[Chimera-users] castP, Chimera and atom numbers

Eric Pettersen pett at cgl.ucsf.edu
Wed May 29 17:14:58 PDT 2013


Hi Boaz,
	It's not really that the serial numbers have to be consecutive, but the serial numbers in the .poc and .mouth files have to match the serial numbers in the PDB file.  When I wrote this code back in '08, I was concerned that a non-standard PDB file with blank chain IDs would be impossible to match up uniquely with it's .poc and .mouth files, which is why I chose to match on serial numbers.  Nowadays I might choose to believe that chain IDs will always be there and match on atom names and residue information instead.
	I'm sorry this decision caused problems for you.

--Eric

On May 26, 2013, at 8:38 AM, Boaz Shaanan <bshaanan at exchange.bgu.ac.il> wrote:

> Hi,
> 
> Apparently Chimera insists on consecutive serial atom numbers (the first column after ATOM in the pdb file) when it reads in castp files. If that's not the case (as most often happens when hydrogens are attached during the refinement run but are not written out to the final pdb) Chimera complains about incompatibility between the mouth file and coordinates and refuses to read in the castp files. This is my first encounter with a program that cares about the atom number column but I learnt it the hard way.
> 
> Cheers,
> 
>             Boaz
> 
> Boaz Shaanan, Ph.D.                                        
> Dept. of Life Sciences                                      
> Ben-Gurion University of the Negev                          
> Beer-Sheva 84105                                            
> Israel                                                      




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