In my pdb file, there are 6 chain identifier. How can i select 2 identifier using vmd or pymol? then i will do md simulation. I want to take B and F identifier and will run for md simulaiton. I have attached my pdf file. can anyone help me about it ?
No need to bother with VMD or PyMOL when simple Linux commands will do it.
grep " B " 1brs.pdb > chain_b.pdb
grep " F " 1brs.pdb > chain_f.pdb
No need to bother with VMD or PyMOL when simple Linux commands will do it.
grep " B " 1brs.pdb > chain_b.pdb
grep " F " 1brs.pdb > chain_f.pdb
There are multiple ways you can do it. You can use the method of grep " B " suggested by Mr. Justin Lemkul for this case (PDB: 1brs). Note that there is one space before B and another space after. But I still suggest you to use one of my following methods because this method doesn't work well for PDB files which contain residue numbers greater than 999.
(1) As you asked about Pymol, you can use the command "select 1brs and chain B" for chain B; or the command "select 1brs and (chain B or chain F)" if you want 2 chains. You can create an object by this selection and save this object (molecule) as pdb file. Using VMD, you can find similar commands on Internet, so I don't repeat here.
(2) As a bioinformatician, a more standard way is to write a script/program using Python, Perl, JAVA or whatever you like. You can even use a number of Linux commands, including grep. The idea is grep all the lines where the beginning is "ATOM" or "HETATM" and chainID (column 22) is what you want ("B" or "F" in your case). Here, I give you my python 2.x script (python 2.6 or 2.7). Use "get...chains.py -i 1brs.pdb -c B -o 1brs_B.pdb" or "get...chains.py -i 1brs.pdb -c BF -o 1brs_BF.pdb". Type -h for help message.
(3) An easy way: edit your PDB file as a text file. Just select the part of your interest by seeing the column 22 and delete other parts.
There are certainly more elegant ways to do it, but I will note that my grep command has spaces before and after the chain identifiers, e.g. " B " not "B" so it will not, in fact, get lines containing CB. I verified that this works exactly as intended on the OP's PDB file.
Dear Mr Justin Lemkul,
I'm very sorry that I hadn't noticed the spaces in your response. I modified my answer accordingly. Definitely, you method will work for this PDB file. However, it can raise some errors for other PDB files. I'd like to suggest other methods which I think more secured for a general purpose.
You can use "UCSF CHIMERA".
In command line insert "delete:.a" and this will automatically remove your "a" protein chain. In the similar way, you can replace a with c, d and e.
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