[Chimera-users] findclash "batch" calculations

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 7 11:42:55 PST 2011

On Feb 4, 2011, at 9:54 AM, Elaine Meng wrote:

>> Second chimera does not open more than 9999 residues, the pseudo  
>> pdb have nearly 100 000 residues. Is there a way to get around that.

This is a limitation of PDB format -- 4 characters allocated to the  
residue-number columns.  I think your options are:

1) Use another format that has no limit for the pseudo structure, such  
as Mol2.

2) Use MODEL records.  MODEL records also have a 4-digit "limit" but  
Chimera ignores the number given in the MODEL record and just numbers  
them sequentially from 1.  Therefore you can have 100,000  
"MODEL        1" records in your file (with corresponding ENDMDL  
records) and Chimera will open the file as 100,000 separate models  
(e.g. #2.1 through #2.100000).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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