Hi Garib,
This is a side-question. What you just said writing to Abhinav explains
why I have problem of some repulsion between identical ligands with
different tail conformations when I try to refine them at 25% and 25%
occupancy. In my case the overall occupancy of the ligand is not
expected to be 100% (the ligand is naturally partially lost) so in
order to have the well behaving refinement I will have to change these
occupancies to 50-50, right? And just pay the price with the higher B
factors? Or is there any other way to deal with this situation?
Aleks
On 30 Jul 2008, at 16:15, Garib Murshudov wrote:
If sum of occupancies of atoms is less than or equal to one and atoms
are not in the same residue with the same alt code then they do not
see each other. Otherwise they see each other and there is vdw
repulsion between them. this has not changed substantially since the
first version.
Waters are not good way of modelling unknown ligands.
If you want to model unknown model then you can use DUM atoms with DUM
residue name (just like the arp/warp uses it). Then atoms can come
much closer to each other (up to 1.2A or so. this value can be
controlled)
Garib
On 30 Jul 2008, at 16:05, Kumar, Abhinav wrote:
I have had a similar experience.
I was trying to model a bunch of waters to simulate an unknown ligand
(UNL) in an unmodeled density. The waters were all in different
alternate conformations of the same residue number. When the
occupancies of these waters were set to 0.5, the vdw repulsion became
absent; waters stayed within density at close distances. But, as soon
as the occupancies were changed to anything but 0.5, waters got
pushed out of density due to vdw repulsion.
So my feeling is that at 0.5 occupancy the atom does not see vdw
repulsion (?). Change it to something else and atom should crawl back
into its density.
I was using refmac5 version 5.2.0019.
Thanks
Abhinav
Stanford Synchrotron Radiation Laboratory
Joint Center for Structural Genomics
Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf
Of Garib Murshudov
Sent: Wednesday, July 30, 2008 5:18 AM
To:[EMAIL PROTECTED]
Subject: Re: [ccp4bb] Preventing close contact between protein and
ligand
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.
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