Yes, from Python:
cmd.transform_selection( selection,
[m0, m1, m2, ax,
m3, m4, m5, ay,
m6, m7, m8, az,
bx, by, bz, 1])
where b(xyz) is a pre-translation (applied before the rotation) and a(xyz) is a
post-translation (applied after the rotation). This is that we call a T
Hi Warren,
I only have CRYST1, SCALE, ATOM and END lines in my pdb file. The file
originally came out of ccp4's refmac & pdbset. I can email it and my
conformers.pml script to you privately if it would help.
Simon
On 27 Mar 2009, at 14:45, Warren DeLano wrote:
Simon,
You're triggerin
Simon,
You're triggering some special-purpose annotated PDB code from many years back.
Are there USER records in your PDB files by chance? Getting rid of those
should solve the problem.
Cheers,
Warren
-Original Message-
From: Simon Kolstoe [mailto:s.kols...@ucl.ac.uk]
Sent: Fri 3/27
Dear PyMOL list,
I am trying to visualise 20 docked ligand conformations using PyMOL. I
have been opening PyMOL as the GUI, setting up a view of my protein,
and then running the following script to load my ligand conformations:
load conformer000.pdb, conf0
load conformer001.pdb, conf1
load
Hi Cedric,
In general terms, you can do such things with alter_state. More
specifically, you may want to start scripting, reading in the file
(assuming it's from a file) and doing the transformation. One thing
that's not directly clear is whether t is pre- or post-shifting. You
can directly read
Dear All,
Is there any command to move a molecule using this type of matrix ?
rotation matrix to rotate Chain-1 to Chain-2 --
i t(i) u(i,1) u(i,2) u(i,3)
1-59.0140477207 0.5936510259 -0.4271312489 0.6820097915
2 26.6732874752 -0.792
Hi Thomas,
Joel gave some pointers using the menus. But the reason for giving
spheres and mentioning that as a generic way is that spheres will work
for connected as well as non-bonded atoms. In the case of sulphate you
probably want to have a stick representation. The hydrogen bonds can
be drawn
Dear Jhon,
You want to use the show sticks option. Using the sequence viewer, this will
show your ligands etc. Select these by clicking on them in the sequence viewer
then under selection pick show sticks. From this point once you have displayed
the selected residues it would be best to use the
