyz format. > I do not have the initial configuration data for these trajectory files. > I tried loading these trajectory files into VMD and playing around the > Graphic Representation Tools. > However, I couldn't get the atoms to appear. I chose the VDW molecule type. > Is it possible to visualize the atoms and bonds only from .pdb or .xyz files > ? > or do I need to get the initial configuration too ? no. both file formats, .xyz and. pdb, contain coordinate information. please have a close look at the VMD console and check if there are any error messages. VMD will do a best effort to parse files according to the available "standards" and some commonly used variants, but if the format strays too far, the corresponding plugin may reject reading the files. if there is no message visible, please provide small example files demonstrating the issue. cheers,     axel. > Thanks, > Erik Winardi -- Dr. Axel Kohlmeyer Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.