Hi Alireza -
For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of
choice. If your protein is chain A, the command would look something like this:
pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb <<EOF
renum 1 chain A
EOF
To remove the extraneous stuff within PyMOL, you could also use applicable
selectors (http://www.pymolwiki.org/index.php/Single-word_Selectors) to remove,
e.g. heteroatoms, solvent, organic (ligand) molecules, etc. using one or more
of these commands, depending on what it is you’re trying to remove.
remove het
remove solvent
remove all and not polymer
remove organic
remove metals
As an alternative (pun intended), instead of removing those items, you could
change their chain IDs using the `alter` command:
alter (chain A and not polymer), chain=“Z”
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Dec 13, 2014, at 1:54 PM, Alireza Kashani
<alireza.kashanip...@gmail.com<mailto:alireza.kashanip...@gmail.com>> wrote:
Thanks for your prompt answer,
numbers resets in every chain - and there is a lot of nucleobases in the
beginning (A,C,U,G) and MG at the end and these atoms mess up the residues
number additionally !
can I remove them via pymol ? Thank you
<http://en.wikipedia.org/wiki/Nucleobase>
On Sat, Dec 13, 2014 at 5:45 PM, Andreas Warnecke
<4ndreas.warne...@gmail.com<mailto:4ndreas.warne...@gmail.com>> wrote:
Hi,
There is a script available on the pymol wiki called "zero_residues". This will
allow you to easily renumber any AA sequence.
As far as other heteroatoms are concerned you could consider removing them
(remove hetatm), or extract them into a second object.
Another alternative is to simply adjust the coloring command according to the
pdb.
Hope that helps,
Andreas
On Dec 13, 2014 4:41 PM, "Alireza Kashani"
<alireza.kashanip...@gmail.com<mailto:alireza.kashanip...@gmail.com>> wrote:
Dear All,
I would like to colour different regions of a protein in different colour; say
region one, amino acid number 1 to 100 and region two amino acid 101 to 150;
However, when I look into a pdb file using pymol; by displaying the residuals,
I see the residue number 1, does not correspond to the first amino acid; I
assume, because of other atoms (metals, ions and etc).
I was wondering if I should filter the pdb file, beforehand to be free from
these metals, or is there any command that I can put them away and make a
selection based on set of amino acids ?
I appreciate your help,
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