> 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
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
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,
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 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,
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
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
"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
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 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 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 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 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
13 matches
Mail list logo
