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 m
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, I
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,
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 this into python script.
I tried many varieties including something like
cmd.select( prot, (VAL or PRO or /
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
"Warren L. DeLano" wrote:
>
> You've got choose either real-time manipulation with OpenGL-quality
> rendering or prerendered movies without manipulation. We need another
> 100-1000 fold increase in CPU performace before real-time raytracing will
> become possible.
>
> -Warren
Dear Warren,
Do
Hi, dear Pymolers,
It is great to see the cross-eye stereo support in 0.82.
I am also very much interested in knowing the new selection operators.
The documentation seems to be a little bit behind?
Actually as we play more and more with pymol,
it is easily realized that the selection functions are
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 count
Dear Nat,
Thanks for the trick.
This sounds like a good method, in general.
I will do this when I finish debugging my code
and start to work on many files.
I was just curious if we can do this in a program.
Perhaps this is actually a Python problem,
not a Pymol specific problem.
Regards,
K.K.Lian
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 lik
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 f
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 calc
> Date: Wed, 13 Nov 2002 15:26:22 -0500
> From: Michael Ford
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #210 - 2 msgs
>
> This list really needs a reflector (ala AMBER mail reflector) so that we
> can benefit from each others pains. It would really b
13 matches
Mail list logo
