From: Axel Kohlmeyer (
Date: Wed May 20 2009 - 16:34:45 CDT

On Wed, 2009-05-20 at 13:36 -0500, Lalit wrote:


> However, when I wanted to see the 'protein' (within/around the lipid
> bilayer):
> i) As Coloring Method: Structure & Drawing Method: NewCartoon I was
> NOT able to visualize it.
> ii) Also, with Drawing Method: Cartoon; NewRibbons, Ribbons,
> Tube,Trace; it wasn't visuable (A faint/very small part/structure was
> showing on the openGL).
> iii) Though it was showing the full protein's structure in Licorie,
> cpk, vdw, points, Hbonds, Dynamicbonds, Bonds,Line; drawing methods.

please provide a saved state file with the corresponding .pdb file(s)
that demonstrates the bad behavior, so that we can track it down and
investigate who/what is to blame.

one potential problem is the fact that secondary structure assignment
is done by calling the (external) stride program which tends to react
rather sensitive when processing non-amino acid or other unusual
residues. so you may want to try using a selection for only the protein
and then use the "NewCartoon" representation on it. and then additional
representations for the rest. or you can even set the secondary
structure assignment manually for residues where this has failed.

> Which one do not want!
> I am using VMD 1.8.6 version. Both RedHat Enterprise 4 as well as
> Windows version is showing exactly the same problem.

OS should not be the origin of your problem.


> Please help.
> Many Thanks,
> --- Lalit
> On Tue, May 19, 2009 at 11:00 AM, David Tanner <>
> wrote:
> A PDB file ends with the line 'END'. If you use the 'cat'
> command to concatenate 2 PDB files, you still need to remove
> the 'END' and other non-ATOM lines from the middle of the PDB
> file. Did you already remove these lines?
> Thank you,
> David E. Tanner
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> (217) 244 - 2905
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> On Mon, May 18, 2009 at 6:07 PM, Lalit <>
> wrote:
> Hi,
> I have a situation.
> I got two separate pdb files. one - A lipid bilayer
> with water on both sides, plus Z & minus Z direction,
> and say, named as BL1_WAT.pdb. Second - a protein pdb
> file, say, named as prot_only.pdb.
> Now, I want to put the protein manually 'at a
> particular place' within the lipid bilayer. This I
> was able to do (using moveby command). Once, I placed
> the protein wherever I wanted to, I saved the
> prot_only.pdb file as say, prot_only_final.pdb file.
> Here, so far, whenever, I visualized the protein's pdb
> file I was using: Coloring Method: Structure & Drawing
> Method: NewCartoon AND it was looking OK as it should
> be.
> However, when I just added/concatenated/copied &
> pasted the two pdb files, likewise, BL1_WAT.pdb and
> prot_only_final.pdb INTO a single pdb file, say,
> BL_and_prot.pdb file and then made the selection:
> "protein" within Graphical Representation (after
> loading the file: BL_and_prot.pdb) and wanted to 'see'
> the protein using--> Coloring Method: Structure &
> Drawing Method: NewCartoon, it wasn't possible?
> So, the situation is that when I have two separate pdb
> files (one of then is a common protein's pdb file) I
> was able to visualize the protein using: Coloring
> Method: Structure & Drawing Method: NewCartoon BUT
> when I just add this protein's pdb file with another
> system's (equilibrated lipid bilayer with water &
> ions) pdb file, I wasn't able to make the selection
> (for protein or corresponding residue IDs) as:
> Coloring Method: Structure & Drawing Method:
> NewCartoon.
> I know, initially, there are lots of
> clashes/overlapping between protein's residues and
> water/lipid residues (and I expect to remove these
> steric clashes during equibrium) but still I want to
> 'visualize' the protein (as Coloring Method: Structure
> & Drawing Method: NewCartoon ) and I know its a common
> practice!
> Let, me also add that, when my protein was, say, 10
> Angstrom away from one of the sides of the bilayer I
> was able to 'visulize' the protein as Coloring Method:
> Structure & Drawing Method: NewCartoon. However, as
> the protein approaches the bilayer and as such I
> adjusted the protein the way I wanted it to place (at
> the lipid/water interface) I wasn't able to
> 'visualize' the protein as Coloring Method: Structure
> & Drawing Method: NewCartoon.
> I am missing something here. Please help.
> Many Thanks,
> --- Lalit
> Note: I don't want topology/parameters for the
> combined (protein & lipid bilayer) system or don't
> need to use combine.tcl script(s) as I am getting
> parameters/topology files from amber.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.