pymol-users

[PyMOL] transforming PDB in Pairfit or align

[Ravi B. <boj...@ya...>]

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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Re: [PyMOL] transforming PDB in Pairfit or align

[Andy P. <a.p...@ma...>]

Quoting Ravi Bojja <boj...@ya...>:

> 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,
>    

Hi Ravi,

I suggest using Secondary Structure Matching to align the helices (see
http://www.ebi.ac.uk/msd-srv/ssm/). You can then load the fitted pdbs into
Pymol for visualisation. I don't know if there is a Pymol plugin for SSM
though. Personally, I use Coot to run the SSM and then load the files into
Pymol for making pretty pictures!!

Andy

-- 
"We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry."
+---------------------------------------------------------------------+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail   a.p...@ma...                   |
+---------------------------------------------------------------------+


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Re: [PyMOL] transforming PDB in Pairfit or align

[sivaram m. <mv...@gm...>]

Hi Ravi,

You could use the DALI-LITE (EMBL) server to align both pdbs, then open the
new (aligned) pdbs generated by DALI into PYMOL - that should align the
identical helices perfectly and show you the differences in the loops.

Sivaram.


On 3/12/07, Andy Purkiss <a.p...@ma...> wrote:
>
> Quoting Ravi Bojja <boj...@ya...>:
>
> > 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,
> >
>
> Hi Ravi,
>
> I suggest using Secondary Structure Matching to align the helices (see
> http://www.ebi.ac.uk/msd-srv/ssm/). You can then load the fitted pdbs into
> Pymol for visualisation. I don't know if there is a Pymol plugin for SSM
> though. Personally, I use Coot to run the SSM and then load the files into
> Pymol for making pretty pictures!!
>
> Andy
>
> --
> "We are the Kitten. Lower your weapons and open your arms.
> Your refrigerators and sofas will be utilized for our comfort.
> Your society will be assimilated to nurture and care for our own.
> Resistance is Furry."
> +---------------------------------------------------------------------+
> |  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
> |           E-mail   a.p...@ma...                   |
> +---------------------------------------------------------------------+
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
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-- 
Sivaram Mylavarapu.
mv...@gm...
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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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