Can you send a bit of your PDB including the CA and CL? Eleanor
Louise Gourlay wrote:
Dear All,
I installed CCP4 on my Mac OS X Leopard system using fink. I have some problems
with Refmac, it doesn't refine calcium or chlorine atoms, or any non-protein
atom in general. In the log file it doesn't recognize them and says:
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /sw/share/xtal/ccp4-6.0.2/lib/data/atomsf.lib
No match for atom ID CL subtracting one character
No match for atom ID CA subtracting one character
Thanks,
Louise
----- Messaggio Originale -----
Da: Garib Murshudov <[EMAIL PROTECTED]>
Data: Mercoledi', Luglio 30, 2008 2:28 pm
Oggetto: Re: [ccp4bb] Preventing close contact between protein and ligand
A: CCP4BB@JISCMAIL.AC.UK
Dear Snageetha
1) Could you check please if specified atoms have zero
occupancy.
Atoms with zero occupancy are considered as absent and there are
not
restraints on them
2) symm y at the end of instructions means that the program
check all
possible symmetry operators and finds minimal distance. Most
probably
5.024 is the distance between symmetry related atoms
3) to remove antibumping between different chains there is
an
undocumented keyword. It can be used. the keyword is (as an example)
vdwrestraints exclude between chains A B
Please let me know if this instruction does not work.
NB: This option should not be used unless you know what you are
doing
(that is the reason why it has not been documented). If there
are
clashes between chains then there are reasons for that. For example
if ligand has half occupancy then it is very likely that
surrounding
atoms also have multiple conformation and you should model them.
regards
Garib
On 29 Jul 2008, at 18:24, Sangeetha Vedula wrote:
Dear bb users,
I am refining a protein-ligand complex (at 1.68 A resolution)
in
which the ligand lies on a 2-fold crystallographic symmetry
axis.
The ligand occupancy is, therefore, 0.5 in each asymmetric unit.
I am almost at the end of the refinement but one problem has
me
stumped. Refmac keeps moving a carbon in the ligand too close
to a
serine OG and an oxygen too close to an arginine CD. Given
that the
ligand is at the interface, the density is not perfect.
However, I
rebuild the ligand to eliminate close contacts and still be
within
density and refmac pulls it right back close to the protein.
The
refined position does not even look better than the rebuilt
one! It
almost always looks worse! Would refmac put less weight on
close
contacts with the ligand because it is only partially occupied?
I tried to use external restraints between the ligand and
the
residues so that they are kept further away.
Upon searching the net, I found this command line:
external distance first chain [ch] residue [res] insertion
[ins] -
atom [n] [altcode [a]] second chain [ch] residue [res]
insertion
[ins]-
atom [n] [altcode [a] ] value [v] sigma [s] [symm y/n]
I thought (hoped) that the distance herein is the minimum
distance
of approach between the specified atoms, I added these lines
from
within "Developer options" in refmac interface:
exte dist first chain A resi 59 atom CD seco chain X resi 2001
atom
O1 valu 3.2 sigm 0.02 symm Y
exte dist first chain A resi 27 atom OG seco chain X resi 2001
atom
C10 valu 3.2 sigm 0.02 symm Y
It didn't recognize these restraints at all.
However, when I change these lines to:
exte dist first chain A resi 59 atom CA seco chain X resi 2001
atom
O1 valu 3.2 sigm 0.02 symm Y
exte dist first chain A resi 27 atom OG seco chain X resi 2001
atom
C10 valu 3.2 sigm 0.02 symm Y
Refmac recognizes the first line but not the second - lines
from
log file:
Bond distance deviations from the ideal >10.000Sigma will be
monitored>
A 59 ARG CA . - X
2001 DIE O1 . mod.= 5.024 id.= 3.200 dev=
-1.824 sig.= 0.020
This raises two concerns:
Concern 1: From the first line of output: the restraints here
don't
seem to be minimizing close contact at all; it seems to think
they
are bonded somehow (the distance between these atoms is not
5.024;
it is 6.26 A; I don't know what 5.024 A is!).
I am missing something here. It'd be great if someone can tell
me
what that is!
Concern 2: This command only works when the first atom
specified is
a C-alpha atom (or maybe a main chain atom; I didn't try
using
other main chain atoms). Why is that?
AND ULTIMATELY,
is there some way I can tell refmac not to make the ligand
and
protein clash?
I'd really appreciate any help!
Thanks,
Sangeetha.
Louise Gourlay Ph.D Dep. of Biomolecular Sciences and Biotechnology, Università
degli Studi di Milano Via Celoria 26 Milano 20133
http://users.unimi.it/biolstru/Home.html Italy
