Dear Thomas,
Many thanks! I copied and saved the script as a dot txt but can not run it from
file> run on pymol. Do I need yo save the file in a special folder? I am
actually really new with pymol and not vey good in scripting
Thanks for your understanding
Sincerely
Chi
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Hi Anke -
Try `as surface`, which is the equivalent of `hide everything; show surface`.
Hope that helps.
Cheers,
Jared
Sent from my iPhone
> On May 19, 2017, at 6:43 AM, Anke Schultz
> wrote:
>
> Hi Thomas,
>
> thanks for the explanation on adjusting view, it works fine. This leaves
> me
Hi Celestine,
Did you run the "get_raw_distances.py" script first? You can do that by:
run
https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/get_raw_distances.py
Or better: Download it to your computer and run it from there ("run" command or
"File > Run Script..." from t
Hi Thomas,
thanks for the explanation on adjusting view, it works fine. This leaves
me with one question: How do I get a .wrl-file containing only faces?
Using "show surface" and setting surface_type to 2 (triangles) gives me
sticks and spheres in the .wrl-file (sticks as edges, spheres at the
Hi Thomas,
I am also interesting in getting bond distances between two pairs of molecule.
I tried running the commands to suggested but I get an error message e.g
When I tried the following (see below) the fist command was well executed but
the second gave an error message “ SyntaxError: invalid
Hi Anke,
surface_type 0 will produce faces (solid triangles).
There are no triangle faces in surface_type 2, only edges.
Thomas
> On May 19, 2017, at 12:43 PM, Anke Schultz
> wrote:
>
> Hi Thomas,
>
> thanks for the explanation on adjusting view, it works fine. This leaves me
> with one qu
Hi Ahmad,
Unfortunately there is no proper API for this. But I can think of two
approaches. Note that the results can differ because the two method do slightly
different h-bond detection!
1) Use "cmd.find_pairs" with mode=1 on "donors" and "acceptors" selection.
Example:
sele1 = "chain A & (d
Hi Kingsley,
The b-factor is a result of the X-ray crystallography experiment. If you have
X-ray data, I suggest to consult the CCP4BB mailing list
(http://www.ccp4.ac.uk/ccp4bb.php). If you don’t have such data, then you can’t
calculate a b-factor.
There are computational methods which analyz
Hi Dolev,
The difference is that the menu action only aligns on C-alpha atoms. Since
PyMOL 1.8 the menu label says “align > to molecule (*/CA)” to make this more
obvious.
The exact command which is executed by the menu action is:
align 4A11 & name CA & polymer, 3W15 & name CA & polymer,
objec
Hi Anke,
The obvious difference I can see in your two samples is that the first one
contains sticks and spheres representations, and the second one only has faces
(could be surface or cartoon).
The other difference is the viewport z position (zoom distance), which is 0.0
in the second sample.
Hello
I have noted that using action -> align -> to molecule via the GUI gives
(sometimes radically) different result then running align on the same
structures via command line.
For examples, for PDB structures 4A11 and 3W15, the command
align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.5
Hi Marko,
Have you tried this?
select zplane, z > 6.377 and z < 7.139
This works since PyMOL 1.6 (I think).
Cheers,
Thomas
> On May 19, 2017, at 9:49 AM, Marko Sever wrote:
>
> Hello everyone! Could someone help me figure out, how I could do a residue
> selection along specific z-axis coo
Hello everyone! Could someone help me figure out, how I could do a residue
selection along specific z-axis coordinates, for example from 6,377-7,139 on
the z-axis, etc..Like that it selects all residues in that plane.
Marko Sever, PhD student
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