Liyang,
This will only be of use to you if you happen to be a PyMOL subscriber,
but there is an example movie script somewhat like this in the official
online documentation:
http://delsci.info/dsc/dokuwiki/doku.php?id=example:animation:granzyme_h
ydrolysis
Cheers,
Warren
-Original
Martin,
It is remarkable that a question like this hasn't come up before, but it
reveals a rather large whole in PyMOL's selection language: though we have
some proximity operators, we are not currently able to select atoms based on
absolute or relative coordinate vector relationships.
So
Am 04.03.2009 um 06:46 schrieb Warren DeLano:
Hey Warren,
It is remarkable that a question like this hasn't come up before,
but it reveals a rather large whole in PyMOL's selection language:
though we have some proximity operators, we are not currently able
to select atoms based on
Hello,
I have experimental phases/map_coeff's in a .phs file. Can anyone tell me
how to most easily get them read read into PyMol to display electron
density? I assume I need to convert the file somehow first, I usually use
mapman for this utility but don't see an option for .phs files.
Hi,
I have a couple of quick notes about your specific application:
This works well when bilayers are flat. So, it works well for small bilayers
and it works well at the beginning of a simulation. For medium to large
bilayers, undulations throughout the simulation will cause this algorithm to
Dear pymol users
I am running SMD simulation. I want to draw arrow/spring to display
direction of pulling of my ligand. i know it is possible with VMD. but i am
more attracted to graphics in Pymol. is it some way i can draw arrow or
spring connecting two atoms. please let me know
--
Falgun H
Am 04.03.2009 um 17:32 schrieb Michael Lerner:
Hey Michael
You probably know all of this, but I thought I'd mention it in case
someone was tempted to just take your code and apply it individually
to each frame of a simulation without really thinking about it.
Unfortunately, I've seen
I have a homodimer. I place it at an arbitrary place on the screen,
where it looks nice.
Now move the monomers apart from each other in x. translate [10, 0,
0], object molA translate [-10, 0, 0], object molB
Then I want to rotate each monomer 90 deg so that each monomer's
contribution
Falgun,
We don't have an arrow primitive, but you can use the distance command
to connect two atoms:
dist spring, selection1, selection2, label=0
for example:
fragment val
dist spring, valCG1, valCG2, label=0
Cheers,
Warren
Hi,
I have experimental phases/map_coeff's in a .phs file. Can anyone tell me
how to most easily get them read read into PyMol to display electron
density? I assume I need to convert the file somehow first, I usually use
mapman for this utility but don't see an option for .phs files.
Colleagues,
If the PDB file contains only Ca atoms and PyMOL shows them as
non-bonded atoms what one should do to display them as a ribbon? The
1rh2 entry is one of them.
Thank you.
___
Vaheh
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