[Chimera-users] Making PDBs with over 10,000 residues

[Eric Pettersen]

Hi Ryan,
	It seems you mean residues rather than atoms, so I changed the subject line.  Chimera will basically never treat residues with different chain IDs as being in the same chain, but rather as two separate chains that happen to have some covalent bonding (e.g. disulphide bonds), so the approach you are trying is just going to lead to frustration.  However, Chimera allows two different PDB “cheats” to get past the 10,000 residue limit.  The first cheat is that if the column just to the right of the residue number (the “insertion code”) is a digit rather than a letter, it will treat it as if it were a 5-digit residue number rather than a 4-digit residue number with a numeric insertion code.  The second “cheat” is that you can use the “Hybrid-36” numbering scheme to fit up to 2,436,111 residue numbers into the 4-digit residue field.  The Hybrid-36 scheme is described here: hybrid-36: PDB serial and sequence numbers <http://cci.lbl.gov/hybrid_36/>.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Aug 7, 2019, at 8:20 AM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> 
> Hi Chimera,
>  
> I am trying to make a PDB with over 10,000 atoms. Currently we have this marked as a limitation to our project. I am researching to see if there is a way around this. Our current idea is to make the next 10,000 atoms another chain. Although when I apply this to a sample I get a break point between chain A and chain B. I do want them connected and to be different chains. So: 9,998.A 9,999.A 0.B 1.B connect.
>  
> In addition, I would need helices and sheets to span over these two chains. So helix or sheet would start at 9,998.A and end at 1.B.
>  
> Best,
> Ryan Harlich
>  
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>  
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