From: Dr. STEPHEN SIN-YIN, CHUI
Date: 2011/12/8
Dear All,
I have a protein crystal co-crystallized with a rigid molecule (solved by
small-molecule X-ray method). The color of that crystal is orange (native is
colorless) after 2d cocrystallization experiment. Then I collected synchrotron
data with a resolution at 1.25 Ang. I can solve it by MR. After I re-build
slightly the protein and add some known ions/water, i found there are +ve
connected blobs in the known active site of that protein. At first I suspect
they are water/ion/EDO but many of them are partially connected within C-C/C-O
distances (1.4-1.6 Ang) and in some part, i may imagine some broken
six-membered ring, that are presumably found in that rigid molecule.
How can I "dock" or "confirm" that rigid molecule using CCP4 software or COOT
smartly? I tried to look at all density regions bit by bit, but the density for
the protein atoms always interfere with my vision. Is it possible to mask out
the density of protein atoms, leaving the residue density of interest for the
rest atoms (maybe the rigid molecule)?
many thanks in advance.
stephen
--
Dr. Stephen Sin-Yin Chui (徐先賢)
----------
From: Ed Pozharski
Isn't that what difference density map is for?
Usually one simply generates the ligand model by using prodrg and/or
sketcher (which would give you a monomer description) and then tries to
manually dock it into the density in coot. Some automation is available
(e.g. coot can search for a ligand in the difference map throughout the
cell), but I believe it does not substitute for the manual inspection
(and, imho, neither is such complete replacement possible or even
desirable).
Things appear to be tricky in your case - at 1.25A a well ordered ligand
should produce clearly interpretable density. What you are describing
sounds like either disordered ligand or indeed solvent molecules, or the
mix of the two (the worst-case scenario). Ultimately, it is up to you
to interpret the density, but be careful to curb your imagination.
You may be able to get a better advice if you post the density
snapshots.
Cheers,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
Date: 2011/12/8
Dear All,
I have a protein crystal co-crystallized with a rigid molecule (solved by
small-molecule X-ray method). The color of that crystal is orange (native is
colorless) after 2d cocrystallization experiment. Then I collected synchrotron
data with a resolution at 1.25 Ang. I can solve it by MR. After I re-build
slightly the protein and add some known ions/water, i found there are +ve
connected blobs in the known active site of that protein. At first I suspect
they are water/ion/EDO but many of them are partially connected within C-C/C-O
distances (1.4-1.6 Ang) and in some part, i may imagine some broken
six-membered ring, that are presumably found in that rigid molecule.
How can I "dock" or "confirm" that rigid molecule using CCP4 software or COOT
smartly? I tried to look at all density regions bit by bit, but the density for
the protein atoms always interfere with my vision. Is it possible to mask out
the density of protein atoms, leaving the residue density of interest for the
rest atoms (maybe the rigid molecule)?
many thanks in advance.
stephen
--
Dr. Stephen Sin-Yin Chui (徐先賢)
----------
From: Ed Pozharski
Isn't that what difference density map is for?
Usually one simply generates the ligand model by using prodrg and/or
sketcher (which would give you a monomer description) and then tries to
manually dock it into the density in coot. Some automation is available
(e.g. coot can search for a ligand in the difference map throughout the
cell), but I believe it does not substitute for the manual inspection
(and, imho, neither is such complete replacement possible or even
desirable).
Things appear to be tricky in your case - at 1.25A a well ordered ligand
should produce clearly interpretable density. What you are describing
sounds like either disordered ligand or indeed solvent molecules, or the
mix of the two (the worst-case scenario). Ultimately, it is up to you
to interpret the density, but be careful to curb your imagination.
You may be able to get a better advice if you post the density
snapshots.
Cheers,
Ed.
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
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