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 list. 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 > filename.pdb --Eric