Question: How extract coordinates of surface atoms of a protein from a pdb file?
0
gravatar for sluggishcrow
4.0 years ago by
United States
sluggishcrow0 wrote:

Hi everyone,

I have a pdb file that contains a single protein information.

I want to extract the coordinates of the atoms that are on the surface of protein and by that i dont mean the set of atoms of surface residues because that set may contain atoms that are deeply buried inside the protein.

Is there any tool that can do this?

Thanks

protein atom surface pdb • 2.3k views
ADD COMMENTlink modified 4.0 years ago by a.polo88100 • written 4.0 years ago by sluggishcrow0
3
gravatar for João Rodrigues
4.0 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:
Use NACCESS. It outputs both residue and atom accessibility.
ADD COMMENTlink written 4.0 years ago by João Rodrigues2.5k
1
gravatar for sluggishcrow
4.0 years ago by
United States
sluggishcrow0 wrote:

Adding to what João Rodriguesmentioned there is another free program (non commercial use) called MSMS that given a set of spheres S and a probe radius rp ,computes the Reduced Surface and the analytical model of the Solvent Excluded Surface ( SES ).

 

ADD COMMENTlink written 4.0 years ago by sluggishcrow0

hello, I also want to extract all the residues on the surface of a PDB file. I agree to that people can do that by MSMS. But I do not kown why I cann't open the web www.scripps.edu/sanner/html/msms_man.html and download it. Can you give me a link which is available, or mail me(address: yuehuiy@mail.ustc.edu.cn).Thank you !

ADD REPLYlink written 2.5 years ago by yuehuiy0
0
gravatar for venu
4.0 years ago by
venu6.0k
Germany
venu6.0k wrote:

Try in this way

  • make a list of residues (3-letter code) which have high propensity to be on the surface (search literature).
  • extract the coordinates of those resdiues.

Something like this will work.

$ awk '$1=="ATOM"' pdbFile.pdb | grep -Fwf list | awk '{print$7"\t"$8"\t"$9}' > coOrdinates.txt

It extracts the coordinates of all surface residue atoms, you can extract only 'CA' atoms(represents a residue in coarse grained simu.) coordinates by modifying '$1=="ATOM" && $3=="CA"'.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by venu6.0k

thank you but i said: "i dont mean the set of atoms of surface residues because that set may contain atoms that are deeply buried inside the protein."

ADD REPLYlink written 4.0 years ago by sluggishcrow0
0
gravatar for a.polo88
4.0 years ago by
a.polo88100
Italy
a.polo88100 wrote:

I'm agree with Joao for the use of NACCCES. otherwise there are graphic molecular software e.g. swisswiev that have incorporated the module for calculate what do you ask.

ADD COMMENTlink written 4.0 years ago by a.polo88100
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