[PyMOL] Rotation/Translation

2010-05-29 Thread J. Fleming
Hello,

I've been using 'super' to align the C-alphas within one domain of two
different models of the same protein while leaving the second domain
to move freely.  I can do this using:

super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca)

What I would like to do is determine the rotation and translation of
model B's second domain as it moves away from A's second domain.

I can output a matrix after running super using:

print cmd.get_object_matrix(A)

How do I go from the matrix to an angle and distance?

Thanks for any thoughts,
Jon

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[PyMOL] Pymol and APBS

2010-04-15 Thread J. Fleming
Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
few weeks now on multiple linux systems (RedHat and Fedora).  I've
Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
it is a PDB2PQR server generated file APBS runs and states X atoms
did not have properties assigned and to either remove or fix the
atoms.  How can I fix them?  The problem residues are just regular
amino acids; no split confrimations etc.  I've also tried editing out
the PDBs chain name before converting to the PDB to PQR but that
didn't work.

Another things I've tried is using APBSTools 2 but it errors as soon
as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

I really need to get this to work but I have no clue what to try next.

Thanks in advance for any thoughts.
-Jon

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[PyMOL] Cartoon backbone nitrogens

2010-03-05 Thread J. Fleming
Hi all,

  Is there a good method to display backbone nitrogens while in cartoon
mode?  I tried using spheres on the backbone nitrogen positions but it
doesn't look right.  Sticks also looked strange as the transition from
cartoon to sticks was broken.  Perhaps there is a way to color just the
cartoon backbone nitrogen blue?

I'm open to any ideas.  Thanks,
Jon
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