you can try the 'hide cell' command. This should hide the unit cell box,
however, I don't know why it is not displayed in your 'unrendered' gui...
Cheers,
Johannes
2017-12-11 23:47 GMT+01:00 Cygler, Miroslaw :
> Hi,
> When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part
> o
Hi,
When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part of
the protein all is well until I use the RAY command. In the ray traced image I
see the unit cell box that does not show on the image in the normal view. How
can I remove the box from the ray traced image?
Thanks fo
Hi Lindsey,
The following should work:
select sele, obj1 and not (obj1 like obj2)
or to match all identifiers, not only resi/name:
select sele, obj1 and not (obj1 in obj2)
There are also actual "diff" and "symdiff" commands available from PSICO
(https://pymolwiki.org/index.php/Psico). Try
Hello!
Does anyone know how to select residues in object 1 that are different from
object 2? I know how to select residues that are similar ("select name, obj1
like obj2") but can't figure out how to do the opposite. I am running PyMOL on
a Mac.
Thank you,
Lindsey
Hi Sebastiano
2012/5/18 Sebastiano Pasqualato
>
> Hi all,
>
> is there a way in Pymol to have a loop/tube representation of the protein
> backbone that would pass through the N-CA-C-N(+1)-CA(+1)-C(+1) atoms rather
> than CA-CA(+1) atoms?
>
I know this is possibly not what you are after, but wha
Hi all,
is there a way in Pymol to have a loop/tube representation of the protein
backbone that would pass through the N-CA-C-N(+1)-CA(+1)-C(+1) atoms rather
than CA-CA(+1) atoms?
I remember something like this (a loop vs turn representation) in Molscript or
Ribbons, but can't find it in Pymol
Hi Chris,
set cartoon_side_chain_helper=1, HISA
should be
set cartoon_side_chain_helper=1
That setting cannot yet be applied just to a specific set of atoms:
it's a global setting. This is something we should add to our to-do
list.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Mana
Hi Christopher,
I saw your script and there's many ways to the same destination. Here's how
my brain thinks:
load A.pdb
hide everything, A
show cartoon, A
[cmds for whatever else I like: fancy helices etc. etc.]
Option 1:
show sticks, A and resi 197-199
Option 2:
And if you hate that the backbo
Hi,
I'm a little stuck with a Pymol script. I'd like to represent my protein
with fancy helices and B-sheets, and in a looped domain I want to show a
few residues, but only the side chains.
In my script I tried using "set cartoon_side_chain_helper, on, HISA" on
the selection of residues I want t
Firstly, I think in Pymol there is no true electrostatic potential
calculator, but only a "charge-smoothed" surface presentation (
http://www.pymolwiki.org/index.php/Protein_contact_potential).
So, If you want to calculate the real electrostatic potential in Pymol (by
Possion-Boltzman method), you
Dear Maher,
as far as I know pymol uses the APBS (http://www.poissonboltzmann.org) for the
calculations and your question is answered in the FAQ:
http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential
(kT/e)
I don't know if this also answers
Hi everyone, I have two questions:
1- Does anybody know what are the units on the display ruler after you
calculate the vaccum electrostatics using pymol?
2- What are the default kT/e values used by pymol?
Thank you,
Maher
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