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] MERGING THREE DATASETS
If you still have the input to scalepack you can rerun it to get an unmerged file for both sets of data.. You dont need to change the SG unless of course there is a different indexing convention for the sets.. pointless should handle that - you can generate a mtz file for each data set, then ask to match the indexing to the first Then you can combine the 3 mtz files, and get a single one ready for input to scala (or aimless) .. Eleanor On 12/22/2011 03:30 PM, Yuri Pompeu wrote: I was actually trying to do the same thing. I have to data sets processed in p21 that I would like to merge as one contains higher resolution data. They were processed and merged using the HKL suite. So I have the two .sca files I guess the first step for me would be to create a fake unmerged set of both using Combat, as suggested by prof. Dodson and others. Practically speaking, do I accomplish that by changing the space group to P1 while keeping my cell dimensions constant in combat? Thanks a lot
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 low resolution REMARK
Hi Bernhard So what's new? See http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html (17-Nov-11). Cheers -- Ian On 2 January 2012 06:58, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Dear Developers, it seems to me that at least Refmac 5.6.0117 does not report the actual lowest resolution used in refinement, but instead the lowest resolution of the hkl index range generated by the default cif import script instead. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.63 --- The data go only to 28.66 A according to mtzdump as well as xprep as far as I can tell, cif2mtz does it right and reports * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.00122 0.25305 ( 28.660 - 1.988 A ) - then the script calls unique which pads the reflections up * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 33.1300 57.2300 38.6500 90. 91.9400 90. * Resolution Range : 0.00067 0.25302 ( 38.628 - 1.988 A ) - which then propagates to CAD and FREEFLAG into the MTZ header where it is picked up by refmac. OVERALL FILE STATISTICS for resolution range 0.001 - 0.253 === Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC -16 16 0 100.00 0.1 6.3 38.63 1.99 H H 2 NONE 0 28 0 100.00 10.5 10.5 38.63 1.99 H K 3 NONE 0 19 0 100.00 7.3 7.3 38.63 1.99 H L 4 NONE 0.0 9.0 0 100.00 4.50 4.50 38.63 1.99 I FREE 5 NONE 7.7 707.8 361 96.40 102.76 102.76 28.66 1.99 F FP - this is the right number! 6 NONE 1.6 37.3 361 96.40 8.84 8.84 28.66 1.99 Q SIGFP I have noticed that other PDB/sf file sets (not mine) seem to be affected as well. Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. -
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 low resolution REMARK
So what's new? Alzheimer's and late night senile dementia :-) BR PS: nice site! -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Monday, January 02, 2012 4:34 AM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] refmac low resolution REMARK Hi Bernhard So what's new? See http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html (17-Nov-11). Cheers -- Ian
