Re: [PyMOL] transforming PDB in Pairfit or align

[<hu...@us...>]

Ravi,

Do you use "pairfitting" or "align" command in PyMol? Align works well 
for me even for different (but homologous) proteins.
Another popular alternative is to use Stamp (U. of Dundee) for the 
alignment of the PDBs 
(http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html)
Hugo

Ravi Bojja wrote:
> Hi,
>  
> I have an unique problem with pairfitting, My Protein  is comprised of 
> helices and loops,
> In active and inactive forms there are no changes in helical 
> structures, but only loops orientation are changed
>  
> after pairfitting, one the structure is shifted about 0.5 angstroms,
>  
> Is there any command to shift the 0.5 angstroms of one structure, so I 
> that I can see both
> PDB structures as one uniform helix with disoriented loops in active 
> and inactive form,
>  
> thanks
>  
> Ravi
>
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-- 
Hugo G. de Teran, PhD.
Departmento de Farmacología / Instituto de Farmacia Industrial
Universidade Santiago de Compostela

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