Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
On Sun, 28 Dec 2014 15:37:22 -0600, Igor Petrik petr...@illinois.edu wrote: ... DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93 DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 CRYSTAL TO DETECTOR DISTANCE (mm) 259.04 LAB COORDINATES OF DETECTOR X-AXIS 1.00 0.00 0.00 LAB COORDINATES OF DETECTOR Y-AXIS 0.00 1.00 0.00 ... (XDS defines spindle as X and beam as Z) ... Hi Igor, XDS does not define the geometry by itself; rather, the definition is specified by the _user_ , in XDS.INP! The trouble with improperly self-defining things is that one can get e.g. the wrong sign of the anomalous signal, which is why tested XDS.INP examples are provided. Thus, I would redefine beam as Y and spindle as Z using: DIRECTION_OF_DETECTOR_X-AXIS= 0 0 1 ! instead of 1 0 0 DIRECTION_OF_DETECTOR_Y-AXIS= 1 0 0 ! instead of 0 1 0 INCIDENT_BEAM_DIRECTION= 0 1 0 ! instead of 0 0 1 ROTATION_AXIS= 0 0 1 ! instead of 1 0 0 (this is a circular permutation so should be safe), and index with that. Finally, there is (in orthorhombic settings) a choice of 8 equivalent settings of the crystal. best, Kay
Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
Yes, unfortunately an orientation matrix is completely useless without a frame of reference. All it does is tell you where the cell axes lie relative to X, Y and Z, but X may be the x-ray beam, or sometimes that is Z and X is the spindle axis. Different people have different and strongly-held opinions about this. The fast and slow axes on the detector are also a matter of widely-varying convention. The origin of the detector could be the first pixel in the image file, the upper-left corner, or it could be in cameraman view vs sample view and the beam center is also only meaningful relative to whatever the origin is. Also, if you are at one of the four beamlines in the world that rotates their spindle the opposite direction of everyone else, then you may have to reverse the sign of one axis as well, usually Y, or there may be an option such as REVERSEPHI. XDS lets you define all these things manually and there are formally no default settings. To be fair, it is difficult for developers to keep track of what all ~150 beamlines around the world, plus commercial home lab equipment manufacturers are doing. I've been trying to some time to assemble a library of recent lysozyme datasets from as many beamlines as possible, but my collection is still far from complete: http://bl831.als.lbl.gov/example_data_sets/ That said, I have written a few jiffies for inter-converting XDS and mosflm conventions, and posted them here: http://bl831.als.lbl.gov/~jamesh/orientation_matrix/ Instructions are at the top of each awk script. For example, mosflm2xds.awk takes the first three lines to be the *.mat file from mosflm, but also needs the mosflm input script after that to figure out how to convert it into XDS conventions. Use it like this: cat auto.mat mosflm.inp | ./mosflm2xds.awk XDS.INP You can convert the resulting XDS keywords into an XPARM.XDS file using xds2xparm.awk, which can be useful for feeding into some pipelines. If you already have an XPARM.XDS, you can convert it back into XDS keywords using xparm2xds.awk, and these keywords can, in turn, be fed into xds2mosflm.awk to get a mosflm *.mat file again. Note, however, that there can be some information loss here. The *.mat file does NOT contain the full description of the detector and spindle geometry that XDS may be using. I make some guesses in these scripts if not all the relevant XDS keywords are provided. It works with my setup at ALS 8.3.1, but I have not tested it thoroughly with other cameras. I would be interested if you find any bugs! As for what you're missing, could it perhaps be a reversed phi direction? That might look like a 180-degree rotation. Good luck! -James Holton MAD Scientist On 12/28/2014 3:12 PM, Igor Petrik wrote: Takanori and Pierre, Thank you for your quick responses. If you read my post you will see that I used the xds2mos.py script to convert the xds orientation to Mosflm format, but this gives me a result that is inconsistent with the matrix calculated directly by moslfm or DENZO. For orthorombic space group P222 there are only a hand full of equivalent matrices related by changing sign of one of the vectors. The matrices generated by XDS and Mosflm do not seem equivalent. Or maybe I'm missing something. Thanks, - Igor
[ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
I am working on a small project which requires me to obtain the proper orientation of a crystal lattice with respect to the gonistat and source. I have until now successfully used the matrices from Mosflm and DENZO, which are consistent with each other and define the orientation of the reciprocal lattice in the lab space when the spindle is at 0deg. I am trying to use the orientation computed by XDS, but this seems to not be consistent with the others. Here is an example: mosflm .mat file: -0.00458796 -0.01054146 -0.01052990 0.00600652 0.01617284 -0.00696834 0.02352343 -0.00618559 -0.00027442 0.000 0.000 0.000 -0.1856881 -0.5200068 -0.8337343 0.2431015 0.7978011 -0.5517381 0.9520617 -0.3051332 -0.0217278 39.6412 48.3160 77.5507 90. 90. 90. 0.000 0.000 0.000 SYMM P222 (top part is reciprocal matrix in the format: a*x b*x c*x a*y b*y c*y a*z b*z c*z where x is the x-ray beam axis and z is the spindle axis) DENZO (HKL2000) gives an equivalent matrix. XDS orientation parameters: CORRECT.LP ... REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 30955 INDEXED SPOTS REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS STANDARD DEVIATION OF SPOTPOSITION (PIXELS) 0.70 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)0.08 SPACE GROUP NUMBER 16 UNIT CELL PARAMETERS 39.52848.15377.542 90.000 90.000 90.000 E.S.D. OF CELL PARAMETERS 4.0E-02 3.3E-02 3.8E-02 0.0E+00 0.0E+00 0.0E+00 REC. CELL PARAMETERS 0.025299 0.020767 0.012896 90.000 90.000 90.000 COORDINATES OF UNIT CELL A-AXIS -37.65011.269-4.236 COORDINATES OF UNIT CELL B-AXIS14.62441.546 -19.461 COORDINATES OF UNIT CELL C-AXIS-1.764 -32.374 -70.439 CRYSTAL MOSAICITY (DEGREES) 0.211 LAB COORDINATES OF ROTATION AXIS 0.62 0.007232 -0.004834 DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93 DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 CRYSTAL TO DETECTOR DISTANCE (mm) 259.04 LAB COORDINATES OF DETECTOR X-AXIS 1.00 0.00 0.00 LAB COORDINATES OF DETECTOR Y-AXIS 0.00 1.00 0.00 ... (XDS defines spindle as X and beam as Z) Converted to reciprocal lattice orientation matrix in mosflm axis conventions: (output from xds2mos; manual calculation is consistent with this output) -0.00273114 -0.00809777 -0.01150308 -0.00724876 -0.01754758 0.00521075 -0.02353677 0.00634416 -0.00027012 0.000 0.000 0.000 -0.11022162 -0.39811300 -0.91068616 -0.29254071 -0.86269689 0.41252918 -0.94988163 0.31189970 -0.02138535 39.5280 48.1530 77.5420 90. 90. 90. 0.000 0.000 0.000 As you can see they are different. You can note that the component of each vector along the mosflm-Z (spindle) axis is consistent, suggesting that it is only the angle of rotation around the spindle axis that is inconsistent between the two. I know that for mosflm and DENZO the orientation matrix defines the orientation of the reciprocal lattice when the spindle is at 0 deg. XDS seems to be using a different reference point. Why is this and what is the proper way to obtain the absolute reciprocal orientation at 0 deg from XDS? (If anyone wants to test this on their own, I can provide the frames I used to obtain these files.) Thanks, - Igor Petrik University of Illinois
Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
(I think) these matrices are roughly 180 degrees apart, so they may just correspond to different signs of the axes Phil On 28 Dec 2014, at 21:37, Igor Petrik petr...@illinois.edu wrote: I am working on a small project which requires me to obtain the proper orientation of a crystal lattice with respect to the gonistat and source. I have until now successfully used the matrices from Mosflm and DENZO, which are consistent with each other and define the orientation of the reciprocal lattice in the lab space when the spindle is at 0deg. I am trying to use the orientation computed by XDS, but this seems to not be consistent with the others. Here is an example: mosflm .mat file: -0.00458796 -0.01054146 -0.01052990 0.00600652 0.01617284 -0.00696834 0.02352343 -0.00618559 -0.00027442 0.000 0.000 0.000 -0.1856881 -0.5200068 -0.8337343 0.2431015 0.7978011 -0.5517381 0.9520617 -0.3051332 -0.0217278 39.6412 48.3160 77.5507 90. 90. 90. 0.000 0.000 0.000 SYMM P222 (top part is reciprocal matrix in the format: a*x b*x c*x a*y b*y c*y a*z b*z c*z where x is the x-ray beam axis and z is the spindle axis) DENZO (HKL2000) gives an equivalent matrix. XDS orientation parameters: CORRECT.LP ... REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 30955 INDEXED SPOTS REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS STANDARD DEVIATION OF SPOTPOSITION (PIXELS) 0.70 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)0.08 SPACE GROUP NUMBER 16 UNIT CELL PARAMETERS 39.52848.15377.542 90.000 90.000 90.000 E.S.D. OF CELL PARAMETERS 4.0E-02 3.3E-02 3.8E-02 0.0E+00 0.0E+00 0.0E+00 REC. CELL PARAMETERS 0.025299 0.020767 0.012896 90.000 90.000 90.000 COORDINATES OF UNIT CELL A-AXIS -37.65011.269-4.236 COORDINATES OF UNIT CELL B-AXIS14.62441.546 -19.461 COORDINATES OF UNIT CELL C-AXIS-1.764 -32.374 -70.439 CRYSTAL MOSAICITY (DEGREES) 0.211 LAB COORDINATES OF ROTATION AXIS 0.62 0.007232 -0.004834 DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93 DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 CRYSTAL TO DETECTOR DISTANCE (mm) 259.04 LAB COORDINATES OF DETECTOR X-AXIS 1.00 0.00 0.00 LAB COORDINATES OF DETECTOR Y-AXIS 0.00 1.00 0.00 ... (XDS defines spindle as X and beam as Z) Converted to reciprocal lattice orientation matrix in mosflm axis conventions: (output from xds2mos; manual calculation is consistent with this output) -0.00273114 -0.00809777 -0.01150308 -0.00724876 -0.01754758 0.00521075 -0.02353677 0.00634416 -0.00027012 0.000 0.000 0.000 -0.11022162 -0.39811300 -0.91068616 -0.29254071 -0.86269689 0.41252918 -0.94988163 0.31189970 -0.02138535 39.5280 48.1530 77.5420 90. 90. 90. 0.000 0.000 0.000 As you can see they are different. You can note that the component of each vector along the mosflm-Z (spindle) axis is consistent, suggesting that it is only the angle of rotation around the spindle axis that is inconsistent between the two. I know that for mosflm and DENZO the orientation matrix defines the orientation of the reciprocal lattice when the spindle is at 0 deg. XDS seems to be using a different reference point. Why is this and what is the proper way to obtain the absolute reciprocal orientation at 0 deg from XDS? (If anyone wants to test this on their own, I can provide the frames I used to obtain these files.) Thanks, - Igor Petrik University of Illinois
Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
Hi, xdsme has xds2mos.py script. https://code.google.com/p/xdsme/ https://code.google.com/p/xdsme/source/browse/XOconv/xds2mos.py Best regards, Takanori Nakane On 2014/12/29 6:37, Igor Petrik wrote: I am working on a small project which requires me to obtain the proper orientation of a crystal lattice with respect to the gonistat and source. I have until now successfully used the matrices from Mosflm and DENZO, which are consistent with each other and define the orientation of the reciprocal lattice in the lab space when the spindle is at 0deg. I am trying to use the orientation computed by XDS, but this seems to not be consistent with the others. Here is an example: mosflm .mat file: -0.00458796 -0.01054146 -0.01052990 0.00600652 0.01617284 -0.00696834 0.02352343 -0.00618559 -0.00027442 0.000 0.000 0.000 -0.1856881 -0.5200068 -0.8337343 0.2431015 0.7978011 -0.5517381 0.9520617 -0.3051332 -0.0217278 39.6412 48.3160 77.5507 90. 90. 90. 0.000 0.000 0.000 SYMM P222 (top part is reciprocal matrix in the format: a*x b*x c*x a*y b*y c*y a*z b*z c*z where x is the x-ray beam axis and z is the spindle axis) DENZO (HKL2000) gives an equivalent matrix. XDS orientation parameters: CORRECT.LP ... REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM 30955 INDEXED SPOTS REFINED PARAMETERS: DISTANCE BEAM ORIENTATION CELL AXIS STANDARD DEVIATION OF SPOTPOSITION (PIXELS) 0.70 STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)0.08 SPACE GROUP NUMBER 16 UNIT CELL PARAMETERS 39.52848.15377.542 90.000 90.000 90.000 E.S.D. OF CELL PARAMETERS 4.0E-02 3.3E-02 3.8E-02 0.0E+00 0.0E+00 0.0E+00 REC. CELL PARAMETERS 0.025299 0.020767 0.012896 90.000 90.000 90.000 COORDINATES OF UNIT CELL A-AXIS -37.65011.269-4.236 COORDINATES OF UNIT CELL B-AXIS14.62441.546 -19.461 COORDINATES OF UNIT CELL C-AXIS-1.764 -32.374 -70.439 CRYSTAL MOSAICITY (DEGREES) 0.211 LAB COORDINATES OF ROTATION AXIS 0.62 0.007232 -0.004834 DIRECT BEAM COORDINATES (REC. ANGSTROEM) 0.003134 0.005401 1.020962 DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM1230.87 1260.93 DETECTOR ORIGIN (PIXELS) AT 1226.25 1252.96 CRYSTAL TO DETECTOR DISTANCE (mm) 259.04 LAB COORDINATES OF DETECTOR X-AXIS 1.00 0.00 0.00 LAB COORDINATES OF DETECTOR Y-AXIS 0.00 1.00 0.00 ... (XDS defines spindle as X and beam as Z) Converted to reciprocal lattice orientation matrix in mosflm axis conventions: (output from xds2mos; manual calculation is consistent with this output) -0.00273114 -0.00809777 -0.01150308 -0.00724876 -0.01754758 0.00521075 -0.02353677 0.00634416 -0.00027012 0.000 0.000 0.000 -0.11022162 -0.39811300 -0.91068616 -0.29254071 -0.86269689 0.41252918 -0.94988163 0.31189970 -0.02138535 39.5280 48.1530 77.5420 90. 90. 90. 0.000 0.000 0.000 As you can see they are different. You can note that the component of each vector along the mosflm-Z (spindle) axis is consistent, suggesting that it is only the angle of rotation around the spindle axis that is inconsistent between the two. I know that for mosflm and DENZO the orientation matrix defines the orientation of the reciprocal lattice when the spindle is at 0 deg. XDS seems to be using a different reference point. Why is this and what is the proper way to obtain the absolute reciprocal orientation at 0 deg from XDS? (If anyone wants to test this on their own, I can provide the frames I used to obtain these files.) Thanks, - Igor Petrik University of Illinois
Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO
Takanori and Pierre, Thank you for your quick responses. If you read my post you will see that I used the xds2mos.py script to convert the xds orientation to Mosflm format, but this gives me a result that is inconsistent with the matrix calculated directly by moslfm or DENZO. For orthorombic space group P222 there are only a hand full of equivalent matrices related by changing sign of one of the vectors. The matrices generated by XDS and Mosflm do not seem equivalent. Or maybe I'm missing something. Thanks, - Igor
