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
bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov
Sent: Wednesday, July 30, 2008 5:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Preventing close contact between protein and ligand
Dear Snageetha
1) Could you check please if specified atoms have zero occupancy
[mailto:[EMAIL PROTECTED] On Behalf
Of Garib Murshudov
Sent: Wednesday, July 30, 2008 5:18 AM
To: CCP4BB@JISCMAIL.AC.UK
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
On Wed, Jul 30, 2008 at 8:17 AM, Garib Murshudov [EMAIL PROTECTED]wrote:
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
They do not have zero occupancy.
2) symm y at
I am looking at my ligand library file that ProDRG generated. I do not see
any column id that indicates that it is a restraints weight or such. Could
you tell me exactly which one I should edit?
Thanks,
Sangeetha.
On Tue, Jul 29, 2008 at 3:23 PM, Robert Immormino [EMAIL PROTECTED]wrote:
There should be something like:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
MAN-b-D O1 C1single 1.4100.020
MAN-b-D C2 C1single 1.524
: (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
[mailto:[EMAIL PROTECTED] On
Behalf Of Garib Murshudov
Sent: Wednesday, July 30, 2008 5:18 AM
To: CCP4BB@JISCMAIL.AC.UK
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
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
