[Chimera-users] Fwd: Aligning two residues same name

[Elaine Meng]

Hi  Francesco,
The RMSD from the command "match" is reported in the Reply Log  
(Favorites... Reply Log).
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
Best,
Elaine

On Feb 4, 2008, at 7:26 AM, Francesco Pietra wrote:

> Changing residue name works. Deleted membrane, saved pdb without  
> membrane.
> Loaded the two models. Command line: match :XXX :YYY
>
> How to put the difference in quantitative terms (rmsd)?
> Thanks
> francesco
>
>
>
> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
>
>> Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST)
>> From: Francesco Pietra <chiendarret at yahoo.com>
>> Subject: Aligning two residues same name
>> To: chimera <chimera-users at cgl.ucsf.edu>
>>
>> Task: compare/align a single-residue molecule before docking (naked  
>> molecule,
>> mol2 or pdb file) with same residue as ligand in a protein after  
>> docking/MD
>> (pdb file of a snapshot for complex embedded in a bilayer  
>> membrane). Should I
>> change the residue name in one of the two models? Same name poses  
>> to me
>> problems. Or there is a direct way?
>> Thanks
>> francesco pietra
>>
>>
>>
>>
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