Dear pymolers,
I have to study the outcome from our MD calculations on
a protein surrounded by about 1700 water molecules.
There are 12000 such PDB files, each for one specific moment of time.
Now the problem is, when I tried to load some of the PDB files
into a movie, pymol will link the water
Dear Warren,
Thanks for the message and thanks for the pymol program.
It is one of the most interesting programs that I worked with.
I tried to make all of the atoms in the waters HETATM,
and after all of the records of the atoms, I put CONECT
for all of the water molecules.
In the Win version,
Dear Warren,
Just to tell you the good news,
I have got version 0.80 installed and everything looks just great.
(I have got well-behaved water molecules flowing now)
I have to study the manual better to play with other functions now.
Thanks again for the great program.
Regards,
K.K.Liang
Dear pymolers,
Yesterday I asked the question about selection.
After studying python manual I figure out what I should do.
I can select some residues in my protein in the command prompt
by saying for example
select prot = (VAL or PRO or GLY)
but now I have trouble translating
Dear Pymolers,
I have studied how to use selections and I have done some
very interesting analysis for my own research.
However, there is one thing that I wish to be able to improve.
Since I have to deal with thousands of PDB files,
do about ten to twenty selections on each of them,
and then
Dear Pymolers,
In the on-line help (of `iterate_state'), I found examples that
one can iterate through atoms and obtain their x value.
But I tried on my local installations (both Win and Linux),
an error was there when I tried to access 'x' value, for example.
But I can access other properties
Dear Pymolers,
Well I asked about the possibility of supressing some output
from pymol earlier.
I'm so happy that I found something important.
In my case, what bothered me is that I have to do a lot of
selections and analyze the selected residues.
There are roughly 10,000 selection for each pdb
Dear pymolers,
Many of you are interested in SS.
I think you must be experts on this.
So, although this is not a pymol problem,
I hope that you can give me some information.
I've got some MD simulation results,
and I calculated the phi-psi angles of each amino acid.
(Yeah I know that phi-psi
