how can merge two PDB

From: Afshan Begum
Date: 19 October 2011 14:13

Hello CCP4 user

I have collected a data set 2.1 for my complex. Actually after  first run of Rafmac i can see the density for my inhibitor but the problem is my inhibitor is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already crystallize with other protein molecule present in PDB data bank so how can i put in to that electron density i mean are there any ways to combine two Pdb in one molecule?

I would be thankful for your help

 

Best Regards

AFSHAN

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From: Tanner, John J.


3 ways:

cat mol1 mol2 > mol3

Use an editor such as nedit to cut and paste.

Coot merge molecules function.

Sent from Jack's iPad

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From: Ed Pozharski


Why not do the molecular replacement - 6kDa is rather small but it most
likely will work

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

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From: Bosch, Juergen

why don't you read in that chain in Coot and run the find ligand option with flexible ligand turned on and select that 6kDa ligand ? You should also choose Fo-Fc map to fit the ligand to maybe at 2.7 sigma. You might have to split up the ligand into pieces, not sure what the limitations in Coot/Find Ligand are.

You already have a MR solution of the rest of your protein right ? So you are just asking how to make your life easier to not built de novo 45-50 residues ?

Jürgen

......................

Jürgen Bosch

Johns Hopkins University

Bloomberg School of Public Health

Department of Biochemistry & Molecular Biology

Johns Hopkins Malaria Research Institute

615 North Wolfe Street, W8708

Baltimore, MD 21205

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From: Afshan Begum

 Dear Juergen

Many thank for your response yes you have excatly understand my question we  have a MR solution of the rest of our protein and  just asking how to make my life easier to not built de novo 45-50 residues. so i could not find the option in coot find ligand so, from where i get it?

Best Regards

AFSHAN

 

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From: Miller, Mitchell D.


Hi Afshan,
in Coot  select calculate --> other modeling tools --> find ligands
In 0.6.2, there is a message that ligands are limited to 400 atoms or less.
Regards,
Mitch