Dear,
cealign,super,super_all cannot make an alignment object , as the most
important thing is to obtain
the alignment file out of all this exercise remains unresolved ,Please
suggest me structure based
alignment method in PyMol wherein I can use multiple structures at a time
(with low sequence
PAVAN PAYGHAN wrote, On 12/29/11 13:23:
> Dear ,
>
> "A > align > all to this" and "alignto" both are the same or different?
> If different in what context.
It's different.
The first method uses "align" and gives you an alignment object (uses
util.mass_align function).
The second uses "ceal
Hi Jacob,
regarding "alignto" and states' iter-relations, this has recently been
fixed in open-source pymol.
"align" and "super" both take arguments "mobile_state" and
"target_state" and also preserve states' iter-relations.
Example:
align 1d7q, 2oqk, mobile_state=7, target_state=1
The matrix
Dear List,
I want to superpose a series of 30 states on another (single-state)
model in the following way:
--Superpose the best (closest-fitting) state first. (I know which one this is)
--Output that transformation matrix
--Transform other states by same matrix to preserve states' inter-relation.
Dear ,
"A > align > all to this" and "alignto" both are the same or different?
If different in what context.
Pavan Payghan
On Thu, Dec 29, 2011 at 4:23 PM, zjxu wrote:
> Dear Pavan,
>
>
> align 4-5 structures at a time (with low sequence identity).
>
> check cealign:
> http://www.pym
Dear Pavan,
align 4-5 structures at a time (with low sequence identity).
check cealign: http://www.pymolwiki.org/index.php/Cealign
In pymol1.4, you could use 'alignto':
PyMOL>help alignto
DESCRIPTION
NOTE: This feature is experimental and unsuspported.
"alignto" aligns all other loaded objects t
Dear,
Thanks a lot for the information. As you mentioned super is only for
aligning two structures while with super_all to align the multiple
structures, but the most important thing is to obtain the alignment file
out of all this excercise, can it be possible with super, super_all?
If not whic
Hi Vivek.
I will suggest looking at:
http://pymolwiki.org/index.php/Rotkit
Best
Troels Linnet
2011/12/29 Jason Vertrees
> Vivek,
>
> Yes, it is. Please read the web page I suggested.
>
> Cheers,
>
> Jason
>
> Sent from my android.
> On Dec 28, 2011 9:04 PM, "Vivek Ranjan" wrote:
>
>> Is it p
