Re: [ccp4bb] imosflm with multiple data sets
Thanks Frank, Luke forgot to tell me that he had actually implemented this ! For those wishing to use this option, the Matrix line has to be dragged and dropped on the Sector line of the segment of data that you want to assign the matrix to, NOT to the Matrix line of that sector. I agree Frank, it is very tedious to have to have to drag past all the images, we will change things so that the collapsing the sector still leaves the Matrix visible. While on this topic, Clemens Vonrhein kindly pointed out to me that I had not read the original Email carefully enough, in that the second sector of data had an oscillation range of 0-180, the same as the first sector, but the phi value had been changed by 180 degrees between the two runs. Thus, in order to get the matrix from the first sector to correctly predict images from the second sector, 180 degrees needs to be added to the phi values of each image. This is easily done by manually entering the phi values for the first image of the second sector, then this will be automatically propagated for all following images. Andrew On 18 Aug 2009, at 06:55, Frank von Delft wrote: Actually, drag-and-drop DOES work, and is *dead* handy! (But a considerable annoyance: you HAVE to open the sector to be able to click on the matrix line -- and then you have to drag that matrix past all the 300 (or whatever) images to get to the next sector. For many images, this really slow. Better to put matrix and images on separate sub-nodes.) Andrew Leslie wrote: Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way. Then read in the second segment of data. You will notice that in this second segment, underneath the Sector name, there is a line starting Matrix and this will be Unknown. If you go to the Matrix line of the first segment, the matrix will have a name (based on the image template). Double click on the name of the matrix. A popup window (Matrix properties) will appear. Click on the save matrix file icon (a blue disc) and save the matrix with an appropriate filename. Now go to the Matrix line of the second segment, double click (on Unknown) as before and this time click on the Open matrix file icon (a folder) and read in the matrix that you saved from the first sector. You can now process the second segment using this matrix. It would be even nicer if you could drag and drop the matrix, this is on our to do list. Best wishes, Andrew On 17 Aug 2009, at 13:33, Brett, Thomas wrote: I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
Re: [ccp4bb] imosflm with multiple data sets
Hi Hari, This is slightly different, and was indeed a bug in imosflm version 1.0.0. In the new version, released last week (1.0.3) this bug is fixed, so that if images from multiple sectors are used in indexing, the same matrix is defined for all those sectors (ie they will not be marked as Unknown. Best wishes, Andrew On 17 Aug 2009, at 14:53, hari jayaram wrote: I didnt realize the following: You read in images from the two wedges collected with the same crystal orientation. mydata_1_###.img mydata_101_###.img Now when you index ,if you say use images from both datasets mydata_1_###.img use image 1,90 mydata_101_###.img use image 30 , 120 The matrix for the second wedge (mydata_101_###.img) is still marked unknown? Isnt this different from the behaviour in the X- mosflm . SHould the matrixes be the same since the orientation was calculated using images from both. Now , If I did not force the second wedge to have the same matrix , using the save to file and read from file method you just described , does the new imosflm use the last calculated matrix from the running session or calculate a new matrix ?..I guess I have to check some of the data I processed with my erroneous assumption to make sure that the matrixes for the two wedges are the same . Thanks for clarifying this.. hari On Mon, Aug 17, 2009 at 9:13 AM, Andrew Leslieand...@mrc-lmb.cam.ac.uk wrote: Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way. Then read in the second segment of data. You will notice that in this second segment, underneath the Sector name, there is a line starting Matrix and this will be Unknown. If you go to the Matrix line of the first segment, the matrix will have a name (based on the image template). Double click on the name of the matrix. A popup window (Matrix properties) will appear. Click on the save matrix file icon (a blue disc) and save the matrix with an appropriate filename. Now go to the Matrix line of the second segment, double click (on Unknown) as before and this time click on the Open matrix file icon (a folder) and read in the matrix that you saved from the first sector. You can now process the second segment using this matrix. It would be even nicer if you could drag and drop the matrix, this is on our to do list. Best wishes, Andrew On 17 Aug 2009, at 13:33, Brett, Thomas wrote: I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
[ccp4bb] imosflm with multiple data sets
I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
Re: [ccp4bb] imosflm with multiple data sets
Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way. Then read in the second segment of data. You will notice that in this second segment, underneath the Sector name, there is a line starting Matrix and this will be Unknown. If you go to the Matrix line of the first segment, the matrix will have a name (based on the image template). Double click on the name of the matrix. A popup window (Matrix properties) will appear. Click on the save matrix file icon (a blue disc) and save the matrix with an appropriate filename. Now go to the Matrix line of the second segment, double click (on Unknown) as before and this time click on the Open matrix file icon (a folder) and read in the matrix that you saved from the first sector. You can now process the second segment using this matrix. It would be even nicer if you could drag and drop the matrix, this is on our to do list. Best wishes, Andrew On 17 Aug 2009, at 13:33, Brett, Thomas wrote: I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
Re: [ccp4bb] imosflm with multiple data sets
I didnt realize the following: You read in images from the two wedges collected with the same crystal orientation. mydata_1_###.img mydata_101_###.img Now when you index ,if you say use images from both datasets mydata_1_###.img use image 1,90 mydata_101_###.img use image 30 , 120 The matrix for the second wedge (mydata_101_###.img) is still marked unknown? Isnt this different from the behaviour in the X- mosflm . SHould the matrixes be the same since the orientation was calculated using images from both. Now , If I did not force the second wedge to have the same matrix , using the save to file and read from file method you just described , does the new imosflm use the last calculated matrix from the running session or calculate a new matrix ?..I guess I have to check some of the data I processed with my erroneous assumption to make sure that the matrixes for the two wedges are the same . Thanks for clarifying this.. hari On Mon, Aug 17, 2009 at 9:13 AM, Andrew Leslieand...@mrc-lmb.cam.ac.uk wrote: Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way. Then read in the second segment of data. You will notice that in this second segment, underneath the Sector name, there is a line starting Matrix and this will be Unknown. If you go to the Matrix line of the first segment, the matrix will have a name (based on the image template). Double click on the name of the matrix. A popup window (Matrix properties) will appear. Click on the save matrix file icon (a blue disc) and save the matrix with an appropriate filename. Now go to the Matrix line of the second segment, double click (on Unknown) as before and this time click on the Open matrix file icon (a folder) and read in the matrix that you saved from the first sector. You can now process the second segment using this matrix. It would be even nicer if you could drag and drop the matrix, this is on our to do list. Best wishes, Andrew On 17 Aug 2009, at 13:33, Brett, Thomas wrote: I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
Re: [ccp4bb] imosflm with multiple data sets
Actually, drag-and-drop DOES work, and is *dead* handy! (But a considerable annoyance: you HAVE to open the sector to be able to click on the matrix line -- and then you have to drag that matrix past all the 300 (or whatever) images to get to the next sector. For many images, this really slow. Better to put matrix and images on separate sub-nodes.) Andrew Leslie wrote: Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way. Then read in the second segment of data. You will notice that in this second segment, underneath the Sector name, there is a line starting Matrix and this will be Unknown. If you go to the Matrix line of the first segment, the matrix will have a name (based on the image template). Double click on the name of the matrix. A popup window (Matrix properties) will appear. Click on the save matrix file icon (a blue disc) and save the matrix with an appropriate filename. Now go to the Matrix line of the second segment, double click (on Unknown) as before and this time click on the Open matrix file icon (a folder) and read in the matrix that you saved from the first sector. You can now process the second segment using this matrix. It would be even nicer if you could drag and drop the matrix, this is on our to do list. Best wishes, Andrew On 17 Aug 2009, at 13:33, Brett, Thomas wrote: I am an imosflm novice and have a relatively simple question. I have a 360 deg data set collected in two swathes of 180 deg (one with phi=0 and omega going 0-180 and the second with phi = 180 and omega going 0-180). What is the easiest way to process the two datasets using a matching orientation matrix (or one rotated by 180 deg as it were) so that all the data can be merged together. Is there an easy way to do it in imosflm or must one process the two sets separately and then manipulate later with pointless before scalling and merging everything together? Thanks in advance. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110
