[phenixbb] Zinc-cysteine bond refinement in phenix_refine
Ralf Grosse-Kunstleve
rwgrosse-kunstleve at lbl.gov
Wed Aug 31 10:23:28 PDT 2011
phenix.refine does not work with the LINK lines in any way (long story).
Could you send me (off-list) the inputs?
I suspect something must be pushing the ZN the wrong way. It will be much
easier for me to diagnose your problem if I have the inputs for
phenix.refine.
If you don't want to share the data, I could probably do without, but the
other files are essential.
Ralf
On Wed, Aug 31, 2011 at 10:05 AM, Zhang yu <phenixzyfish at gmail.com> wrote:
> Dear all,
>
> I have been stuck in the problem for a while. I appreciate any suggestions.
>
> I have two zinc binding domain in my 3A structure which are Cys4 type.
> The geometry is OK for one domain, but it is not refined properly in the
> other one.
>
> The problems during phenix refinement are
> 1. Zinc is always refined to position ~0.5A off from its correct position
> 2. The refined bond lengths of four Cys-Zn are all below 2.3
> 3. Sometimes, distances between SG atoms of nearby cysteines are too close,
> and coot just connect them as disulfate bond.
> 4. Sometimes, I get the following message showing that all bond angles are
> outliers with >8 sigmas, I listed part of the outliers.
>
> Top angle outliers (sorted by deviation):
> atoms ideal model difference
> deviation (sigma)
>
> ----------------------------------------------------------------------------
> SG CYS D1204 57.894 104.470 46.576
> 9.32
> ZN ZN D2001
> SG CYS D1112
>
> SG CYS D1201 50.842 92.496 41.654
> 8.33
> ZN ZN D2001
> SG CYS D1204
>
> SG CYS D1204 126.952 92.496 -34.455
> -6.89
> ZN ZN D2001
> SG CYS D1201
>
> SG CYS D1201 52.183 86.105 33.922
> 6.78
> ZN ZN D2001
> SG CYS D1112
>
> SG CYS D1194 152.275 119.729 -32.546
> -6.51
> ZN ZN D2001
> SG CYS D1112
>
> SG CYS D1112 89.273 119.729 30.456
> 6.09
> ZN ZN D2001
> SG CYS D1194
>
> I also post my metal.edit file for refinement
>
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq
> 1201
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
>
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq
> 1194
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
>
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq
> 1112
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
>
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq
> 1204
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1194
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1201
> angle_ideal = 112.172178
> sigma = 5
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1112
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1201
> angle_ideal = 87.092184
> sigma = 5
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1112
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1194
> angle_ideal = 118.116518
> sigma = 5
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1201
> angle_ideal = 91.677138
> sigma = 5
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1194
> angle_ideal = 130.829256
> sigma = 5
> }
> }
>
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq
> 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1112
> angle_ideal = 104.886672
> sigma = 5
> }
> }
>
>
> Questions,
> 1. Why the ideal bond angle are different in the metal.edit file and final
> model ? How does phenix determine the ideal bond_angle?
> For example, in the metal.edit file
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq
> 1112
> The angle_ideal = 104.886672
>
> But in the final model
>
> atoms ideal model difference
> deviation (sigma)
>
> ----------------------------------------------------------------------------
> SG CYS D1204 57.894 104.470 46.576
> 9.32
> ZN ZN D2001
> SG CYS D1112
>
> 2. Do I need to put the following LINK in the pdb header to run refinement?
> LINK ZN ZN D2001 SG CYS D1201 1555 1555
> 2.34
> LINK ZN ZN D2001 SG CYS D1112 1555 1555
> 2.33
> LINK ZN ZN D2001 SG CYS D1194 1555 1555
> 2.38
> LINK ZN ZN D2001 SG CYS D1204 1555 1555
> 2.37
>
> 3. After phenix refinement, the output pdb doesn't contain these LINK lines
> no matter what the inpout pdb is. Does phenix_refine use these restrains of
> LINK lines?
>
> Thanks.
>
> Yu Zhang
> Postdoc fellow
> Rutgers University
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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