[Chimera-users] HELIX/SHEET/CONECT records for non-existent bonds/atoms are being inserted into file.pdb when pdbrun nouser cat > file.pdb is run

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 7 17:14:01 PST 2005

On Mar 7, 2005, at 2:50 PM, Sabuj Pattanayek wrote:

> Hi,
> If I load a pdb, display only selected atoms/bonds, then do pdbrun 
> nouser cat > file.pdb, the outputted pdb file also has 
> HELIX/SHEET/CONECT records for non-existent bonds/atoms (as if the pdb 
> file in its entirety was written out). Is this a bug or a feature? Is 
> there some way to completely turn off output of HELIX/SHEET/CONECT 
> records?

Hi Sabuj,
	Chimera ships out the same headers that it received as input, 
including HELIX/SHEET records.  Doing anything else with HELIX/SHEET 
records is a can of worms, since if you try to output such records to 
reflect the state of Chimera, then you have to account for 
reassignments of secondary structure that the user may have made and/or 
mid-helix/sheet residue deletions.  Also, HELIX records include the 
"helix type" (3-10, etc.) that Chimera would just have to make up if 
not using the original records.  Similarly, SHEET records are single 
strands with a "sheet number" that organizes them -- Chimera doesn't 
really have an idea of a sheet per se, just strands.
	In the pdbrun case, should HELIX/SHEET records be output if only part 
of the helix/sheet is shown?  You can see how the whole thing is a 
morass.  On the other hand, we could certainly suppress CONECT records 
for bonds that aren't in the pdbrun output.  I'll put that on a to-do 
	On the bright side, it isn't hard to screen out HELIX/SHEET/CONECT 
records completely if that is what you want.  Use this command:

	pdbrun nouser grep -v HELIX | grep -v SHEET | grep -v CONECT > 



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