On Apr 19, 2009, at 21:32, JOE wrote:
Thanks a lot for the replies I have received so far!
I have one homodimer in each ASU. What I intended to do is to show
the electron density for each monomer in different colors (only for
presentation purpose). I guess the only way to achieve this is to
individually create (not sure it is a right word) the map for each
monomer and then display them in pymol or coot. Any better solutions?
I am afraid this email came a few minutes after I could not resist to
already comment on this practice in more brief manner.
My two cents following the joke before:
I am sure you have noble motifs, but all the people that intentionally
or accidentally have presented such 'carved' maps, have done it for
presentation purposes, for presenting their paper to referees and the
journal. Thus, I still think its wrong practice.
Having two different colors for the two 'halves' of the map is still
wrong, even if you clearly want to use for illustrating your point
better. The reason I think it is wrong, is that it has no connection
to your experiment, your map is experimental evidence, and your map
does not have direct information for which monomer it corresponds to.
That information comes from your interpretation, your model.
Thus, I would suggest that the best way to do what you intend is to
show the map in one color and your model in two different colors: that
is perfectly fine. Your model is your interpretation of the
experimental density, and thus you can assign it a color to present
best its properties as a model that best explains your experiment.
Best.
Tassos
Thanks,
Joe
On Sun, Apr 19, 2009 at 11:06 AM, JOE CRYSTAL <[email protected]>
wrote:
Hi,
I want to generate maps only covering atoms in the pdb file. I tried
fft-creat map in ccp4i (output map to cover all atoms in pdb), but
it actually also generated map in places other than pdb atoms. Are
there any other ways to do this? Thank you.
--
Best regards,
Joe
--
Best regards,
Joe
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
