I like to add that PyMOL will only work as expected with upper and lower case
chain identifiers if the "ignore_case" setting is off.
http://pymolwiki.org/index.php/Ignore_case
Cheers,
Thomas
On 07 Jul 2015, at 11:59, Steve Darnell wrote:
> Hi Yeping,
>
> Just to clarify on Jose’s comment.
Dear all,
Is possible to calculate volume of the space sampled by ligand in MD
simulation, either from Amber trajectory or by loading multiple PDB files
of ligand ( PDB of each conformation of ligand extracted from simulation) ?
In brief, I have an octahedral simulation box, where I am simulatio
Hi Emily,
No, it takes them from the selection.
Cheers,
Tsjerk
On Jul 7, 2015 4:09 PM, "Emilia C. Arturo (Emily)" wrote:
> To be extra clear/redundant:
> >
> > The default value passed is None. If Pymol finds that the argument is
> None,
> > it takes the minimum/maximum value from the list of
Hi Yeping,
Just to clarify on Jose’s comment. The valid chain identifiers for the PDB
format are [A-Za-z0-9], which allows up to 62 identifiers. This should be
sufficient for your current usage. I agree with Jose, mmCIF format is the
currently recommended format.
~Steve
From: Jose Manuel Duar
Hello
I have a question about find_pairs argument, angle. Especially when I'm
trying to find all hydrogen bonds with a script like this:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/list_hbonds.py
I'd like to know what angle is there? It is not very clear neither from
pymol documentation
To be extra clear/redundant:
>
> The default value passed is None. If Pymol finds that the argument is None,
> it takes the minimum/maximum value from the list of values,
...do you mean that it takes the minimum/maximum values from the list
of b-values from within that pdb file? So that for each p
Hi all,
I installed PyMOL on a CentOS 6.6 machine and I got this error when I ran
it. Can anyone help? Thanks so much in advance.
$ ./pymol
Traceback (most recent call last):
File "/opt/pymol-svn/modules/pymol/__init__.py", line 71, in
import pymol
File "/opt/pymol-svn/modules/pymol/__in
Hi Emily,
The default value passed is None. If Pymol finds that the argument is None,
it takes the minimum/maximum value from the list of values, otherwise it
will take the value provided. The interpolation is indeed linear.
Hope it helps,
Tsjerk
On Tue, Jul 7, 2015 at 4:11 AM, Emilia C. Arturo
