I am not absolutly certain to understand the steps that you followed.
But if it doesn't work with the nucleotid as "reference" and "target", maybe if you face two GTPase, you can find some conserve
residues in the binding pocket. In this cas, you can use these residues as ref. and target.
To be more helpful, i think we need more information about the output message givent by superpose. I assume that it take correctly all the pdb files in count but it was not able to superpose, am i right ?
One other solution is to use one of the solution descibed here : http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html
or here : http://wishart.biology.ualberta.ca/superpose/
Or maybe directly in the chimera soft (tools =>structure comparison) (it's not as good as lsqkab (superpose)).
regards.
Nicolas
________________________________________
De : vijay srivastava [[log in to unmask]]
Envoyé : mardi 26 mai 2015 14:56
À : FOOS Nicolas
Objet : Re: [ccp4bb] Hi
Dear Nicolas,
I ahd tried in superpose but it is not alligning and simultaenousli I had given only the pdb
containing only the nucleotide but both of them dosen't work.
regards
Vijay
On Tuesday, 26 May 2015 6:22 PM, FOOS Nicolas <[log in to unmask]> wrote:
Dear Vijay,
Have you try to use superpose in ccp4 ? In superpose it's possible to select exactly what you want (atoms, residues...) .
In your case if you use only the atoms or the nucleotids that you want to be superpose, it could be ok.
Hope to help.
Nicolas
________________________________________
De : CCP4 bulletin board [[log in to unmask]<mailto:[log in to unmask]>] de la part de vijay srivastava [[log in to unmask]<mailto:[log in to unmask]>]
Envoyé : mardi 26 mai 2015 14:41
À : [log in to unmask]<mailto:[log in to unmask]>
Objet : [ccp4bb] Hi
Dear All,
I want to superpose the nucleotide form one GTPase on to the nucleotide of other GTPase in order to study
the interaction in the nucleotide binding pocket. I tried to superpose but it is superposing on the basis of secondary structure as a
result both the nucleotides from two structutres are not properly aligned. I want to superpose both the nucleotide, so that I will get the matrix, which I want to apply on my desired strcuture and study the interacting residues.
Do any one have the align program with you or any other program which can solve this problem.
waiting for your kind response
regards
vijay
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