Carlos,
> Is it possible to output to the console the superposition matrix after pair
> fitting?
# yes, for example:
load $TUT/1hpv.pdb
extract chA, chain A
extract chB, chain B
align chA, chB
print cmd.get_object_matrix("chA")
# which dumps the 4x4 homogenous transformation matrix
> 2
Rotem,
Try starting with the script below. It will produce output like:
PRO A 1Chi-1: 20.6
GLN A 2Chi-1: -178.8
LEU A 5Chi-1: -64.6
TRP A 6Chi-1: -55.6
GLN A 7Chi-1: -59.6
ARG A 8Chi-1: -83.1
PRO A 9Chi-1: 34.9
LEU A 10 Chi-1: -53.5
...
Cheers,
Warren
---
Hi,
I would like to do the following task:
I have three complexes of three different ligands with the same enzyme and
I would like to rotate/translate the electron density maps of two of these
complexes in order to superpose them onto the first complex. I need to do
the superposition bas
Dear Warren and Martin,
Thank you for your answers.
I'm using the free version 0.99rc6, so the function "matrix_copy" is
not available.
However, I performed my alignment, saved my pdb file and redid the
process PBD2PQR+ABPS. After that, I'm able to load the PQR files and
the correspondin
Hi Charles,
It is better to reply on the mailing list as this will ensure that the
discussions are archived. That way, many biologists will be able to
search for answers to their questions before posting themselves ;)
The font settings can be controlled with 'set'. If you type 'set
label' in the
Hi,
I think that it probably is possible to do this from within pymol, and
probably quite convenient for single molecules.
However, there are two other possible approaches, which would be
helpful for multiple molecules.
Firstly, there is a program called 'dang' made by the Richardson group:
htt
Hi,
I'm looking for a way to calculate set of torsion angels from
selected residues (for example Chi1 dihedral of all His residues). Is
it possible to write PyMOL script for such task ? Any hints to write
such script will be appreciated!
Thank you
Rotem
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