Hi ,

Rather than using atom selection macros (/1jff//a/etc.../), the easiest way is probably to execute the following command, which takes advantage of PyMOL's built-in "hetatm" single-word selector:
select just_protein, ! hetatm

The "hetatm" selector consists of all atoms from the PDB file's HETATM lines, so it's negated in the above command in order to select only the ATOM lines (which I assume are only protein).  A really paranoid way to select only protein atoms is to try the following:
select CAs, name ca
select just_protein, byres CAs
Here we first select just the C-alphas ("CAs") and then use PyMOL's selection algebra to expand this selection into a new object ("just_protein") that consists of only C-alphas and all atoms in C-alpha-containing residues (i.e., entire protein).  These two methods should produce equivalent selections except in the unusual cases of (1) having 'CA' atoms in HETATM lines of the PDB file or (2) having HETATM lines that contain protein residues that you'd like to include in your selection (whether they have 'CA' atoms or not).  See http://pymol.sourceforge.net/newman/user/S0220commands.html#7 for more info.

This reminds me of a related question I once had -- does anyone know if there's a way to create selections based loosely (and very generally) on bond connectivity criteria, in a somewhat similar manner as specified in force fields used for proteins.  It would be neat to be able to select all groups of atoms in all residues that are topologically connected (i.e. by any number of bonds) as separate groups, in the absense of chain IDs of course... there's probably a clever way of doing this via byobject, byresi, etc. commands?


=== Hanspeter Niederstrasser wrote (on 04/17/2004 01:03 PM): ===
I'm trying to create an object of a protein from a PDB file that doesn't
give a chain ID (pdb is 1BG2).

I normally do something like:

create atub=(/1jff//a/)

to pull a specific chain out of a PDB file, but 1BG2 doesn't have a chain
name.  And if i use "create kin=(/1BG2////)", the object kin gets ALL the
elements from 1BG2, including the waters, nucleotide, and ions, which is
exactly what I'm trying to not do.

How can I create an object out from a nameless chain?


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Cameron Mura