Hi,
I was wondering if I have unnatural amino acids in beta sheet mimicking
peptides, is there a way to have them show up as a beta sheet in the
cartoon representation? I understand the code:
alter 1-11/, ss='S'
as an example of assigning residues 1-11 as a beta sheet but how do I
tackle artific
I have a pdb file, with only Alpha carbon atoms.
I want to display the secondary structure. Given that pymol
uses the backbone to define SS elements is there a way
i can draw the cartoon.
i have tried explicitly defining ss using alter command
but without success. i want to a
i am wanting to highlight a number of residues on a virus capsid. i have 60
states (objects), and wanted to only select particular residues (say resi
23,45,46 from 3 chains across all
60 objects) that are within say 20A or 40A from a fixed point (or residue).
could i get advice on
Hi Jon,
this can be done by enabling "cartoon_trace_atoms".
set cartoon_trace_atoms
show cartoon
You can also enable it for your particular object, if you have other
objects loaded for which the setting should not apply.
set cartoon_trace_atoms, 1, yourcaonlyobject
Hope that helps.
Cheers,
Hi John,
here is something to start with:
# put everything in state 1 (convert states to objects)
split_states capsid
delete capsid
# specify the fixed residue
select fixedresidue, capsid_0001 and chain D and resi 30
# select residues of interest within given radius
select s1, chain A+B+C and r
Hi Balaji,
you need to upgrade your PyMOL installation. The 0.99rc6 version has a
quite old version of python build-in and does not use your python-2.7
installation.
Cheers,
Thomas
On 11/14/2012 06:58 AM, Ban Arn wrote:
> Dear Pymol Users
>
> I am using pymol v-0.99rc6 (in windows).
>
> I'm
