[ccp4bb] Expanding p4212 coordinates to p1
Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
[ccp4bb] copy FreeR - maintain resolution
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I would like to copy the freeR-flags from B.mtz to A.mtz. B.mtz has higher resolution. As far as I can tell the ccp4 utilities for doing so extend the resolution from A to match the resolution of B which results in mtzdmp displaying the wrong resolution of the data which I find very annoying. Is there a tool or switch to freerflag which only tags those reflections which are actually present in A? I am aware of the 'resolution' keyword in most of those programs but this is not what I want, because it might still alter the reflection list. Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPhpmzUxlJ7aRr7hoRAqxFAKCtWQyPxjoh/YeNQOU/vPnwJDdTcQCeJp5R krRZlS1cYIwlUOOfqKH2pvw= =FJYt -END PGP SIGNATURE-
[ccp4bb] Reminder: BCA Summer School 2012
This is a reminder that applications for the BCA/CCP4 Summer School in Protein Crystallography close ***1st May 2012***. The school will take place at Diamond from Tuesday 28th August - Sunday 2nd September 2012. Students and postdocs are welcome from wherever they are studying or working (not just if they are UK based). Lectures and computer tutorials will cover protein crystallographic methods from data collection to structure validation. Elspeth Garman will run a crystal cryo-cooling and manipulation workshop. Social activities will include a walking tour of Oxford, an evening boat cruise on the Thames, and a conference dinner. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Page.html
Re: [ccp4bb] copy FreeR - maintain resolution
Hi Tim I did not try it myself but it seems to be what you need: - import free-R flag from higher-resolution mtz as usual - remove reflections with missing FP: sftools (READ .mtz; SELECT ONLY COLUMN FP PRESENT; WRITE yyy.mtz) Andrey On 12 Apr 2012, at 10:00, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, I would like to copy the freeR-flags from B.mtz to A.mtz. B.mtz has higher resolution. As far as I can tell the ccp4 utilities for doing so extend the resolution from A to match the resolution of B which results in mtzdmp displaying the wrong resolution of the data which I find very annoying. Is there a tool or switch to freerflag which only tags those reflections which are actually present in A? I am aware of the 'resolution' keyword in most of those programs but this is not what I want, because it might still alter the reflection list. Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPhpmzUxlJ7aRr7hoRAqxFAKCtWQyPxjoh/YeNQOU/vPnwJDdTcQCeJp5R krRZlS1cYIwlUOOfqKH2pvw= =FJYt -END PGP SIGNATURE-
Re: [ccp4bb] copy FreeR - maintain resolution
TIm, As far as I can tell the ccp4 utilities for doing so extend the resolution from A to match the resolution of B which results in mtzdmp displaying the wrong resolution of the data which I find very annoying. I wasn't aware that mtzdump displays the wrong resolution: I thought I had fixed that problem years ago. Are you looking in the right place in the output? The resolution values on the RESO keyword in the header (use 'less' or a text editor on the MTZ file to see it, the 'header' is actually right at the end of the file - so it's really a 'trailer'!) refers to the resolution limits (d_max and d_min) calculated from the hkl values in the file, regardless of the contents of the data columns. That has always been the case: mtzdump is only reporting what's in the file header/trailer. Then the table printed out by mtzdump (see below for example) shows the d_max d_min for data in each column excluding NaNs (undefined values). These could well be different from the d_max d_min in the header/trailer and indeed from each other. So in the example below the d_max d_min for the hkl's is 64.829 1.4, and the values for each individual column, some of which are different from these, are shown in the table. Are you seeing something different from this, if so there's a bug somewhere that we should fix? Cheers -- Ian * Resolution Range : 0.000240.51020 ( 64.829 - 1.400 A ) * Sort Order : 1 2 3 0 0 * Space group = 'P 21 21 21' (number 19) OVERALL FILE STATISTICS for resolution range 0.000 - 0.510 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 39 0 100.00 14.8 14.8 64.83 1.40 H H 2 NONE 0 44 0 100.00 16.5 16.5 64.83 1.40 H K 3 NONE 0 92 0 100.00 34.6 34.6 64.83 1.40 H L 4 NONE0.019.0 0 100.00 9.51 9.51 64.83 1.40 I FreeR_flag 5 NONE0.0 311.5 62138 31.1848.8448.84 19.96 2.00 F F 6 NONE0.014.6 62138 31.18 2.11 2.11 19.96 2.00 Q SIGF
Re: [ccp4bb] Expanding p4212 coordinates to p1
Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.chwrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
'echo symm x,y | cad' gives: Data line--- symm x,y **SYMMETRY OPERATOR ERROR** Error in interpreting symop X,Y I. On 12 April 2012 12:03, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
On 2nd thoughts I guess you could do it in a space group that's a supergroup of the plane group say with all l and all z = 0. Then you could use symm x,y,z and it would just ignore the z components (I think?). I. On 12 April 2012 12:11, Ian Tickle ianj...@gmail.com wrote: 'echo symm x,y | cad' gives: Data line--- symm x,y **SYMMETRY OPERATOR ERROR** Error in interpreting symop X,Y I. On 12 April 2012 12:03, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
[ccp4bb] SUMMARY [ccp4bb] copy FreeR - maintain resolution
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, you are right, the table lists the correct resolution limits, although this is not what my question aimed at. Andrey's suggestion sftools (READ .mtz; SELECT ONLY COLUMN FP PRESENT; WRITE yyy.mtz) is the solution I was looking for with FP replaced by the correct column label in .mtz Thanks for all replies, Tim On 04/12/12 12:29, Ian Tickle wrote: TIm, As far as I can tell the ccp4 utilities for doing so extend the resolution from A to match the resolution of B which results in mtzdmp displaying the wrong resolution of the data which I find very annoying. I wasn't aware that mtzdump displays the wrong resolution: I thought I had fixed that problem years ago. Are you looking in the right place in the output? The resolution values on the RESO keyword in the header (use 'less' or a text editor on the MTZ file to see it, the 'header' is actually right at the end of the file - so it's really a 'trailer'!) refers to the resolution limits (d_max and d_min) calculated from the hkl values in the file, regardless of the contents of the data columns. That has always been the case: mtzdump is only reporting what's in the file header/trailer. Then the table printed out by mtzdump (see below for example) shows the d_max d_min for data in each column excluding NaNs (undefined values). These could well be different from the d_max d_min in the header/trailer and indeed from each other. So in the example below the d_max d_min for the hkl's is 64.829 1.4, and the values for each individual column, some of which are different from these, are shown in the table. Are you seeing something different from this, if so there's a bug somewhere that we should fix? Cheers -- Ian * Resolution Range : 0.000240.51020 ( 64.829 - 1.400 A ) * Sort Order : 1 2 3 0 0 * Space group = 'P 21 21 21' (number 19) OVERALL FILE STATISTICS for resolution range 0.000 - 0.510 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 39 0 100.00 14.8 14.8 64.83 1.40 H H 2 NONE 0 44 0 100.00 16.5 16.5 64.83 1.40 H K 3 NONE 0 92 0 100.00 34.6 34.6 64.83 1.40 H L 4 NONE0.019.0 0 100.00 9.51 9.51 64.83 1.40 I FreeR_flag 5 NONE0.0 311.5 62138 31.1848.8448.84 19.96 2.00 F F 6 NONE0.014.6 62138 31.18 2.11 2.11 19.96 2.00 Q SIGF - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPhsbgUxlJ7aRr7hoRAoiQAJ40iW5HQkMGb0V261CtftQdy5HmBgCgxiDX UNPKF9di9WgjiwkKah+N4ho= =JtG1 -END PGP SIGNATURE-
Re: [ccp4bb] .CBF raw images in iMOSFLM- error
Dear all The problem was indeed the distance being written in mm rather than m, so some of our internal maths gave surprising results. This will be fixed in the next versions of iMosflm and Mosflm - barring finding any killer bugs I hope this will be released next week. On 11 Apr 2012, at 16:43, Harry wrote: Hi Yuri If you can put some of the images on our ftp site (instructions sent separately) we'll have a look. There was a problem a while ago when some Pilatus detectors changed from writing the distance in metres to writing it in millimetres, but no-one told us until iMosflm started having problems. On 11 Apr 2012, at 16:08, Yuri Pompeu wrote: Hello everyone, I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM utility and I get the following error message: Distance has refined to an unreasonable value This causes the program to freeze and not open the rest of the frames. Also it is not picking up the X and Y beam positions. It looks to me like its just simply not reading the image file HEADER properly. Anyone has encountered this before and has any ideas on how to get around/fix this? Thanks a lot! Yuri Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] Last call: CCP4 summer school at APS, in USA
Dear Colleagues, This is friendly but final reminder that Tuesday, April 17 is the application deadline for the fifth annual CCP4 Summer School From data collection to structure refinement and beyond. On-line application and all details about the school can be found on its web site: http://www.ccp4.ac.uk/schools/APS-2012/index.php We are looking forward to seeing you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: Sanishvili, Ruslan Sent: Tuesday, April 03, 2012 5:15 PM To: CCP4BB@JISCMAIL.AC.UK Cc: Sanishvili, Ruslan Subject: Application deadline approaching: CCP4 summer school at APS, in USA Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School From data collection to structure refinement and beyond is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world's leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
[ccp4bb] Defining consensus pattern for searching a motif in protein database(s)
Dear All I want to search SUMO interacting motif (SIM) in different protein data bases and also in the given protein sequences. Does anyone can provide me the PROSITE AC and/or ID for the SIM motif? I will be grateful if you provide me MATRIX for the SIM motif profile. I do not know much about how to define the amino acid sequence ‘pattern’ for searching the motif in the ‘Prosite’ tool. For an example AP endonuclease contains following consensus pattern D-[ST]-[FY]-[RP]-[KHQ]-x(7,8)-[FYWD]-[ST]-[FYW] (2) What is the meaning of x(7,8) and (2) in the above example. Any literature or article regarding this topic is most welcome. Thank you in advance Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
Re: [ccp4bb] .CBF raw images in iMOSFLM- error
Thank you Harry for letting us know about this! Could you please send an update to the list when the new version is out? (I would also like to process images from BNL x25 (Pilatus 6M), and I'm sure there are others in the same boat). Best wishes, Kip On Thu, 12 Apr 2012 15:39:48 +0100 Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Dear all The problem was indeed the distance being written in mm rather than m, so some of our internal maths gave surprising results. This will be fixed in the next versions of iMosflm and Mosflm - barring finding any killer bugs I hope this will be released next week. On 11 Apr 2012, at 16:43, Harry wrote: Hi Yuri If you can put some of the images on our ftp site (instructions sent separately) we'll have a look. There was a problem a while ago when some Pilatus detectors changed from writing the distance in metres to writing it in millimetres, but no-one told us until iMosflm started having problems. On 11 Apr 2012, at 16:08, Yuri Pompeu wrote: Hello everyone, I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM utility and I get the following error message: Distance has refined to an unreasonable value This causes the program to freeze and not open the rest of the frames. Also it is not picking up the X and Y beam positions. It looks to me like its just simply not reading the image file HEADER properly. Anyone has encountered this before and has any ideas on how to get around/fix this? Thanks a lot! Yuri Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] Yeast plasmid DNA miniprep problem
Sorry for the non-ccp4 question. I am having trouble to miniprep plasmid from yeast. The plasmid is pCTCON2 and the yeast strain is EBY100. I am using Zymoprep Yeast Plasmid Miniprep II kit. I grow the culture in SDCAA medium to OD0.3 and spin down 1.5ml cells. The pellet was resuspended in solution 1 supplemented with Zymolyase and was incubated for 1 hr. I followed the manual exactly for the rest steps. However, I have never been able to recover any plasmid. There is nothing or smear in the agarose gel and there is no colony after transformation to DH5alpha after one overnight incubation at 37. The existence of the plasmid in the yeast has been confirmed by the ability to grow in the nutrition deficient medium SDCAA and the expression of plasmid protein in SGCAA medium was observed by FACS. I am wondering if someone here can shine some light on this issue. Any thoughts or suggestions are welcome. Thank you. Zhen The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] Expanding p4212 coordinates to p1
I am confused by the discussion on this message. Although it says plane group I assume it really is a normal 3D tetragonal space group, P42(1)2 So Eleanor's suggestion should work and sftools expand command will do the job as well. Bart On 12-04-12 05:03 AM, Eleanor Dodson wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and "generate chains by symmetry operators" eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with "expand 1" to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command "expand 1", and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA,
Re: [ccp4bb] Expanding p4212 coordinates to p1
Yes I was also confused by the fact that P4212 is obviously a space group (upper case 'P') whereas p4 and p1 are plane groups (lower case 'p'), as stated. Not sure what 'p2121' is though, I assumed it was somehow related to the p2gg plane group (no 8). Also there's no plane group 'p6212', but then there's no space group 'P6212' either. Perhaps the original poster could clarify and take care with his P's and p's? Cheers -- Ian On 12 April 2012 16:51, Bart Hazes bha...@ualberta.ca wrote: I am confused by the discussion on this message. Although it says plane group I assume it really is a normal 3D tetragonal space group, P42(1)2 So Eleanor's suggestion should work and sftools expand command will do the job as well. Bart On 12-04-12 05:03 AM, Eleanor Dodson wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
[ccp4bb] RESEARCH DIRECTOR IN STRUCTURAL BIOLOGY/BIOPHYSICS TENURE-TRACK GROUP LEADERS, Helsinki
- please do not reply to me but to the email address mentioned. www.biocenter.helsinki.fi/bi RESEARCH DIRECTOR IN STRUCTURAL BIOLOGY/BIOPHYSICS The lnstitute of Biotechnology is a leading European research institute with a mission to increase knowledge in cross- disciplinary biology and biotechnology. The Institute has a budget of 23 M€ and state-of-the-art facilities in imaging, model organisms, proteomics, genomics, crystallography and NMR. We seek a proven leader for a Research Director level position in Structural Biology/Biophysics. The successful candidate has an outstanding track record as a Principal Investigator in research on any aspects of structural biology and biophysics, including (but not limited to): X-ray crystallography, NMR spectroscopy, electron microscopy, bioenergetics, single molecule studies, and computational methods. The successful candidate is expected to develop an independent externally funded line of research and to take responsibility for developing the area of Structural Biology/Biophysics at the Institute of Biotechnology. Appointments are expected to lead to tenure. A globally competitive remuneration package and 3-year startup funds are negotiable. Applications should include a presentation of past achievements (max 2 pages; contributions made and recognition received) and research interests (max. 5 pages), curriculum vitae, list of 20 publications (with citation numbers), and three letters of reference. Applications and letters of reference are to be submitted at www.biocenter.helsinki.fi/bi/ recruit no later than 10 June 2012. For further information and detailed contacts, please visit www.biocenter.helsinki. fi/bi/recruit or contact Director Tomi P. Mäkelä directly: bi-direc...@helsinki.fi, tel. +358 9 19159359. TENURE-TRACK GROUP LEADERS The lnstitute of Biotechnology is a leading European research institute with a mission to increase knowledge in cross- disciplinary biology and biotechnology. The Institute has a budget of 23 M€ and state-of-the-art facilities in imaging, model organisms, proteomics, genomics, crystallography and NMR. We seek outstanding candidates for tenure-track Group Leader positions in Molecular Cell Biology, Genomics and Quantitative Biology, Plant Biology, Developmental Biology, or Structural Biology and Biophysics. Successful candidates have a suitable strong track record including a PhD/ MD and post-doctoral experience in an international setting and are expected to develop an independent externally funded line of research. Appointments are for a six-year period with a possibility for extensions based on evaluations every 4 years and tenuring after 12 years. A globally competitive remuneration package and 3-year startup funds are negotiable. Applications should include a presentation of past achievements (max 2 pages; contributions made and recognition received) and research interests (max. 5 pages), curriculum vitae, list of no more than 20 publications (with citation numbers), and three letters of reference. Applications and letters of reference are to be submitted at www. biocenter.helsinki.fi/bi/recruit no later than 10 June 2012. For further information and detailed contacts, please visit www.biocenter.helsinki.fi/bi/recruit or contact Director Tomi P. Mäkelä directly: bi-direc...@helsinki.fi, tel. +358 9 19159359. CURRENT GROUP LEADERS Structural Biology and Biophysics Arto Annila Dennis Bamford Sarah Butcher Adrian Goldman Hideo Iwai Perttu Permi Markku Varjosalo Mårten Wikström Core facilities: Cryo-EM NMR Protein Crystallisation Proteomics Developmental Biology Jukka Jernvall Ulla Pirvola Mart Saarma Osamu Shimmi Irma Thesleff Genomics Quantitative Biology Petri Auvinen Mikko Frilander Yrjö Helariutta Liisa Holm Ari Löytynoja Ari Pekka Mähönen Tomi Mäkelä Alan Schulman Core facilities: DNA Sequencing Genomics Genome Biology unit Molecular Cell Biology Ville Hietakangas Eija Jokitalo Jussi Jäntti Pekka Lappalainen Päivi Ojala Maria Vartiainen Core facilities: Electron Microscopy Light Microscopy
Re: [ccp4bb] Expanding p4212 coordinates to p1
Hi,
I was referring to P42(1)2, which is the CCP4 symmetry number 90.
I am working on 2D membrane protein crystals and cryo-electron microscopy
images of these, where I initially deal with two-dimensional projection images,
which are eventually merged into a 3D dataset. Therefore my sloppy formulation.
Thanks for the suggestions from several people on this list.
What I am doing now, and what works well, is:
\rm -f SCRATCH/merge3Dref-clean.mtz
#
${bin_ccp4}/sftools eof
read SCRATCH/merge3Dref.mtz
sort h k l
set spacegroup
${CCP4_SYM}
select phaerr
select invert
purge
y
write SCRATCH/merge3Dref-clean.mtz
quit
eof
#
\rm -f SCRATCH/merge3Dref-clean-p1.mtz
#
${bin_ccp4}/cad hklin1 SCRATCH/merge3Dref-clean.mtz hklout
SCRATCH/merge3Dref-clean-p1.mtz eof
reso overall 1 1
outlim spacegroup 1
labin file 1 all
end
eof
#
\rm -f merge3Dref.mtz
#
${bin_ccp4}/sftools eof
read SCRATCH/merge3Dref-clean-p1.mtz
sort h k l
set spacegroup
1
reduce matrix 1 0 0 0 1 0 0 0 1
write merge3Dref.mtz
quit
eof
#
All the best,
Henning.
On Apr 12, 2012, at 6:10 PM, Ian Tickle wrote:
Yes I was also confused by the fact that P4212 is obviously a space
group (upper case 'P') whereas p4 and p1 are plane groups (lower case
'p'), as stated. Not sure what 'p2121' is though, I assumed it was
somehow related to the p2gg plane group (no 8). Also there's no plane
group 'p6212', but then there's no space group 'P6212' either.
Perhaps the original poster could clarify and take care with his P's and p's?
Cheers
-- Ian
On 12 April 2012 16:51, Bart Hazes bha...@ualberta.ca wrote:
I am confused by the discussion on this message. Although it says plane
group I assume it really is a normal 3D tetragonal space group, P42(1)2
So Eleanor's suggestion should work and sftools expand command will do the
job as well.
Bart
On 12-04-12 05:03 AM, Eleanor Dodson wrote:
Apologies - I didn't notice the plane group..
Although I think if the sym ops are correctly listed in the P4121 file they
will just be applied as given..
Eleanor
On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote:
I didn't realise the CCP4 suite could handle the plane groups: where
are they listed (they're not in symop.lib or syminfo.lib)? Or are
they doing some clever projections of the space groups?
Cheers
-- Ian
On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Cad will do this correctly
Reflection utilitied - merge mtz ( rather confusing job title - sorry..)
mtz in - the P4121.mtz data
Output - P41212-ext.mtz
Defne mtz output
Select define limit for refl;action by Laue code select P1
then you will get a list of all P1 reflections with phases correctly
modified.
If you really want to work in P1 you will need to change the space group
in
P41212-ext.mtz
Easiest way is
mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz
SYMM P1
end
DONT change the G of P41212.mtz before doing the extension - the program
needs the P41212 sym ops to change the phases correctly..
If you want the coordinates extended too
use pdbset to get a P1 set of cds.. (Coordinate utilities
Edit pdb
select pdbset and generate chains by symmetry operators
eleanor
Eleanor
On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch
wrote:
Hi Everybody,
I am working in a P4212 plane group, which is a p4 symmetric structure
with a screw axis in addition. My map has in the unit cell two 4-fold
symmetric structures, one if which is upside-down with respect to the
other
one. If using expand in sftools, then the resulting map is p4
symmetrized
in the center between two p4-symmetric structures, which is wrong. This
is
probably the phase origin problem referred to here:
http://www.ccp4.ac.uk/dist/html/sftools.html#expand
Would anybody have a suggestion how I can expand the p4212 MTZ file to
full p1, but with properly respecting the symmetry phase origin?
My illiterate guess would be to either
1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then
use
sftools with expand 1 to create the full reflection sets in p1; then
shift
back by (180.0;0.0); or
2) use sftools with the command expand 1, and then modify (invert?)
the
phases of the reflections in the quadrants that have wrong phases.
In option 1) I am not sure if it is possible to shift phase origin,
while
staying in p4212 symmetry. How could I do that?
In option 2) I would probably get into deep water the next time I work
with another symmetry, like p6212, or p2121, where I would have to deal
not
with quadrants but with triangles of 60deg angle?
Any suggestions would be highly appreciated.
All the best,
Henning.
Henning Stahlberg, PhD
Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
http://c-cina.org | Tel. +41-61-387 32 62
[ccp4bb] symmetry related molecules
Hi guys, Does any body know if there is a software that would analyse the interface between a protein molecule and its symmetry related molecules in the crystal structure? Thank you, Maher
Re: [ccp4bb] symmetry related molecules
CONTACT (CCP4) , PISA, ProFunc What do you mean by analyse ? Residues contacting each other, surface complementarity, buried surface area ? Jürgen On Apr 13, 2012, at 12:15 AM, Maher Alayyoubi wrote: Hi guys, Does any body know if there is a software that would analyse the interface between a protein molecule and its symmetry related molecules in the crystal structure? Thank you, Maher .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
