Hi everyone,
I want to color C-alpha atoms of a selection in a specified colour (red) and
and the cartoon representation in a separate color(grey). When i try colouring
the calpha's in red, the same color leaks onto to the cartoon representation
also, making it look grey with patches of red.
Dear users,
I was interested in knowing if there is an option or setting in PyMOL which is
able to make an outline to spheres.
I am aware of the show spheres command and have used it extensively to show
C-alpha atoms of amino acids as spheres.
I am curious to know how I could make an outline
Hi everyone,
How to write PyMol commands in Python script, save a session and then save a
.png file of the same ?
I have an input file which has the protein information i.e name, chain, and a
list of residues.
I want to plot the C-alpha atoms of these residues for each protein calculate
, 1a55_Q.pdb, 1a55_R.pdb
Also, in case I have a large number of multiple chain PDB files, how could I go
about splitting each of them?
Please help.
- Anasuya Dighe
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draw_links.py?
Where am I going wrong?
- Anasuya Dighe
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Hi,
I am representing C-alpha atoms of binding site as spheres.
I am using the set sphere_mode command to adjust the radius of the spheres. I
use the sphere_mode as 4.
However, when I do a ray tracing, no matter how small the spheres I set, they
appear very large once the ray tracing is carried
Hi Pymol-users,
I need to select only the atoms [and NOT complete amino acid residues] which are
lying in a radius of 4.5 Angstroms from the ligand from a ligand-bound protein
structure.
I am aware that the command: select site, br. resn FAD and chain A and resi 45
around 4.5 and not HET
Hi Pymol Users,
I was trying to use the findSurfaceResidues.py script listed on PyMOLwiki
(http://www.pymolwiki.org/index.php/FindSurfaceResidues), to find out which
residues which are present on the surface of the protein.
These are the steps I have followed:
1) Made a file called
Hello,
I wanted to know what is the command-line syntax for finding out the number of
residues which fall within a selection made in PyMOL.
Once the selection is made, the command line shows the number of atoms selected,
but I wanted to know the number of residues present in such subsequent
What's going wrong with this code?
___CODE___
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select(target,(resn %s and chain %s and resi %s)%(res,chain,num))
cmd.select(zone2,(br. (target expand 9 and not (target expand 4.5)) and not
Hi,
I am running this code on some pdb files: 12gs.pdb, 182l.pdb, 183l.pdb
CODE
from pymol import cmd
def process_line(x):
pdbid,res,chain,num = x.split()
cmd.load(pdbid)
cmd.select(target,(resn %s and chain %s and resi %s)%(res,chain,num))
cmd.select(zone2,(br. (target expand 9 and
Hello ,
I want to extract out complete amino acid residues which fall within a radius
of 4 to 9 Angstroms from the ligand.
What do I do in such a case, given the pdb id's, chain ID, the name of the
ligand and its residue id?
PS: I want to avoid, extracting out cmplete residues within a 0-4.5A
how do i put a protein molecule inside a cube with x-axis spanning till the
largest x-coordinate, y-axis spanning till the largest y-coordinate, and z-axis
spanning till the largest z-coordinate?
Once i do this, can i divide the larger cube(i.e. the one holding the entire
protein) into smaller
Hello,
I have a .txt file which has data in the following fashion:
19gs BSP A 1
1a2d PYX A 117
9rsa ADU A 125
7kme PRR J 382
1a0r ACE B 1
1a0r FAR G 72
.
.
.
Fields: PDB ID LIGAND NAME CHAIN TO WHICH IT
hi all,
I am writing this email with regards to the following problem.
Statement of the problem:
I have around 19,200 unique PDB files. Each of them have one or more ligands in
it.
For each ligand, I have to extract a zone which contains complete residues
within 4.5Angstroms of the ligand [ i.e.
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