[ccp4bb] P21221 to P21212 conversion
Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya
Re: [ccp4bb] P21221 to P21212 conversion
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] P21221 to P21212 conversion
Hi, My case is old b is changed to c (scenario 2 as you explained) or hkl is changed to hlk. Thanks for the help Shya On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt merr...@u.washington.eduwrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] P21221 to P21212 conversion
On 5/7/12 4:09 PM, Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya Hi Shya - Under the Scale tab of HKL2000, you'll see a button near the bottom labeled Reindex. Clicking this brings up a dialog box with the reindexing conventions appropriate to your spacegroup. For P orthorhombic, there are only two choices: hkl - klh, or hkl - lhk. If you have P21221, and want to go to P21212, you want hkl -lhk. HOWEVER, there seems to be a bug in this particular reindexing (or maybe the options are written confusingly). You want to choose the wrong option (number 2 in the list presented), as the two options seem to be reversed. You'll know that you got it right by inspection of the scaling log file - look at the systematic absence table at the bottom. Also check that the unit cell axes were permuted in the correct way - you want your old b axis to be your new c axis. Once you select the correct reindexing (make sure you apply it to all datasets being scaled at the same time), you click Reindex in the popup dialog, and this triggers another round of scaling with the reindexing included. This reindexing is sticky - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] P21221 to P21212 conversion
On Monday, May 07, 2012 01:42:58 pm Shya Biswas wrote: Hi, My case is old b is changed to c (scenario 2 as you explained) or hkl is changed to hlk. Thanks for the help hkl - hkl gives an inverted coordinate system. You don't want that. Ethan Shya On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt merr...@u.washington.eduwrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] P21221 to P21212 conversion
Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.eduwrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
HKL or most probably SCALEPACK know nothing above point group if you do not tell it. But even in GUI one can use hkl matrix with the needed transformation matrix :-\ What is nice about it that it will never let you to change the handedness of the data, so anomalous signal is safe… FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 7, 2012, at 23:48 , Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
Forget to tell that all is done in the menu Macros : - ( FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 7, 2012, at 23:48 , Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
The program that does the indexing in HKL is Denzo. Denzo doesn't care about the space group. It cares about the point group (cf. Ethan's point) and the cell dimensions, because it integrates the data without regard to the symmetry expressed in the intensities - however it does take notice of the restrictions placed on cell dimensions by point groups. Denzo therefore picks primitive orthorhombic cells in abc. Scalepack scales the integrated data but does not reindex the data if you tell it the space group is P22121. Therefore unit cell choice in HKL is by default driven by cell edge size. Scalepack has the ability to reindex the data, for those of us that like to work in P21212 rather than P22121. On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt Scaling is done in a point group, not a space group. My quibble with this statement is that the output reflection data from Scalepack differs depending on what space group you tell it, since systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. The number of reflections affected is quite small, of course. Phil Jeffrey Princeton On 5/7/12 4:48 PM, Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu mailto:merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
If one make a proper transformation :-/ and supply a correct space group, absent reflections will be printed in the end of scale.log Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 8, 2012, at 24:00 , Phil Jeffrey wrote: The program that does the indexing in HKL is Denzo. Denzo doesn't care about the space group. It cares about the point group (cf. Ethan's point) and the cell dimensions, because it integrates the data without regard to the symmetry expressed in the intensities - however it does take notice of the restrictions placed on cell dimensions by point groups. Denzo therefore picks primitive orthorhombic cells in abc. Scalepack scales the integrated data but does not reindex the data if you tell it the space group is P22121. Therefore unit cell choice in HKL is by default driven by cell edge size. Scalepack has the ability to reindex the data, for those of us that like to work in P21212 rather than P22121. On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt Scaling is done in a point group, not a space group. My quibble with this statement is that the output reflection data from Scalepack differs depending on what space group you tell it, since systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. The number of reflections affected is quite small, of course. Phil Jeffrey Princeton On 5/7/12 4:48 PM, Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu mailto:merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
Why do you like P21212 better than P22121? JPK On Mon, May 7, 2012 at 4:00 PM, Phil Jeffrey pjeff...@princeton.edu wrote: The program that does the indexing in HKL is Denzo. Denzo doesn't care about the space group. It cares about the point group (cf. Ethan's point) and the cell dimensions, because it integrates the data without regard to the symmetry expressed in the intensities - however it does take notice of the restrictions placed on cell dimensions by point groups. Denzo therefore picks primitive orthorhombic cells in abc. Scalepack scales the integrated data but does not reindex the data if you tell it the space group is P22121. Therefore unit cell choice in HKL is by default driven by cell edge size. Scalepack has the ability to reindex the data, for those of us that like to work in P21212 rather than P22121. On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt Scaling is done in a point group, not a space group. My quibble with this statement is that the output reflection data from Scalepack differs depending on what space group you tell it, since systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. The number of reflections affected is quite small, of course. Phil Jeffrey Princeton On 5/7/12 4:48 PM, Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu mailto:merritt@u.washington.**edu merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- * Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu mailto:j-keller2@**northwestern.eduj-kell...@northwestern.edu * -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
On Monday, May 07, 2012 02:00:43 pm Phil Jeffrey wrote: On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt Scaling is done in a point group, not a space group. My quibble with this statement is that the output reflection data from Scalepack differs depending on what space group you tell it, since systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. The number of reflections affected is quite small, of course. The statement is correct, but the scalepack behavior is IMHO a bad thing. Therefore I always tell it to scale in the pointgroup (P222 in this case) and I correct the space group later. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] P21221 to P21212 conversion
Hi Matt, It worked really well in HKL 2000 reindex option, sorry about the confusion before, I wanted hkl to lhk. as you pointed out the second one gave me what I wanted. thanks, Shya On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mfrank...@nysbc.orgwrote: On 5/7/12 4:09 PM, Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya Hi Shya - Under the Scale tab of HKL2000, you'll see a button near the bottom labeled Reindex. Clicking this brings up a dialog box with the reindexing conventions appropriate to your spacegroup. For P orthorhombic, there are only two choices: hkl - klh, or hkl - lhk. If you have P21221, and want to go to P21212, you want hkl -lhk. HOWEVER, there seems to be a bug in this particular reindexing (or maybe the options are written confusingly). You want to choose the wrong option (number 2 in the list presented), as the two options seem to be reversed. You'll know that you got it right by inspection of the scaling log file - look at the systematic absence table at the bottom. Also check that the unit cell axes were permuted in the correct way - you want your old b axis to be your new c axis. Once you select the correct reindexing (make sure you apply it to all datasets being scaled at the same time), you click Reindex in the popup dialog, and this triggers another round of scaling with the reindexing included. This reindexing is sticky - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] P21221 to P21212 conversion
Hi, i just repeated the MR using the reindexed dataset (hkl to lhk) and it gave me the right solution. thanks, Shya On Mon, May 7, 2012 at 5:39 PM, Edward A. Berry ber...@upstate.edu wrote: Now given that the MR soluiton was obtained in the (preparing to duck) nonstandard setting, what is the transform to apply to that solution in pdbset to get the solution in the standard setting? Or is it easier to just repeat the MR? eab Shya Biswas wrote: Hi Matt, It worked really well in HKL 2000 reindex option, sorry about the confusion before, I wanted hkl to lhk. as you pointed out the second one gave me what I wanted. thanks, Shya On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mfrank...@nysbc.org mailto:mfrank...@nysbc.org wrote: On 5/7/12 4:09 PM, Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya Hi Shya - Under the Scale tab of HKL2000, you'll see a button near the bottom labeled Reindex. Clicking this brings up a dialog box with the reindexing conventions appropriate to your spacegroup. For P orthorhombic, there are only two choices: hkl - klh, or hkl - lhk. If you have P21221, and want to go to P21212, you want hkl -lhk. HOWEVER, there seems to be a bug in this particular reindexing (or maybe the options are written confusingly). You want to choose the wrong option (number 2 in the list presented), as the two options seem to be reversed. You'll know that you got it right by inspection of the scaling log file - look at the systematic absence table at the bottom. Also check that the unit cell axes were permuted in the correct way - you want your old b axis to be your new c axis. Once you select the correct reindexing (make sure you apply it to all datasets being scaled at the same time), you click Reindex in the popup dialog, and this triggers another round of scaling with the reindexing included. This reindexing is sticky - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374 tel:%28212%29%20939-0660%**20ext.%209374
