[Chimera-users] Proper display of oligosaccharide

[Greg Couch]

Actually, chimera accepts 4 character residue names, it's a non-standard 
extension that we first had in our previous software, MidasPlus.

The bad PDB records are the bogus AUTHOR, REMARK, and CONNECT records.
AUTHOR and REMARK records have particular formats to be standard.  And
CONNECT is supposed to be spelled CONECT, and when it is, chimera uses 
those records for connectivity.

That said, we'd still like to see the example that fails.

 	Greg Couch
 	UCSF Computer Graphics Lab

On Wed, 18 Apr 2007, Elaine Meng wrote:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: R. Andrew Byrd <rabyrd at ncifcrf.gov>
> Cc: chimera-users at cgl.ucsf.edu
> Date: Wed, 18 Apr 2007 09:21:03 -0700
> Subject: Re: [Chimera-users] Proper display of oligosaccharide
> Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted
>     mechanism)
> Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted
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> 
> 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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