Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/
[ccp4bb] hi
Hello to every one Can any body send me the information in concise form about history of protein crystallization along with what is the properties of protein crystal in lattice parameters. Thanks In advance Sanjit Kumar
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I would say that 0.333 (in a scientific context) implies that I am confident about this number up to the third decimal point, i.e. 0.3325 = x = 0.3334. This gives you an idea of the precision. 1/3 is not a scientific format, but a mathematical one, unless for some constraint you know that value is exactly 1/3, then there is no error associated with it. Cheers, Tim On 07/23/2014 09:57 PM, James Holton wrote: Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org mailto:b...@ruppweb.org b...@hofkristallamt.org mailto:b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0NofUxlJ7aRr7hoRAjEHAKDHJB/iHYgx6qJyr/k3U5TI5y6YSACguJli rWda+amIYdVWnT40WGw8dPA= =taoT -END PGP SIGNATURE-
[ccp4bb] hi
Hello to every one Can any body send me the information in concise form about history of protein crystallization along with some idea about the properties of protein crystal in lattice parameters. Thanks In advance Sanjit Kumar
Re: [ccp4bb] moleman2 install problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0NqrUxlJ7aRr7hoRAugrAJ9wv3WIDOL+1Ti+BBbvuYCnu/JObwCgpmhj W8vdmVM22yJXmF+4vumooFk= =aYck -END PGP SIGNATURE-
Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/ - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0NuIUxlJ7aRr7hoRAuorAKDaX42345ovf1SIrVIPzAuO1g1UkwCglBsF NoX6cxLs99wWwd0KZyaZ9XE= =buQc -END PGP SIGNATURE-
[ccp4bb] 2014: Crystal (cl)Year gentle reminder
Dear all, the early bird registration deadline (July 30th) is approaching fast! Register the soonest to have a discounted fare. Students and young researchers: there are some slots available for oral presentations and some funds left for travel grants. Submit your abstracts http://www.nettab.org/2014/CCY/ . We are looking forward to seeing you in Turin! Regards Camillo
Re: [ccp4bb] hi - history of protein crystallization
Hi Sanjit, These two reviews throw some light on the history of protein crystallization: http://www.ncbi.nlm.nih.gov/pubmed/24165393 http://www.ncbi.nlm.nih.gov/pubmed/25005076 I didn't understand what you exactly mean by properties of protein crystal in lattice parameters . HTH Raghu From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sanjit Roy Sent: Thursday, July 24, 2014 15:28 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] hi Hello to every one Can any body send me the information in concise form about history of protein crystallization along with what is the properties of protein crystal in lattice parameters. Thanks In advance Sanjit Kumar
[ccp4bb] Problem in molecular replacement
DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. Please suggest. Thanks Yang zhang
Re: [ccp4bb] Problem in molecular replacement
Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ - - - - - - - - - - - - - - - - - - email: antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 http://www.sussex.ac.uk/lifesci/oliverlab http://tinyurl.com/aw-oliver - - - - - - - - - - - - - - - - - - On 24 Jul 2014, at 12:50, dusky dew duskyde...@gmail.commailto:duskyde...@gmail.com wrote: DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. Please suggest. Thanks Yang zhang
Re: [ccp4bb] moleman2 install problem
Hi Tim, I download it again through command line and got another error message:” -bash: /Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable It seems the software does match my CPU. The processor of my computer is: 2.3 GHz Intel Core i7 Do you know how to solve this ? Thank you so much! Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn On Jul 24, 2014, at 6:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0NqrUxlJ7aRr7hoRAugrAJ9wv3WIDOL+1Ti+BBbvuYCnu/JObwCgpmhj W8vdmVM22yJXmF+4vumooFk= =aYck -END PGP SIGNATURE-
Re: [ccp4bb] Problem in molecular replacement
In addition to that good suggestion, with a model at such high sequence identity and with reasonable resolution data, it would be a good idea to search for smaller models, like a single dimer or even a monomer, because the assembly may have changed conformation. Another possibility you should consider is that the space group may not be correct. Good luck! Randy Read On 24 Jul 2014, at 13:06, Antony Oliver antony.oli...@sussex.ac.uk wrote: Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ - - - - - - - - - - - - - - - - - - email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 http://www.sussex.ac.uk/lifesci/oliverlab http://tinyurl.com/aw-oliver - - - - - - - - - - - - - - - - - - On 24 Jul 2014, at 12:50, dusky dew duskyde...@gmail.com wrote: DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. Please suggest. Thanks Yang zhang -- 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
Re: [ccp4bb] moleman2 install problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yamei, I am not sure where the official site for USF is now, but I would use http://xray.bmc.uu.se/usf/ There you can download OSX_binaries for Lion and Snow Leopard. The file in the tar-archive is called 'usf_osx_bin/moleman2' rather than osx_moleman2, therefore I guess to stumbled across an outdated download location. I hope Gerard Kleywegt will correct me if I am wrong. I hope this helps. Tim On 07/24/2014 02:08 PM, Yamei Yu wrote: Hi Tim, I download it again through command line and got another error message:” -bash: /Users/yamei/xutil_osx/osx_moleman2: Bad CPU type in executable It seems the software does match my CPU. The processor of my computer is: 2.3 GHz Intel Core i7 Do you know how to solve this ? Thank you so much! Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn On Jul 24, 2014, at 6:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear yamei, my guess is that the download was not completed, or your hard disk is about to break. Try downloading it again. You can also copy files from the command line with the cp command. Best, Tim On 07/24/2014 07:19 AM, Yamei Yu wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0PwpUxlJ7aRr7hoRAi4DAJ0YLbbvfBxV5Nj8cmE+laTJ97ploQCg/C70 5KD2nH0qH/MOyUq89ZPQOG4= =nHJU -END PGP SIGNATURE-
Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
Not sure why this qualifies as a flame or who you want to flame - seems reasonable but needs to be done so that the data items are extracted consistently from all programs and can be interpreted again by the refinement (or validation) programs independently of which program they came from. Insular kludges probably won't do. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Donnerstag, 24. Juli 2014 12:10 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/ - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFT0NuIUxlJ7aRr7hoRAuorAKDaX42345ovf1SIrVIPzAuO1g1UkwCglBsF NoX6cxLs99wWwd0KZyaZ9XE= =buQc -END PGP SIGNATURE-
Re: [ccp4bb] moleman2 install problem
Hi Mark Unless you've done something very odd, Snow Leopard binaries should be compatible with Mavericks (and Yosemite, too, when you get to try that). Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 24 Jul 2014, at 13:39, Mark Brooks mark.x.bro...@gmail.com wrote: Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I don't know that Snow Leopard binaries are compatible with Mavericks. (Probably not, judging from all the re-compiling that I seem to have done recently). (Does anyone know better?) See below for instructions from http://xray.bmc.uu.se/usf/ for recompiling, although under OS X 10.6. Mark ---8- The distribution kit can be found here : Distribution_kit Organisation of the distribution kit 35 programs are available, and each has its own directory with the same name as the program, under the parent directory 'usf'. In the top-level 'usf' directory there is a shell script called 'make_all.csh', and big surprise, if you execute that file it will will build all the programs, leaving executables in both the programs' own subdirectories and also in the collective directory 'usf/bin'. Building under OS X The package has been built under Mac OS X v10.6 using the gfortran compiler. The kit is reported to work under 10.7 Lion, but Xcode 4.1 needs to be installed. Thanks to Jacques-Philippe Colletier for the Lion executables. In order to build yourself you will need to install XCODE which can be downloaded from http://developer.apple.com/technology/xcode.html, and gfortran which can be found here http://www.macresearch.org/gfortran-leopard. You will also find a gfortran dmg file in the distribution. Follow the instructions that come with these installation packages. To be able to download these packages, you will have to register as an Apple Developer. Then type make_all.csh in the downloaded USF directory. On 24 July 2014 06:19, Yamei Yu ymyux...@gmail.com wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
Re: [ccp4bb] Problem in molecular replacement
How do I use DNA as search model? Can I use it in molrep or phaser? On Thursday, July 24, 2014, FOOS Nicolas nicolas.f...@synchrotron-soleil.fr wrote: Dear Yang, you should try different search model, for example : 1) DNA only, 1) DNA 2) protein 1)DNA+Prot etc... You can also try to find a partial solution and keep this solution to place the other molecules with another round of MR. Be careful if you use only DNA, if the density doesn't show clear proteic shape, you could have a false positive (a bit like with alpha helix for coil structure) One tips, sometimes the DNA could be organised in infinite Helix in the crystal, you can try to use DNA 2 times longer than you expect especially if your DNA molecules has over-hang. Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de dusky dew [ duskyde...@gmail.com] Envoyé : jeudi 24 juillet 2014 13:50 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Problem in molecular replacement DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. Please suggest. Thanks Yang zhang
Re: [ccp4bb] Problem in molecular replacement
You can use molrep or phaser as you prefer with DNA. To do that, you can edit you pdb file by hand with your favorit text editor (vim, emacs...) And you can cure your pdb file with Edit PDB File in ccp4 coordinate Utilities De : dusky dew [duskyde...@gmail.com] Envoyé : jeudi 24 juillet 2014 14:46 À : FOOS Nicolas Cc : CCP4BB@JISCMAIL.AC.UK Objet : Re: Problem in molecular replacement How do I use DNA as search model? Can I use it in molrep or phaser? On Thursday, July 24, 2014, FOOS Nicolas nicolas.f...@synchrotron-soleil.frmailto:nicolas.f...@synchrotron-soleil.fr wrote: Dear Yang, you should try different search model, for example : 1) DNA only, 1) DNA 2) protein 1)DNA+Prot etc... You can also try to find a partial solution and keep this solution to place the other molecules with another round of MR. Be careful if you use only DNA, if the density doesn't show clear proteic shape, you could have a false positive (a bit like with alpha helix for coil structure) One tips, sometimes the DNA could be organised in infinite Helix in the crystal, you can try to use DNA 2 times longer than you expect especially if your DNA molecules has over-hang. Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] de la part de dusky dew [duskyde...@gmail.commailto:duskyde...@gmail.com] Envoyé : jeudi 24 juillet 2014 13:50 À : CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Problem in molecular replacement DEAR ALL I am trying to solve the structure of a protein DNA complex with molecular replacement. The resolution in about 2.5 angstrom. The spacegroup is P21. The search model has about 50% identity and is a dimer of a dimer. The problem is the unit cell is huge and so the number of molecules in asu becomes 4 or 3. I am not finding any solution with phaser/molrep. Please suggest. Thanks Yang zhang
[ccp4bb] rigaku micromax 007 cooling
Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] rigaku micromax 007 cooling
Dear Andreas, we had a similar issue with our MicroMax 007, with a primary water/water chiller (ATC K3) in between the generator and a secondary inhouse water circuit. After a year of reliable service the K3 would shut off occasionally and dump the 007 with a cooling error. We found that the solution to the issue was to place an additional pump directly in front of the K3. The issue being that the latter would temporarily shut off unless provided with a constant water pressure, which the water circuit wasn't giving apparently. This has now been running fine. Another solution would be a water-air chiller to cool your 007, but in our case that was not an option due to building specs. Hope this helps. I'm happy to provide more details if wanted. Han Han Remaut, PhD Laboratory of Structural Molecular Microbiology VIB / Vrije Universiteit Brussel Building E4, Pleinlaan 2 1050 Brussel han.rem...@vib-vub.be tel. +32-2-629 1923 / +32-499 708050 http://www.vib.be/en/research/scientists/Pages/Han-Remaut-Lab.aspx On 24 Jul 2014, at 17:53, Andreas Förster wrote: Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] rigaku micromax 007 cooling
Dear Andreas, We have a Hyfra water cooled system (VWK50) on our MicroMax 007, but it is probably over-dimensioned because it is also used by a Xstream equipment, a smaller dedicated cooler to the micromax could be better. Daniel Le 24/07/2014 17:53, Andreas Förster a écrit : Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas
Re: [ccp4bb] rigaku micromax 007 cooling
I would warn you that the K3 and K9 chillers have internal hoses which cannot tollerate water pressure above 125 psi. We had a hose fail from the building chilled loop pressure. So, be careful adding any pressure with a pump before the chiller...and maybe consider one after the chiller to pull the water through. Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston From: Han Remaut han_c...@yahoo.co.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 24, 2014 11:07 AM Subject: Re: [ccp4bb] rigaku micromax 007 cooling Dear Andreas, we had a similar issue with our MicroMax 007, with a primary water/water chiller (ATC K3) in between the generator and a secondary inhouse water circuit. After a year of reliable service the K3 would shut off occasionally and dump the 007 with a cooling error. We found that the solution to the issue was to place an additional pump directly in front of the K3. The issue being that the latter would temporarily shut off unless provided with a constant water pressure, which the water circuit wasn't giving apparently. This has now been running fine. Another solution would be a water-air chiller to cool your 007, but in our case that was not an option due to building specs. Hope this helps. I'm happy to provide more details if wanted. Han Han Remaut, PhD Laboratory of Structural Molecular Microbiology VIB / Vrije Universiteit Brussel Building E4, Pleinlaan 2 1050 Brussel han.rem...@vib-vub.be tel. +32-2-629 1923 / +32-499 708050 http://www.vib.be/en/research/scientists/Pages/Han-Remaut-Lab.aspx On 24 Jul 2014, at 17:53, Andreas Förster wrote: Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] rigaku micromax 007 cooling
Thermo scientific has air/water chillers. Google: thermo scientific neslab merlin recirculating chillers brings up the links. We have one of these cooling an Oxford xcalibur. It supplies circulating cold water under pressure which we hook up where the house chilled water would go on the water/waer heat exchanger. On 07/24/2014 12:07 PM, Han Remaut wrote: Dear Andreas, we had a similar issue with our MicroMax 007, with a primary water/water chiller (ATC K3) in between the generator and a secondary inhouse water circuit. After a year of reliable service the K3 would shut off occasionally and dump the 007 with a cooling error. We found that the solution to the issue was to place an additional pump directly in front of the K3. The issue being that the latter would temporarily shut off unless provided with a constant water pressure, which the water circuit wasn't giving apparently. This has now been running fine. Another solution would be a water-air chiller to cool your 007, but in our case that was not an option due to building specs. Hope this helps. I'm happy to provide more details if wanted. Han Han Remaut, PhD Laboratory of Structural Molecular Microbiology VIB / Vrije Universiteit Brussel Building E4, Pleinlaan 2 1050 Brussel han.rem...@vib-vub.be mailto:han.rem...@vib-vub.be tel. +32-2-629 1923 / +32-499 708050 http://www.vib.be/en/research/scientists/Pages/Han-Remaut-Lab.aspx On 24 Jul 2014, at 17:53, Andreas Förster wrote: Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] rigaku micromax 007 cooling
Hi Andreas - My 007HF is cooled by a Haskris R050 chiller which I got from Rigaku. This has a refrigeration loop inside it to extract heat from the closed water loop that goes to the generator; the extracted heat can then go to building chilled water, or even an open loop (city cold water, then down the drain) if your building codes allow it. The advantage of this system is that it can handle unreliable chilled water temperature and flow, with allowable source water temperatures as high as 85 F. If your building water is really unreliable, you can even get an air-cooled Haskris - although your room A/C has to be able to handle the heat load in that case. Contact me off-list if you want more information. The system has been really reliable for me. - Matt On 7/24/14 11:53 AM, Andreas Förster wrote: Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] moleman2 install problem
Hmm. Maybe I'm doing something very wrong, because I get the following when I try those binaries: dyld: Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib Referenced from: /Users/brooks/Downloads/usf_osx_bin/./moleman2 Reason: no suitable image found. Did find: /usr/local/gfortran/lib/libgfortran.3.dylib: mach-o, but wrong architecture Trace/BPT trap: 5 What's that due to? (Stuff seems to break easily nowadays on Macs- perhaps I'm just not as up to speed on libraries, architectures and compilers on Apples as I need to be.) Yamei, I compiled it from source and put a copy here: https://dl.dropboxusercontent.com/u/30290835/bin/moleman2 Download it, then make it executable, run it as follows: chmod a+x ~/Downloads/moleman2 ~/Downloads/moleman2 I hope this helps. Mark P.S. if I run this lipo -info /usr/local/lib/libgfortran.3.dylib it gives: Non-fat file: /usr/local/gfortran/lib/libgfortran.3.dylib is architecture: x86_64 x86_64 is the correct architecture, isn't it? On 24 July 2014 13:45, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: Hi Mark Unless you've done something very odd, Snow Leopard binaries should be compatible with Mavericks (and Yosemite, too, when you get to try that). Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 24 Jul 2014, at 13:39, Mark Brooks mark.x.bro...@gmail.com wrote: Hi Yamei, If you're on OS X version 10.9.3, then I guess you're on Mavericks, not Snow Leopard ( https://www.apple.com/uk/osx/ ). Therefore, I guess you will need to download the source code and recompile it, since I don't know that Snow Leopard binaries are compatible with Mavericks. (Probably not, judging from all the re-compiling that I seem to have done recently). (Does anyone know better?) See below for instructions from http://xray.bmc.uu.se/usf/ for recompiling, although under OS X 10.6. Mark ---8- The distribution kit can be found here : Distribution_kit http://xray.bmc.uu.se/markh/usf/usf_download.php?file=/markh/usf/usf_distribution_kit.tar.gz Organisation of the distribution kit35 programs are available, and each has its own directory with the same name as the program, under the parent directory 'usf'. In the top-level 'usf' directory there is a shell script called 'make_all.csh', and big surprise, if you execute that file it will will build all the programs, leaving executables in both the programs' own subdirectories and also in the collective directory 'usf/bin'. Building under OS XThe package has been built under Mac OS X v10.6 using the gfortran compiler. The kit is reported to work under 10.7 Lion, but Xcode 4.1 needs to be installed. Thanks to Jacques-Philippe Colletier for the Lion executables. In order to build yourself you will need to install XCODE which can be downloaded from http://developer.apple.com/technology/xcode.html, and gfortran which can be found here http://www.macresearch.org/gfortran-leopard. You will also find a gfortran dmg file in the distribution. Follow the instructions that come with these installation packages. To be able to download these packages, you will have to register as an Apple Developer. Then type make_all.csh in the downloaded USF directory. On 24 July 2014 06:19, Yamei Yu ymyux...@gmail.com wrote: Hi all, I’m trying to install a copy of moleman2 for my new Mac. (the version is 10.9.3). while I copy the osx_moleman2 from xutil directory I got the following message: The Finder can’t complete the operation because some data in “osx_moleman2” can’t be read or written. (Error code -36) Could you tell me how to solve this problem? Thank you so much! Best wishes! yamei Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn
Re: [ccp4bb] rigaku micromax 007 cooling
Hi Ours is cooled by a Haskris R250, which is sized for an XStream also. While our heat exchangers have had a couple of issues, overall the Haskris heat exchangers have performed quite well. They redesigned ours when they found out about our building chilled water. I'm not affiliated with and heartily recommend them. As for the water itself, I would ***NEVER*** allow building chilled water into the generator. Our water is extremely dirty and the supply is slightly below spec, so we have a pump downstream of the heat exchanger. There are also 2 filters upstream to pull some of the junk out. Lately, startup has required the use of the pump, which I interpret as buildup in the condenser, so that's eventually going to need a cleanout. That was what the redesign was all about. I imagine ours is an extreme case, but the heat exchanger makes up for a variety of ills. Rigaku also recommends a DI filter to keep conductivity low in the water going into the generator, which improves anode lifetime. Building chilled water will never be able to be as low as desired. Besides, facilities people can change things and you'd never know until it's too late... Ed -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas Förster Sent: Thursday, July 24, 2014 10:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] rigaku micromax 007 cooling Dear all, I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled water supplied rather unreliably through the building infrastructure. I was wondering what alternatives exist. Could other MicroMax 007 users share their experiences with alternative cooling solutions with me? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
[ccp4bb] Scripps LCP workshop
Hello all, I’d like point you all to the LCP Tool and Technologies Workshop that the Scripps Research Institute is hosting in Bedford, MA on October 17th. The workshop is being run by Dr. Vadim Cherezov, and is part of a two day protein crystallography event in Bedford, MA. Please see here for more details: http://formulatrix.com/conference/lcp.html. Have a look around at the LCP Workshop and any other events being hosted on the 16th 17th. Let me know if you have any questions! Thanks, Ellen -- Ellen Gualtieri, PhD | Imager Product Manager | Formulatrix Inc. | Waltham, MA | Office: (781) 788-0228 Ext. 138 | www.formulatrix.com
