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@cgl.ucsf.edu> To: R. Andrew Byrd <rabyrd@ncifcrf.gov> Cc: chimera-users@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 mechanism)
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@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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