pymol-users

[PyMOL] creating objects from pdb w/out chain id

[Hanspeter N. <ni...@OC...>]

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?

Hanspeter

Re: [PyMOL] creating objects from pdb w/out chain id

[Cameron M. <cm...@uc...>]

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?


    Cameron



=== 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?
>
>Hanspeter
>
>
>-------------------------------------------------------
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-- 
Cameron Mura
UCSD

RE: [PyMOL] creating objects from pdb w/out chain id

[Warren D. <wa...@de...>]

Cameron
 
> 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?

There are a set of selection keywords which act on the covalent topology;
(some of these are new in 0.95).

"neighbor" or "nbr." 

   (neighbor selection)

selects all atoms with bonds to a selection, but are not part of that
selection.

   e.g. (neighbor resi 100)


"bound_to" or "bto."

   (bound_to selection)

select all atoms with bonds to a selection, whether or not they are part of
it.

   e.g. (neighbor (resi 123))


"extend" or "xt."

   (selection extend number)

selects all atoms within a certain number of bonds

   e.g.  (name ca extend 2)


"bymolecule" or "bymol" or "bm."

   (bymol selection)

selects all atoms in the covalent tree(s) which contain the selection

   e.g. (bymol resi 100)


"byfragment" or "byfrag" or "bf." 

   (byfrag selection)

   selects all atoms in the covalent tree(s) which contain the selection,
stopping at any and all picked atoms (the pick selections are: pk1, pk2,
pk3, and pk4 -- used mostly for molecular editing).

   e.g. after picking 10/C into pk1, 15/N into pk2, (byfrag 13/CA) would
give you all atoms that are covalently attached to 13/CA up to, but not
including, 10/C and 15/N.  Discounting the presence of disulfide bonds, this
would be all atoms in residues 11, 12, 13, & 14.

   If no atoms are picked by the molecular editor, byfragment works just
like bymolecule.

Cheers,
Warren

Re: [PyMOL] creating objects from pdb w/out chain id

[Jacob C. <jc...@uc...>]

Hi Hanspeter,
If you want to use a stock pdb that does not contain chain IDs, you should create
the object using either a residue or atom selection. For example
(using residue ids for kinesin)
create kin=(/1BG2///3:325/)

However, for your convenience I've attached a modified pdb that
contains different chain IDs for each molecule in the PDB.
kinesin = A
ADP = B
acetate = C
water = W

The new PDB was made using MOLEMAN2 (from the Uppsala Software Factory -
http://alpha2.bmc.uu.se/~gerard/manuals/)


Saturday, April 17, 2004, 1:03:55 PM, you wrote:

HN> I'm trying to create an object of a protein from a PDB file that doesn't
HN> give a chain ID (pdb is 1BG2).

HN> I normally do something like:

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

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

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

HN> Hanspeter


HN> -------------------------------------------------------
HN> This SF.Net email is sponsored by: IBM Linux Tutorials
HN> Free Linux tutorial presented by Daniel Robbins, President and CEO of
HN> GenToo technologies. Learn everything from fundamentals to system
HN> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
HN> _______________________________________________
HN> PyMOL-users mailing list
HN> PyM...@li...
HN> https://lists.sourceforge.net/lists/listinfo/pymol-users