[Chimera-users] Proper display of oligosaccharide

[Elaine Meng]

Hi Andy,
It does not matter what the atom and residue names are, as long as  
they occupy the correct columns of the file.  I often view molecules  
that are not protein or nucleic acids.  Most likely the  
oligosaccharide file does not follow the PDB format specification  
completely.

I went to the SWEET web site and downloaded the first example PDB on  
this page:
http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php? 
left=fexample.html&main=bsp%2Fpdb%2Fpdb.html

Chimera does display all the atoms and bonds for this structure, but  
complained about each line: "bad PDB record."  (I'm using version  
1.2363 on Mac OSX, but I don't think PDB reading has changed much in  
recent versions.) Using a text editor to compare other PDB files with  
the file from SWEET, it is evident that the latter has 4-character  
residue names, while PDB format only includes three columns for  
residue names.  Replacing the last character in the residue name with  
a space (because the subsequent columns are already in the right  
place) should suppress the complaining messages.  However, since this  
file did display in Chimera, perhaps the file(s) you are working with  
have some different or additional problems.  You can mail it to me if  
you'd like us to take a look.

Here is a line from the SWEET example file (need to view this with  
constant width font!)
ATOM      1  C1  adne    1      -0.937  -0.321   0.174  0.00  0.00
and from a different file from the PDB
ATOM      1  N   ALA     1      46.457  12.189  21.556  1.00 56.69

Description of PDB format:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
framepdbintro.html
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
http://www.wwpdb.org/documentation/format23/sect9.html#HETATM

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 17, 2007, at 8:10 PM, R. Andrew Byrd wrote:

> We study protein:carbohydrate interactions, and we use chimera for  
> protein
> displays.  We have a model built for an oligosaccharide using the  
> SWEET
> server at http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php
>
> The file is in pdb format, but it has neither amino acid residue  
> names nor
> nucleotide names.  Hence, the molecule is invisible in Chimera.
>
> How could we make this a recognizable molecule so that we can examine
> various visualizations and modeling efforts using Chimera?
>
> Thanks!
> Andy
>
> P.S. I can send the file if you want.
>
>
>
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