Re: [ccp4bb] Refmac and metal on a two-fold?
Dear Ed, I thought the clumsy way of handling special positions you describe was abandoned after the Xplor days, that even rounding errors could cause special atoms to fly apart, but you may be right. The Mn ion might not really be special, but might have two minima, one closer to one protein molecule and one closer to the symmetry related protein molecule. Supposedly, refmac switches off vd Waals repulsions if the combined occupancies of the the atoms involved does not exceed 1.0. This should take care of the problem but apparently does not. Forcing the ion to have to same position as its symmetry mate may not always be the best representation of the reality in a crystal. The main reason I switched to Buster a few years ago is that in refmac residual repulsions remain, even if the summed occupancies of atoms in alternate positions do not exceed 1.0. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, January 02, 2012 7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and metal on a two-fold? On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Thanks - good to know. Perhaps a good practice is to take care of special positions manually every time just in case. From what I understand, the way refinement software generally treats special positions (other than automatically resetting occupancy to 1/z) is to exclude vdw repulsion to symmetry-related atom which in this case would always push the atom out of position. Exclusion is usually applied to the atom when it is within the cutoff distance (0.1A?) from the corresponding symmetry element. If for whatever reason the atom shifts, the vdw will push it out. Why would such atoms shift varies - I suspect in some cases it is due to hydrogen bonding restraints, in others it could be due to noisy density. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Refmac and metal on a two-fold?
I am surprised that this is such a mess. Small molecule crystallographers frequently encounter special positions and have been able to handle them correctly for many years. A well known small molecule refinement program that I don't need to advertise here has been able to generate the special position constraints for the atom coordinates and anisotropic displacement parameters fully automatically for all special positions in all space groups for the last 20 years, no special user action is required. George On 01/02/2012 12:40 PM, herman.schreu...@sanofi.com wrote: Dear Ed, I thought the clumsy way of handling special positions you describe was abandoned after the Xplor days, that even rounding errors could cause special atoms to fly apart, but you may be right. The Mn ion might not really be special, but might have two minima, one closer to one protein molecule and one closer to the symmetry related protein molecule. Supposedly, refmac switches off vd Waals repulsions if the combined occupancies of the the atoms involved does not exceed 1.0. This should take care of the problem but apparently does not. Forcing the ion to have to same position as its symmetry mate may not always be the best representation of the reality in a crystal. The main reason I switched to Buster a few years ago is that in refmac residual repulsions remain, even if the summed occupancies of atoms in alternate positions do not exceed 1.0. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, January 02, 2012 7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and metal on a two-fold? On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Thanks - good to know. Perhaps a good practice is to take care of special positions manually every time just in case. From what I understand, the way refinement software generally treats special positions (other than automatically resetting occupancy to 1/z) is to exclude vdw repulsion to symmetry-related atom which in this case would always push the atom out of position. Exclusion is usually applied to the atom when it is within the cutoff distance (0.1A?) from the corresponding symmetry element. If for whatever reason the atom shifts, the vdw will push it out. Why would such atoms shift varies - I suspect in some cases it is due to hydrogen bonding restraints, in others it could be due to noisy density. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Refmac and metal on a two-fold?
Dear George, I think for small molecules the situation is much easier as for proteins. With small molecules, the resolution of the data is in general much higher and a water or metal ion will force the small molecules in such a position that the special position is exact. With proteins, the water or metal ion will be in one of many crystal contacts and may not be able to force the much larger proteins in such a position that the special position is exact and what we think is a special position is in fact a mixture of two or more alternative positions. I strongly believe that in these cases one should not force the water or metal ion to be exactly on a symmetry axis, but just switch off the vd Waals repulsions and let the data decide which water or metal ion positions best corresponds with the diffraction data. This switching off of vd Waals repulsions does not seem to always work with refmac. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of George M. Sheldrick Sent: Monday, January 02, 2012 1:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and metal on a two-fold? I am surprised that this is such a mess. Small molecule crystallographers frequently encounter special positions and have been able to handle them correctly for many years. A well known small molecule refinement program that I don't need to advertise here has been able to generate the special position constraints for the atom coordinates and anisotropic displacement parameters fully automatically for all special positions in all space groups for the last 20 years, no special user action is required. George On 01/02/2012 12:40 PM, herman.schreu...@sanofi.com wrote: Dear Ed, I thought the clumsy way of handling special positions you describe was abandoned after the Xplor days, that even rounding errors could cause special atoms to fly apart, but you may be right. The Mn ion might not really be special, but might have two minima, one closer to one protein molecule and one closer to the symmetry related protein molecule. Supposedly, refmac switches off vd Waals repulsions if the combined occupancies of the the atoms involved does not exceed 1.0. This should take care of the problem but apparently does not. Forcing the ion to have to same position as its symmetry mate may not always be the best representation of the reality in a crystal. The main reason I switched to Buster a few years ago is that in refmac residual repulsions remain, even if the summed occupancies of atoms in alternate positions do not exceed 1.0. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, January 02, 2012 7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac and metal on a two-fold? On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Thanks - good to know. Perhaps a good practice is to take care of special positions manually every time just in case. From what I understand, the way refinement software generally treats special positions (other than automatically resetting occupancy to 1/z) is to exclude vdw repulsion to symmetry-related atom which in this case would always push the atom out of position. Exclusion is usually applied to the atom when it is within the cutoff distance (0.1A?) from the corresponding symmetry element. If for whatever reason the atom shifts, the vdw will push it out. Why would such atoms shift varies - I suspect in some cases it is due to hydrogen bonding restraints, in others it could be due to noisy density. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Refmac and metal on a two-fold?
I've seen this happening to water molecules as well (in a somewhat unpredictable fashion). In the latest refmac versions, you can try harmonic restraints, although these will only slow down the atom drift, as the target position is updated every cycle. Perhaps you can use distance restraints against a dummy atom to fix the metal ion in place. Another remedy might be to manually place the metal ion in position followed by zero cycles of refinement to get the final R-values. There is some evidence that excluding isolated atoms from refinement may introduce some systematic error on the rest of the structure, but it is likely very small. Cheers, Ed. On Wed, 2011-12-28 at 13:29 -0600, Dima Klenchin wrote: Hello, I have a metal ion sitting on a two-fold. I assigned it an occupancy of 0.5 but Refmac keeps refining it away from that position so that in the end there is a symmetry-related ion 1.6A away. I thought that this problem has been rectified long ago? Certainly I had several occasions where Refmac would automatically recognize special position and automatically assigned proper occupancy (1/n). Not sure why this particular case is different... This behavior is the same in: Refmac 5.5.0088 (Windows) Refmac 5.5.0102 (Windows) Refmac 5.6.0117 (Windows) Refmac 5.5.0109 (Linux) I also tried leaving it at occupancy 1.0 and also tried renaming MN2+ to water at occupancies of 0.5 and 1.0. All to no avail - the atom is always shifted away from the density. Anything I can do to force Refmac to keep it nice and tidy? Thanks and Happy New Year! - Dima
Re: [ccp4bb] Refmac and metal on a two-fold?
I've seen this happening to water molecules as well (in a somewhat unpredictable fashion). In the latest refmac versions, you can try harmonic restraints, although these will only slow down the atom drift, as the target position is updated every cycle. Perhaps you can use distance restraints against a dummy atom to fix the metal ion in place. Thanks, Ed! Just in case anyone else has the same issue: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Here is the exact command I used: EXTERNAL DISTANCE first chain M residue 3 atom MN - second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y Occupancy set manually to 0.5. - Dima
Re: [ccp4bb] Refmac and metal on a two-fold?
Good to know, thanks. I was actually wondering about this recently. On Sun, Jan 1, 2012 at 1:14 PM, Dima Klenchin klenc...@facstaff.wisc.eduwrote: I've seen this happening to water molecules as well (in a somewhat unpredictable fashion). In the latest refmac versions, you can try harmonic restraints, although these will only slow down the atom drift, as the target position is updated every cycle. Perhaps you can use distance restraints against a dummy atom to fix the metal ion in place. Thanks, Ed! Just in case anyone else has the same issue: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Here is the exact command I used: EXTERNAL DISTANCE first chain M residue 3 atom MN - second chain M residue 3 atom MN value 0.0 sigma 0.00 symm Y Occupancy set manually to 0.5. - Dima
Re: [ccp4bb] Refmac and metal on a two-fold?
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote: With Garib's help, I have forced the atom into its position by using external distance restrains of zero length against the same symmetry-related atom. The cause is unclear because the same program handles special positions in another structure just fine. Thanks - good to know. Perhaps a good practice is to take care of special positions manually every time just in case. From what I understand, the way refinement software generally treats special positions (other than automatically resetting occupancy to 1/z) is to exclude vdw repulsion to symmetry-related atom which in this case would always push the atom out of position. Exclusion is usually applied to the atom when it is within the cutoff distance (0.1A?) from the corresponding symmetry element. If for whatever reason the atom shifts, the vdw will push it out. Why would such atoms shift varies - I suspect in some cases it is due to hydrogen bonding restraints, in others it could be due to noisy density. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
[ccp4bb] Refmac and metal on a two-fold?
Hello, I have a metal ion sitting on a two-fold. I assigned it an occupancy of 0.5 but Refmac keeps refining it away from that position so that in the end there is a symmetry-related ion 1.6A away. I thought that this problem has been rectified long ago? Certainly I had several occasions where Refmac would automatically recognize special position and automatically assigned proper occupancy (1/n). Not sure why this particular case is different... This behavior is the same in: Refmac 5.5.0088 (Windows) Refmac 5.5.0102 (Windows) Refmac 5.6.0117 (Windows) Refmac 5.5.0109 (Linux) I also tried leaving it at occupancy 1.0 and also tried renaming MN2+ to water at occupancies of 0.5 and 1.0. All to no avail - the atom is always shifted away from the density. Anything I can do to force Refmac to keep it nice and tidy? Thanks and Happy New Year! - Dima
