Re: [ccp4bb] Unit Cell of Ensemble must be orthogonal
This means that the unit cell in the MTZ file obtained from the density is non-orthogonal, i.e. the angles are not all 90 degrees. Although in principle we could have made it possible to use non-orthogonal unit cells, it would make things more difficult for us and, since the density has to be cut out and put in a new unit cell with lots of space around it anyway, there's no reason not to choose an orthogonal unit cell. If you use Kevin Cowtan's cmapcut to cut out the density for MR, it will choose an orthogonal unit cell by default. This reminds me that I must update our web page on using electron density as a model! Before Kevin's nice cmapcut program (and Tom Terwilliger's equally nice phenix.cut_out_density procedure) it was a laborious process that required a very long explanation. Best wishes, Randy Read On 17 Jan 2013, at 03:20, Wei Feng wrote: Dear all, When I used PHASER to do a molecular replacement and define ensemble via map (mtz file), the program stoped very soon. The log file showed that Unit Cell of Ensemble must be orthogonal. I tried many ways to generate the map file, but the results are the same. Can anyone help me to solve this problem? Thanks a lot! Wei -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] statistics from a structure factors file
Hi all, maybe a silly question, but I can't figure this out. Is there a piece of software to calculate Table I statistics such as Rsym, Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already containing merged structure factors? That is, if somebody hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] statistics from a structure factors file
Hi Sebastiano, If they hand you an *unmerged* mtz file containing scaled data you can do this, by remerging the data with Scala or Aimless. Equivalently the unmerged output of scalepack or XSCALE (or XDS CORRECT) If however you have merged data then you have lost this information, though completeness and Mn(I/sig) are available, but not Rsym / Rpim / multiplicity etc. Unmerged files are good :o) Cheerio, Graeme On 17 January 2013 09:18, Sebastiano Pasqualato sebastiano.pasqual...@gmail.com wrote: Hi all, maybe a silly question, but I can't figure this out. Is there a piece of software to calculate Table I statistics such as Rsym, Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already containing merged structure factors? That is, if somebody hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] statistics from a structure factors file
Thanks Graeme. Long live and prosper to the unmerged files, then. ciao, s On Jan 17, 2013, at 10:37 AM, Graeme Winter graeme.win...@gmail.com wrote: Hi Sebastiano, If they hand you an *unmerged* mtz file containing scaled data you can do this, by remerging the data with Scala or Aimless. Equivalently the unmerged output of scalepack or XSCALE (or XDS CORRECT) If however you have merged data then you have lost this information, though completeness and Mn(I/sig) are available, but not Rsym / Rpim / multiplicity etc. Unmerged files are good :o) Cheerio, Graeme On 17 January 2013 09:18, Sebastiano Pasqualato sebastiano.pasqual...@gmail.com wrote: Hi all, maybe a silly question, but I can't figure this out. Is there a piece of software to calculate Table I statistics such as Rsym, Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already containing merged structure factors? That is, if somebody hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] statistics from a structure factors file
These days I always ask people to send me the XDS_ASCII.HKL file if they used XDS, then I can be sure that it is really UNMERGED, which has many advantages (and I can read it into hkl2map, shelxc or xprep directly). George On 01/17/2013 10:37 AM, Graeme Winter wrote: Hi Sebastiano, If they hand you an *unmerged* mtz file containing scaled data you can do this, by remerging the data with Scala or Aimless. Equivalently the unmerged output of scalepack or XSCALE (or XDS CORRECT) If however you have merged data then you have lost this information, though completeness and Mn(I/sig) are available, but not Rsym / Rpim / multiplicity etc. Unmerged files are good :o) Cheerio, Graeme On 17 January 2013 09:18, Sebastiano Pasqualato sebastiano.pasqual...@gmail.com wrote: Hi all, maybe a silly question, but I can't figure this out. Is there a piece of software to calculate Table I statistics such as Rsym, Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already containing merged structure factors? That is, if somebody hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Crystallization buffer pH optimization
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mike, I'd be surprised if the book was from Hampton: The pH-value of Hampton solutions refers to the stock solution of the buffer before setting up the final solution, and can differ a lot from your drop's pH - e.g. in the presence of Imidazole or other buffering precipitants. I might be wrong but believe that if you prepare the solution yourself, a chemist should be able to explain to how to do the maths yourself. Regards, Tim On 01/17/2013 06:38 AM, Mike John wrote: Hello, Shameful and sorry for asking this simple question, it looks like this when first starting a new setup in so-called structural biology. I remmeber a book of, probably, Hampton, in which there are tables of pH optimization for many buffers. For example for buffer TRIS, the table will list how many drops NaOH/HCl needed to change pH from 7.0 to 7.2, etc. This is useful for crystallization pH optimization, where can I buy or download this info? Alternatives? Thank you very much! Mike - -- - -- 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/ iD8DBQFQ982/UxlJ7aRr7hoRAldcAKCJCD3q9WGdEMC/UuF7UVKv5k30RgCfR7r1 ajsWl16ZEyXqSASuvIERQWM= =G64g -END PGP SIGNATURE-
Re: [ccp4bb] ccp4 update
Dear Eugene ccp4um doesn't work for me at all (update worked fine up until #012). node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um Traceback (most recent call last): File ccp4um, line 17, in module shutil.copy2 ( fname,fname1 ) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' Did I do something wrong? Or is it just that there's nothing to update? Cheers -- Ian On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote: Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing update :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers, I've come to appreciate the CCP4 update functionality, which, in our multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. Update 012 removed that script with no immediately obvious replacement. Was that on purpose? Is there a way of updating CCP4 from the command line without calling CCP4i? Thanks Andreas (from update.log: [Thu Jan 3 2013 11:00:21] Ready to make changes --- applying update 6.3.0-012 --- update header read --- creating restore package, please wait ... --- done ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical.
Re: [ccp4bb] ccp4 update
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, did you source the ccp4 input script so that variables like CCP4 are set? IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' looks like CCP4 is an empty string. Best, Tim On 01/17/2013 01:44 PM, Ian Tickle wrote: Dear Eugene ccp4um doesn't work for me at all (update worked fine up until #012). node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um Traceback (most recent call last): File ccp4um, line 17, in module shutil.copy2 ( fname,fname1 ) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' Did I do something wrong? Or is it just that there's nothing to update? Cheers -- Ian On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote: Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing update :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers, I've come to appreciate the CCP4 update functionality, which, in our multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. Update 012 removed that script with no immediately obvious replacement. Was that on purpose? Is there a way of updating CCP4 from the command line without calling CCP4i? Thanks Andreas (from update.log: [Thu Jan 3 2013 11:00:21] Ready to make changes --- applying update 6.3.0-012 --- update header read --- creating restore package, please wait ... --- done ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- 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/ iD8DBQFQ9/O7UxlJ7aRr7hoRAhVVAJ4yomsoCO3CeOJ13XteKAt0B95yTgCgoqnq 8PgeNrjcFS3vLeuBk9cBjHM= =IwT/ -END PGP SIGNATURE-
Re: [ccp4bb] ccp4 update
Yes it's my .login so it's always set up: node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-47 echo $CCP4 /software/CCP4-6.3.0/ccp4-6.3.0 Cheers -- Ian On 17 January 2013 12:51, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, did you source the ccp4 input script so that variables like CCP4 are set? IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' looks like CCP4 is an empty string. Best, Tim On 01/17/2013 01:44 PM, Ian Tickle wrote: Dear Eugene ccp4um doesn't work for me at all (update worked fine up until #012). node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um Traceback (most recent call last): File ccp4um, line 17, in module shutil.copy2 ( fname,fname1 ) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' Did I do something wrong? Or is it just that there's nothing to update? Cheers -- Ian On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote: Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing update :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers, I've come to appreciate the CCP4 update functionality, which, in our multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. Update 012 removed that script with no immediately obvious replacement. Was that on purpose? Is there a way of updating CCP4 from the command line without calling CCP4i? Thanks Andreas (from update.log: [Thu Jan 3 2013 11:00:21] Ready to make changes --- applying update 6.3.0-012 --- update header read --- creating restore package, please wait ... --- done ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- 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/ iD8DBQFQ9/O7UxlJ7aRr7hoRAhVVAJ4yomsoCO3CeOJ13XteKAt0B95yTgCgoqnq 8PgeNrjcFS3vLeuBk9cBjHM= =IwT/ -END PGP SIGNATURE-
Re: [ccp4bb] ccp4 update
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, I am not sure, but maybe the error is caused by $PWD being part of your path variable so that when you call 'ccp4um' while your cwd is /software/CCP4-6.3.0/ccp4-6.3.0/bin, python make 'sys.argv[0]' (line 10 in $CBIN/ccp4um) ./ccp4um. This would result in the error you receive. Can you type 'which ccp4um' while being in /software/CCP4-6.3.0/ccp4-6.3.0/bin and while being in some other directory (e.g. $HOME)? Does the error occur if you call 'ccp4um' from e.g. $HOME? Tim On 01/17/2013 01:44 PM, Ian Tickle wrote: Dear Eugene ccp4um doesn't work for me at all (update worked fine up until #012). node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um Traceback (most recent call last): File ccp4um, line 17, in module shutil.copy2 ( fname,fname1 ) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' Did I do something wrong? Or is it just that there's nothing to update? Cheers -- Ian On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote: Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing update :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers, I've come to appreciate the CCP4 update functionality, which, in our multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. Update 012 removed that script with no immediately obvious replacement. Was that on purpose? Is there a way of updating CCP4 from the command line without calling CCP4i? Thanks Andreas (from update.log: [Thu Jan 3 2013 11:00:21] Ready to make changes --- applying update 6.3.0-012 --- update header read --- creating restore package, please wait ... --- done ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- 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/ iD8DBQFQ9/vYUxlJ7aRr7hoRAqXlAJ9qkk3BBNTT6P8eR1HxP6ODEz2GfACgkkvR hUlISdYdsr1v5dryb76tNLg= =kESK -END PGP SIGNATURE-
Re: [ccp4bb] ccp4 update
Tim Eugene node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-58 which ccp4um ./ccp4um node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-59 cd node066:~-60 which ccp4um ccp4um: Command not found. node066:~-61 echo $PATH /software/virtualenv/python2.7/64/cluster/bin: ... :/software/CCP4-6.3.0/ccp4-6.3.0/share/dbccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/ccp4i/bin:/software/CCP4-6.3.0/ccp4-6.3.0/bin:/software/CCP4-6.3.0/ccp4-6.3.0/etc:/software/compilers/linux/intel_v11.7.256/composer_xe_2011_sp1.7.256/bin/ia32:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2core/Test:/software/CCP4-6.3.0/ccp4-6.3.0/share/xia2/xia2/Applications # CBIN is in the path, so we need to rehash after the update: node066:~-62 rehash node066:~-63 which ccp4um /software/CCP4-6.3.0/ccp4-6.3.0/bin/ccp4um node066:~-64 ccp4um WORKS! So I just needed to rehash the PATH after the last update (or I could have logged out in). Thanks to Tim Eugene for suggestions. Cheers -- Ian On 17 January 2013 13:25, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ian, I am not sure, but maybe the error is caused by $PWD being part of your path variable so that when you call 'ccp4um' while your cwd is /software/CCP4-6.3.0/ccp4-6.3.0/bin, python make 'sys.argv[0]' (line 10 in $CBIN/ccp4um) ./ccp4um. This would result in the error you receive. Can you type 'which ccp4um' while being in /software/CCP4-6.3.0/ccp4-6.3.0/bin and while being in some other directory (e.g. $HOME)? Does the error occur if you call 'ccp4um' from e.g. $HOME? Tim On 01/17/2013 01:44 PM, Ian Tickle wrote: Dear Eugene ccp4um doesn't work for me at all (update worked fine up until #012). node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45 ccp4um Traceback (most recent call last): File ccp4um, line 17, in module shutil.copy2 ( fname,fname1 ) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /software/python/python_v2.7.3_64/lib/python2.7/shutil.py, line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: '/libexec/ccp4um' Did I do something wrong? Or is it just that there's nothing to update? Cheers -- Ian On 16 January 2013 15:11, eugene.krissi...@stfc.ac.uk wrote: Dear Andreas, Sorry for late response to your post and confusion with the updater. For technical reasons (Windows does not like names containing update :)), the updater was renamed into ccp4um (ccp4 update manager) and is found in $CCP4/bin. I hope this helps, Eugene Dear CCP4 maintainers, I've come to appreciate the CCP4 update functionality, which, in our multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. Update 012 removed that script with no immediately obvious replacement. Was that on purpose? Is there a way of updating CCP4 from the command line without calling CCP4i? Thanks Andreas (from update.log: [Thu Jan 3 2013 11:00:21] Ready to make changes --- applying update 6.3.0-012 --- update header read --- creating restore package, please wait ... --- done ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed some more blah blah) -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London -- Scanned by iCritical. - -- - -- 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/ iD8DBQFQ9/vYUxlJ7aRr7hoRAqXlAJ9qkk3BBNTT6P8eR1HxP6ODEz2GfACgkkvR hUlISdYdsr1v5dryb76tNLg= =kESK -END PGP SIGNATURE-
Re: [ccp4bb] Crystallization buffer pH optimization
That may be the CALBIOCHEM Buffers Booklet, which is free online as a PDF. On 01/17/2013 12:38 AM, Mike John wrote: Hello, Shameful and sorry for asking this simple question, it looks like this when first starting a new setup in so-called structural biology. I remmeber a book of, probably, Hampton, in which there are tables of pH optimization for many buffers. For example for buffer TRIS, the table will list how many drops NaOH/HCl needed to change pH from 7.0 to 7.2, etc. This is useful for crystallization pH optimization, where can I buy or download this info? Alternatives? Thank you very much! Mike -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] P212121 and P213
I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm http://img.chem.ucl.ac.uk/sgp/large/198az1.htm (Not absolutely sure the above are world viewable) Naively I expected the two structures to roughly align. However they don't there appears to be some change of axes between them. The transform of the P213 onto the P212121 structure is 0.03345 -0.9977 -0.0598 -0.9994 0.03402 -0.08653 0.01066 0.05929 -0.9982 -18.16 -57.18 21.39 This is clearly close to 0 -1 0 -1 0 0 0 0 -1 -0.25 -.75 0.25 in fractionals. Applying either the exact transformation or the regularised one with ether indexing of p213 ie original and k h -l http://www.ccp4.ac.uk/html/reindexing.html the rfactors are well above 50% and don't drop. Any suggestions of what I am doing wrong or is this not going to work (tried MR into the reindexed data and that does not align either- in fact I have tried quite a lot things) The reason for trying to get the two structures on the same axes is to compare the electron densities. The P212121 seems to have some of the disorder loops better defined. Using the Coot transform map by LSQ superpose is quite good BUT it would be better if it were another map other than the refinement map that is transformed as I then want to refine the unmoved structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] P212121 and P213
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicholas, not sure whether it will work - learning by doing: You might integrate the P213 data set in the subgroup P212121 with the real P212121 data as reference data set. At least XDS will then choose consistent indexing. As last step you repeat the CORRECT step with the space group assigned to P213 (CORRECT might actually pick the right lattice symmetry automatically) this should not change the indexing IF XDS considers it possible. Best, Tim On 01/17/2013 03:08 PM, Nicholas Keep wrote: I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm http://img.chem.ucl.ac.uk/sgp/large/198az1.htm (Not absolutely sure the above are world viewable) Naively I expected the two structures to roughly align. However they don't there appears to be some change of axes between them. The transform of the P213 onto the P212121 structure is 0.03345 -0.9977 -0.0598 -0.9994 0.03402 -0.08653 0.01066 0.05929 -0.9982 -18.16 -57.18 21.39 This is clearly close to 0 -1 0 -1 0 0 0 0 -1 -0.25 -.75 0.25 in fractionals. Applying either the exact transformation or the regularised one with ether indexing of p213 ie original and k h -l http://www.ccp4.ac.uk/html/reindexing.html the rfactors are well above 50% and don't drop. Any suggestions of what I am doing wrong or is this not going to work (tried MR into the reindexed data and that does not align either- in fact I have tried quite a lot things) The reason for trying to get the two structures on the same axes is to compare the electron densities. The P212121 seems to have some of the disorder loops better defined. Using the Coot transform map by LSQ superpose is quite good BUT it would be better if it were another map other than the refinement map that is transformed as I then want to refine the unmoved structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick - -- - -- 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/ iD8DBQFQ+Aq1UxlJ7aRr7hoRApI8AJ0SBfsZIFtqsh0eCV5ZzTvV09FcWACfYnAY qF7kTqxZQMTCEhzxxGu+kOI= =Kj8g -END PGP SIGNATURE-
Re: [ccp4bb] P212121 and P213
Hard to say without data - but I would generate the 3 symmetry copies of the molecule you would have in P213, then do rigid refinement of those coordinates with the P212121 cell dimensions and symmetry. There are so many possibilities for origin shifts But you don't say how non-equivalent the axes are; - if -18.16 ~ 1/4 ~ 21.39 that is a pretty big difference? Eleanor On 17 Jan 2013, at 14:08, Nicholas Keep wrote: I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm http://img.chem.ucl.ac.uk/sgp/large/198az1.htm (Not absolutely sure the above are world viewable) Naively I expected the two structures to roughly align. However they don't there appears to be some change of axes between them. The transform of the P213 onto the P212121 structure is 0.03345 -0.9977 -0.0598 -0.9994 0.03402 -0.08653 0.01066 0.05929 -0.9982 -18.16 -57.18 21.39 This is clearly close to 0 -1 0 -1 0 0 0 0 -1 -0.25 -.75 0.25 in fractionals. Applying either the exact transformation or the regularised one with ether indexing of p213 ie original and k h -l http://www.ccp4.ac.uk/html/reindexing.html the rfactors are well above 50% and don't drop. Any suggestions of what I am doing wrong or is this not going to work (tried MR into the reindexed data and that does not align either- in fact I have tried quite a lot things) The reason for trying to get the two structures on the same axes is to compare the electron densities. The P212121 seems to have some of the disorder loops better defined. Using the Coot transform map by LSQ superpose is quite good BUT it would be better if it were another map other than the refinement map that is transformed as I then want to refine the unmoved structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] P212121 and P213
Polymorphs are another possibility. The packing could be very similar but the space group could be different. Enrico. On Thu, 17 Jan 2013 15:30:20 +0100, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Hard to say without data - but I would generate the 3 symmetry copies of the molecule you would have in P213, then do rigid refinement of those coordinates with the P212121 cell dimensions and symmetry. There are so many possibilities for origin shifts But you don't say how non-equivalent the axes are; - if -18.16 ~ 1/4 ~ 21.39 that is a pretty big difference? Eleanor On 17 Jan 2013, at 14:08, Nicholas Keep wrote: I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm http://img.chem.ucl.ac.uk/sgp/large/198az1.htm (Not absolutely sure the above are world viewable) Naively I expected the two structures to roughly align. However they don't there appears to be some change of axes between them. The transform of the P213 onto the P212121 structure is 0.03345 -0.9977 -0.0598 -0.9994 0.03402 -0.08653 0.01066 0.05929 -0.9982 -18.16 -57.18 21.39 This is clearly close to 0 -1 0 -1 0 0 0 0 -1 -0.25 -.75 0.25 in fractionals. Applying either the exact transformation or the regularised one with ether indexing of p213 ie original and k h -l http://www.ccp4.ac.uk/html/reindexing.html the rfactors are well above 50% and don't drop. Any suggestions of what I am doing wrong or is this not going to work (tried MR into the reindexed data and that does not align either- in fact I have tried quite a lot things) The reason for trying to get the two structures on the same axes is to compare the electron densities. The P212121 seems to have some of the disorder loops better defined. Using the Coot transform map by LSQ superpose is quite good BUT it would be better if it were another map other than the refinement map that is transformed as I then want to refine the unmoved structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/ibitecs/simopro/ltmb/cristallogenese http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] P212121 and P213
Dear Nicholas, Why do you want to do the same rebuilding twice? Once in the P212121 map and once guided by the rotated P212121 map? What I usually do in these cases, and which seems more efficient to me, is to first complete rebuilding and refinement of the better defined p212121 structure and then superimpose the refined coordinates onto your P213 molecule. Since you probably have 3 molecules in the asymmetric unit in P212121 and 1 molecule in P213, you could superimpose the 3 p212121 molecules onto your single P213 molecule. Then either you rebuild your P213 molecule, guided by the coordinates of the P212121 structures, or you rebuild one of the P212121 molecules into the p213 structure, just like one does with molecular replacement. My 2 cents, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nicholas Keep Sent: Thursday, January 17, 2013 3:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] P212121 and P213 I have a structure which normally crystallises in P213 but one data set the edges became slightly non-equivalent in length by a couple of angstroms and the data process in P212121 P212121 symmetry operators appears to be a subset of P213 http://img.chem.ucl.ac.uk/sgp/large/019az1.htm http://img.chem.ucl.ac.uk/sgp/large/198az1.htm (Not absolutely sure the above are world viewable) Naively I expected the two structures to roughly align. However they don't there appears to be some change of axes between them. The transform of the P213 onto the P212121 structure is 0.03345 -0.9977 -0.0598 -0.9994 0.03402 -0.08653 0.01066 0.05929 -0.9982 -18.16 -57.18 21.39 This is clearly close to 0 -1 0 -1 0 0 0 0 -1 -0.25 -.75 0.25 in fractionals. Applying either the exact transformation or the regularised one with ether indexing of p213 ie original and k h -l http://www.ccp4.ac.uk/html/reindexing.html the rfactors are well above 50% and don't drop. Any suggestions of what I am doing wrong or is this not going to work (tried MR into the reindexed data and that does not align either- in fact I have tried quite a lot things) The reason for trying to get the two structures on the same axes is to compare the electron densities. The P212121 seems to have some of the disorder loops better defined. Using the Coot transform map by LSQ superpose is quite good BUT it would be better if it were another map other than the refinement map that is transformed as I then want to refine the unmoved structure into the unmoved map guided by the moved map and that involved a lot of changes of map selection. Thanks nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] P212121 and P213
Thanks Eleanor, your tip has got me there. I was attempting the problem the wrong way round. To get it to work I had to reindex the P212121 h=-l k=k l=h Then rigid body refinement of the P213 symmetry generated trimer dropped it to 40% and NCS refinement to around 25% My reasoning for avoiding doing it this way round is that presumably if we deposit the P213 and the P212121 structures the wwPDB will reset to abc (I seem to remember) A quick go at trying to reverse this has not worked. Maybe the radius of convergence of a rigid body is lower in the higher symmetry space group?? For info In P213 a=b=c 75.953 P212121 a=74.504 b=77.473 c=79.894 The SSM fit is 0.79 over virtually all Calphas for the symmetry generated trimer in P213 onto the P212121 structure In response to Herman The final P213 data set is actually higher resolution (we have collected several of these at a range of resolution as we improved cryo/crystal size/sampled more crystals/cooling pathways). The P212121 was the highest at one point and has better density for some loops. Many thanks to all who sent me hints Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] [COOT] favorite linux flavor, or as most of you would say, flavour ;)
A year or two ago we switched from Fedora to Scientific Linux 6. It is a free repackaging of Red Hat Enterprise, so it should be a straightforward shift from Fedora. It is supported long term, and has backing from several large labs (fermilab, CERN, etc) CCP4, Coot, etc. seem to be well-supported in it. Anything package for RH Enterprise should be fine. On 01/17/13 11:33, David Roberts wrote: I'm sorry to re-hash this issue, but I just wanted to know what the present general consensus is on linux flavors. I teach a crystallography class every 2 years, and I have a small cluster of computers running fedora, but the deal is that by the time I get around to my class, fedora has routinely gone up at least 2 levels since my last upgrade, meaning that the latest software and things are difficult at best to load on. I'm OK with any linux, I just want one that will be able to run the majority (if not all) of the typical crystallography packages (cns, ccp4, coot, etc...). I also would like one that works well with nfs and local file sharing. I can upgrade fedora, no problem, but I thought I may branch out if others think there are better flavors out there. Thanks so much Dave Roberts -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] advices
I guess you may have to decide whether you want to modify your current conditions or just start over to find new conditions, to get around this ultra-fast crystallization. I don't know if you have played around all parameters of current condition, such as lower temperature, protein concentration, pH, salt, etc, or ways to slow down vapor diffusion, i.e. covering drop or reservoir by silicon oil. If all these do not help, you might have to find a new condition under which protein crystallizes in a different morphology...However, BEFORE you try out things at the crystallization stage, ask if there is anything that you could improve before crystallization: Is your construct good enough? How is your protein quality--purity/homogeneity? Fine-tuning every step from gene to protein to crystal could eventually lead to good results. Joe On Tue, Jan 15, 2013 at 8:30 PM, Mike John perturb-w...@hotmail.com wrote: Hello, all, My crystal grows very fast even though the protein conc. is now 1.5 mg/ml. The shape of the crystal likes a ruler plate with one side very thin. The crystal quality has diffraction to about 3.5A in a home source of 1.2 KW sealed tube Angilent equipment. But the data can not be indexed due to one direction has poor diffraction and the crystal quality. Seeking advices on improving the crystal quality. Thank you very much Mike -- Best regards, Joe
[ccp4bb] HKL2000 24IDE beam center.
Hi colleagues, We have collected several datasets at APS with detector 24IDE, while processing date, the beam center is obviously not in position. But no matter what values we set in Site Configuration or def.site, it remains about (156, 165). Based on the image, the estimated correct center should be around (156, 157). Does anyone know how to solve this problem? Thanks Niu
Re: [ccp4bb] HKL2000 24IDE beam center.
Hello Niu, Have you tried adding the following line to appropriate areas in the macro tab (indexing, refinement and integration I believe they're called?): x beam 156 y beam 157 Sincerely, Scott Classen On Jan 17, 2013, at 1:19 PM, Niu Tou wrote: Hi colleagues, We have collected several datasets at APS with detector 24IDE, while processing date, the beam center is obviously not in position. But no matter what values we set in Site Configuration or def.site, it remains about (156, 165). Based on the image, the estimated correct center should be around (156, 157). Does anyone know how to solve this problem? Thanks Niu smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] HKL2000 24IDE beam center.
Niu, Could you give me some information about when you came to NE-CAT and I will tell you the beam center. We can do this off the CCP4BB. My email is schue...@anl.gov Thanks, Jon On 01/17/2013 03:19 PM, Niu Tou wrote: Hi colleagues, We have collected several datasets at APS with detector 24IDE, while processing date, the beam center is obviously not in position. But no matter what values we set in Site Configuration or def.site, it remains about (156, 165). Based on the image, the estimated correct center should be around (156, 157). Does anyone know how to solve this problem? Thanks Niu -- Jonathan P. Schuermann, Ph. D. Beamline Scientist, NE-CAT Argonne National Laboratory, 436E 9700 S. Cass Ave. Argonne, IL 60439 Email: schue...@anl.gov Tel: (630) 252-0682
[ccp4bb] Membrane protein overexpression
Dear all I have a general question on membrane protein overexpression in E. coli. Are E. coli proteins expressed in E. coli always better in terms of yield, lipid preservation and so on than another homologous protein? I am aware that it is different for *crystallization* because of flexible loops and thermostability. Thank you. Theresa
Re: [ccp4bb] HKL2000 24IDE beam center.
If you change it in the def.site file, when you start HKL2000 and select the detector type, it has to be the one with the name of the directory of the def.site file that you corrected. If it doesn't have the values that you entered into the def.site file then you are either not choosing the correct one or it is not saving what you updated. Unless the permissions are set for a normal user or you are using the root account, you may not be able to save the values that you changed. what happens if you start HKL2000 then click on the site configuration heading? it should pop up the s.c. window. change the values then just click close. the values should be set. i would uncheck the refine buttons for x beam and y beam to see if it stays at these values. what do you see? if it goes far from these values in the refinement step, then there could be other problems. Where did you get the beam center values. if it was from a different program, then the convention for x and y may be different. some programs rotate the image. so they are not interchangeable. lastly if you change the values in the s.c. window, unless you have the permissions set correctly, it's unlikely that you can save the values. so everytime you restart, you will have to change the values again. -Todd From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [niutou2...@gmail.com] Sent: Thursday, January 17, 2013 3:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HKL2000 24IDE beam center. Hi colleagues, We have collected several datasets at APS with detector 24IDE, while processing date, the beam center is obviously not in position. But no matter what values we set in Site Configuration or def.site, it remains about (156, 165). Based on the image, the estimated correct center should be around (156, 157). Does anyone know how to solve this problem? Thanks Niu
Re: [ccp4bb] Membrane protein overexpression
Hi Theresa, The overexpression of any MP may depend on 100 factors and what you listed below are just a few! toufic On Thu, Jan 17, 2013 at 9:50 PM, Theresa Hsu theresah...@live.com wrote: Dear all I have a general question on membrane protein overexpression in E. coli. Are E. coli proteins expressed in E. coli always better in terms of yield, lipid preservation and so on than another homologous protein? I am aware that it is different for *crystallization* because of flexible loops and thermostability. Thank you. Theresa
Re: [ccp4bb] Unit Cell of Ensemble must be orthogonal
Thanks a lot! Wei At 2013-01-17 17:02:12,Randy Read rj...@cam.ac.uk wrote: This means that the unit cell in the MTZ file obtained from the density is non-orthogonal, i.e. the angles are not all 90 degrees. Although in principle we could have made it possible to use non-orthogonal unit cells, it would make things more difficult for us and, since the density has to be cut out and put in a new unit cell with lots of space around it anyway, there's no reason not to choose an orthogonal unit cell. If you use Kevin Cowtan's cmapcut to cut out the density for MR, it will choose an orthogonal unit cell by default. This reminds me that I must update our web page on using electron density as a model! Before Kevin's nice cmapcut program (and Tom Terwilliger's equally nice phenix.cut_out_density procedure) it was a laborious process that required a very long explanation. Best wishes, Randy Read On 17 Jan 2013, at 03:20, Wei Feng wrote: Dear all, When I used PHASER to do a molecular replacement and define ensemble via map (mtz file), the program stoped very soon. The log file showed that Unit Cell of Ensemble must be orthogonal. I tried many ways to generate the map file, but the results are the same. Can anyone help me to solve this problem? Thanks a lot! Wei -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] R-factors of various kind
Hi, it would be nice if you highlight different type of R-factors used in the literature. I like to understand various kind of R-Factors, their mathematical formula, and relations among them. Thank you. Teri
[ccp4bb] Protein-DNA crystallisation
Dear CCP4 I wish to crystalise a transcription factor in complex with DNA. Are there any good papers you can recommend on protein-DNA crystallisation? Also any helpful tips on protein:DNA ratios, protein concentrations or buffer conditions that have worked for any of you would be most helpful Thanks Careina
