Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?
sorry for repeat. Link I gave in the previous mail should be: www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Garib On 11 Jan 2008, at 19:58, Jie Liu wrote: I've played around for a while, also read the manual and googled the internet, but just couldn't find a way to set up the restraints to the symmetry related atoms in Refmac5. Could anyone please kindly advice me how to do that? Thank you!!! Jie Eleanor Dodson wrote: It needs Garib to answer this! Eleanor Charlie Bond wrote: Eleanor Dodson wrote: It should be more or less equivalent, but better I think to put 1S at 0.5 occ and 2O at occ = 1 At least in REFMAC the restraints to the symmetry atoms should be set up But if you do that, some of the bond angles will be unrestrained, won't they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is refmac cleverer than I think? Cheers, Charlie
Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?
Best way of refining SO4 two-fold axis is to put al occupancies equal to 0.5 and refine like that. You may need to use newer version to deal better with atoms in special position. Have a look: www.ysbl.york.ac.uk/YSBLprograms/index.jsp You can go from this site to latest refmac site. Any further problems with this refinement please let me know. Garib P.S. You can put restraints between symmetry related atoms (you do not need them in this case) using keywords. There are keywords to deal with them. You can find them the same site as the latest refmac. On 11 Jan 2008, at 19:58, Jie Liu wrote: I've played around for a while, also read the manual and googled the internet, but just couldn't find a way to set up the restraints to the symmetry related atoms in Refmac5. Could anyone please kindly advice me how to do that? Thank you!!! Jie Eleanor Dodson wrote: It needs Garib to answer this! Eleanor Charlie Bond wrote: Eleanor Dodson wrote: It should be more or less equivalent, but better I think to put 1S at 0.5 occ and 2O at occ = 1 At least in REFMAC the restraints to the symmetry atoms should be set up But if you do that, some of the bond angles will be unrestrained, won't they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is refmac cleverer than I think? Cheers, Charlie
Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?
I've played around for a while, also read the manual and googled the internet, but just couldn't find a way to set up the restraints to the symmetry related atoms in Refmac5. Could anyone please kindly advice me how to do that? Thank you!!! Jie Eleanor Dodson wrote: > It needs Garib to answer this! > Eleanor > > Charlie Bond wrote: > > Eleanor Dodson wrote: > > > >> It should be more or less equivalent, but better I think to put 1S at > >> 0.5 occ and 2O at occ = 1 > >> > >> At least in REFMAC the restraints to the symmetry atoms should be set up > >> > > > > But if you do that, some of the bond angles will be unrestrained, won't > > they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is > > refmac cleverer than I think? > > > > Cheers, > > Charlie > >
Re: [ccp4bb] Sulfate ion on 2-fold axis - Garib?
It needs Garib to answer this! Eleanor Charlie Bond wrote: > Eleanor Dodson wrote: > >> It should be more or less equivalent, but better I think to put 1S at >> 0.5 occ and 2O at occ = 1 >> >> At least in REFMAC the restraints to the symmetry atoms should be set up >> > > But if you do that, some of the bond angles will be unrestrained, won't > they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is > refmac cleverer than I think? > > Cheers, > Charlie >
Re: [ccp4bb] Sulfate ion on 2-fold axis
Using SHELXL, restraints can be applied to symmetry equivalent atoms so one can easily restrain the sulphate to be a regular tetrahedron by restraining the S-O distances to be equal and the O1..O2, O1'..O2 etc. distances to be equal (with or without target values). For details of a similar example see Acta Cryst. A64 (2008) 112-122. From Eleanor's comment it appears that REFMAC can now do this too, though I was not aware of the facility. If you then wish to refine S anisotropically SHELXL will also automatically generate and apply the constraints required for the special position (in any space group), this can be very useful for high-resolution refinements. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 11 Jan 2008, Charlie Bond wrote: > Eleanor Dodson wrote: > > It should be more or less equivalent, but better I think to put 1S at > > 0.5 occ and 2O at occ = 1 > > > > At least in REFMAC the restraints to the symmetry atoms should be set up > > But if you do that, some of the bond angles will be unrestrained, won't > they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is > refmac cleverer than I think? > > Cheers, > Charlie > -- > Charlie Bond > Professorial Fellow > University of Western Australia > School of Biomedical, Biomolecular and Chemical Sciences > M310 > 35 Stirling Highway > Crawley WA 6009 > Australia > [EMAIL PROTECTED] > +61 8 6488 4406 >
Re: [ccp4bb] Sulfate ion on 2-fold axis
Eleanor Dodson wrote: > It should be more or less equivalent, but better I think to put 1S at > 0.5 occ and 2O at occ = 1 > > At least in REFMAC the restraints to the symmetry atoms should be set up But if you do that, some of the bond angles will be unrestrained, won't they?: O1-S-O2 will be OK, but O1-S-O1' and O2-S-O2' will not. Or is refmac cleverer than I think? Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
Re: [ccp4bb] Sulfate ion on 2-fold axis
Jie Liu wrote: > Dear all > > I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file > one S atom with occu=0.5 and two O atoms with occu=1, or should > I put one S and four O atoms all with occu=0.5? > > Thanks for your inputs. > > Jie > > > It should be more or less equivalent, but better I think to put 1S at 0.5 occ and 2O at occ = 1 At least in REFMAC the restraints to the symmetry atoms should be set up Eleanor
Re: [ccp4bb] Sulfate ion on 2-fold axis
Dear Jie, It also depends on whether you believe the SO4 sits with its internal two-fold along the crystal's two-fold axis. If it does you should probably have a 0.5 occ sulfur and two 1.0 occ oxygen atoms. If the symmetry is not obeyed you will have to have four 0.5 occ oxygen atoms. Be careful, some refinement programs will not be able to handle the bond length and angle restraints if you only supply two oxygen atoms. They will not allow bonds between atoms and symmetry images of atoms. If you are using such a program you will have to supply four oxygen atoms even if this is not what you would otherwise do. Dale Tronrud Charlie Bond wrote: > Hi Jie, > Depending on your resolution, you may be forced use to use S(0.5) and > 4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement. > Cheers, > Charlie > > > Jie Liu wrote: >> Dear all >> >> I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file >> one S atom with occu=0.5 and two O atoms with occu=1, or should >> I put one S and four O atoms all with occu=0.5? >> >> Thanks for your inputs. >> >> Jie >> >> . >> >
Re: [ccp4bb] Sulfate ion on 2-fold axis
Hi Jie, Depending on your resolution, you may be forced use to use S(0.5) and 4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement. Cheers, Charlie Jie Liu wrote: > Dear all > > I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file > one S atom with occu=0.5 and two O atoms with occu=1, or should > I put one S and four O atoms all with occu=0.5? > > Thanks for your inputs. > > Jie > > . > -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
[ccp4bb] Sulfate ion on 2-fold axis
Dear all I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file one S atom with occu=0.5 and two O atoms with occu=1, or should I put one S and four O atoms all with occu=0.5? Thanks for your inputs. Jie
