Re: [ccp4bb] Does Scala merge anomalous/non-anomalous?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 If you don't want scala to keep your Bijvoet-pairs separate, you should uncheck the appropriate button in the ccp4i-GUI. However, since you have SIGF_New, your mtz-file already contains the merged Bijvoet-pairs. Scala is not a refinement programm and you ought to check the input file for phenix where to tell it to use the merged data rather than the unmerged data, and also need to check the phenix log-file to figure out why it calculates the completeness so low. Regards, Tim On 12/04/2012 11:55 PM, Yarrow Madrona wrote: Hello CCP4 users, My column labels from scala include: SIGF_New(+) and F_New as well as F_New(-) and SIGF_new(-) But also contains: SIGF_New, F_New DANO_New and SIGDANOW_NEW When I refine (phenix) using SIGF_NEW(+) and SIGF_New(-) my completeness does not match what comes out of the scala log file (97%). Instead it is only 90% But when I refine using Intensities and let phenix.refine run truncate I get the expected completeness of 97% in my log file. Is there something special you have to do in Scala to tell it to combine anomalous and non-anomalous data for refinement using structure factors? I don't need the anomalous data so I don't need to keep it separate. Thanks. -Yarrow - -- - -- 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/ iD8DBQFQvxVjUxlJ7aRr7hoRAgyeAJ4t8V7H9aDfzuf1lqT3RzULYmSSRQCg8Bj+ zgcEB/KN7LIVONVPcIz0nFg= =fL/K -END PGP SIGNATURE-
Re: [ccp4bb] Does Scala merge anomalous/non-anomalous?
Note that Scala Aimless always put I+, I- and Imean into the output file, which then get propagated through [c]truncate. This is irrespective of whether the Anomalous data flag is switched on: that only affects outlier rejection and some statistics. Note also that Aimless (recent versions anyway) will automatically switch on the Anomalous flag if there appears to be a significant anomalous signal, unless you explicitly tell it not to (to avoid accidentally rejecting good anomalous differences as outliers) Phil On 5 Dec 2012, at 09:35, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 If you don't want scala to keep your Bijvoet-pairs separate, you should uncheck the appropriate button in the ccp4i-GUI. However, since you have SIGF_New, your mtz-file already contains the merged Bijvoet-pairs. Scala is not a refinement programm and you ought to check the input file for phenix where to tell it to use the merged data rather than the unmerged data, and also need to check the phenix log-file to figure out why it calculates the completeness so low. Regards, Tim On 12/04/2012 11:55 PM, Yarrow Madrona wrote: Hello CCP4 users, My column labels from scala include: SIGF_New(+) and F_New as well as F_New(-) and SIGF_new(-) But also contains: SIGF_New, F_New DANO_New and SIGDANOW_NEW When I refine (phenix) using SIGF_NEW(+) and SIGF_New(-) my completeness does not match what comes out of the scala log file (97%). Instead it is only 90% But when I refine using Intensities and let phenix.refine run truncate I get the expected completeness of 97% in my log file. Is there something special you have to do in Scala to tell it to combine anomalous and non-anomalous data for refinement using structure factors? I don't need the anomalous data so I don't need to keep it separate. Thanks. -Yarrow - -- - -- 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/ iD8DBQFQvxVjUxlJ7aRr7hoRAgyeAJ4t8V7H9aDfzuf1lqT3RzULYmSSRQCg8Bj+ zgcEB/KN7LIVONVPcIz0nFg= =fL/K -END PGP SIGNATURE-
Re: [ccp4bb] thanks god for pdbset
Francois, I did not realize Phil Evans is god (perhaps a minor one as he did not yet earn a capital G). I do concur that insertion code is evil. I had to re-refine an old antibody structure recently and it messes up coot sequence window and breaks refmac bond restraints. Evil, evil,.evil. Cheers, Ed. On Wed, 2012-12-05 at 16:58 +0900, Francois Berenger wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] thanks god for pdbset
not god I don't think I wrote that bit! Phil On 5 Dec 2012, at 15:06, Ed Pozharski wrote: Francois, I did not realize Phil Evans is god (perhaps a minor one as he did not yet earn a capital G). I do concur that insertion code is evil. I had to re-refine an old antibody structure recently and it messes up coot sequence window and breaks refmac bond restraints. Evil, evil,.evil. Cheers, Ed. On Wed, 2012-12-05 at 16:58 +0900, Francois Berenger wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] thanks god for pdbset
The last time I tried the pdbset renumber command because of issues with insertion codes in certain programs, it failed to also renumber the LINK, SSBOND CISPEP records. Needless to say, thanking god (or even God) was not my first thought! (more along the lines of why can't software developers stick to the agreed standards?). I haven't tried it with the latest version, maybe it's fixed now. -- Ian On 5 December 2012 07:58, Francois Berenger beren...@riken.jp wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.
Re: [ccp4bb] thanks god for pdbset
Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, December 05, 2012 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset The last time I tried the pdbset renumber command because of issues with insertion codes in certain programs, it failed to also renumber the LINK, SSBOND CISPEP records. Needless to say, thanking god (or even God) was not my first thought! (more along the lines of why can't software developers stick to the agreed standards?). I haven't tried it with the latest version, maybe it's fixed now. -- Ian On 5 December 2012 07:58, Francois Berenger beren...@riken.jp wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.
Re: [ccp4bb] thanks god for pdbset
I had always assumed that ASCII sort order was the standard so ' 128A' comes after ' 128 ' in the collating sequence, and indeed the PDB documentation seems to make it clear that it comes after, e.g. in the section describing the ATOM record: REFERENCE PROTEIN NUMBERINGHOMOLOGOUS PROTEIN NUMBERING - 59 59 60 60 61 62 62 REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING -- 85 85 86 86 86A 86B 87 87 But does it actually matter if the insertion comes before? Surely the sequence is completely defined by the file order, regardless of the residue numbering, not by the alphanumeric sorting order? So if 86A comes immediately before 86 in the file then you must assume that 86A C is linked to 86 N (assuming of course that the bond length is sensible), if after then it's 86 C to 86A N. Cheers -- Ian On 5 December 2012 16:02, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, December 05, 2012 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset The last time I tried the pdbset renumber command because of issues with insertion codes in certain programs, it failed to also renumber the LINK, SSBOND CISPEP records. Needless to say, thanking god (or even God) was not my first thought! (more along the lines of why can't software developers stick to the agreed standards?). I haven't tried it with the latest version, maybe it's fixed now. -- Ian On 5 December 2012 07:58, Francois Berenger beren...@riken.jp wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.
[ccp4bb] Postdoctoral Position in Structural Biology of Immune Receptors
Dear All, I repost this message on behalf of Dr. Jia-huai Wang, as this position needs to be filled as soon as possible. For inquiries please contact Dr. Wang directly at jw...@red.dfci.harvard.edu Postdoctoral Position in Structural Biology of Immune Receptors: There is an immediate opening for a postdoctoral position in protein crystallography at the Dana-Farber Cancer Institute, Harvard Medical School. The research project is focused on the structural and functional investigation of leukocyte integrins, which are cell surface receptors that play a key role in immunity. The successful candidate should have a Ph.D. in structural biology. In addition to a knowledge of X-ray crystallography, the applicant should also have experience in molecular biology, and protein biochemistry. This includes cloning, protein expression and purification, particularly in eukaryotic systems such as baculavirus. Interested candidates should email a CV and three contacts for reference to Dr. Jia-huai Wang at jw...@red.dfci.harvard.edu. For more information regarding the Wang Laboratory, please see the website:http://wang.dfci.harvard.edu Sincerely, lorenzo Lorenzo Ihsan FInci, Ph.D. Postdoctoral Scientist, Wang Laboratory Harvard Medical School Dana-Farber Cancer Institute Boston, MA Peking University The College of Life Sciences Beijing, China -- Scanned by iCritical.
Re: [ccp4bb] thanks god for pdbset
Hi Robbie, On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem. Properly used, the PDB exchange dictionary for mmCIF can indeed sort this out. In addition to the PDB-style residue number + insertion code, it has an item for the residue sequence number in the chain (running from 1 .. n). The relevant item names are: _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code and: _entity_poly_seq.num One thing to be careful of, is cases where the insertion code is a digit (which does happen sometimes). I have seen code many times where an assumption is made that the insertion code is not a digit, and this is assumption is used to separate the residue number from the insertion code (e.g. a user is asked to enter a residue number + insertion code as a single item). If the insertion code is a digit, this won't work. This is easy to handle in the fixed-width PDB format: 85 851 852 86 but if it gets written to mmCIF incorrectly as: loop_ _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code 85 . 851 . 852 . 86 . instead of the correct: loop_ _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code 85 . 85 1 85 2 86 . it can be really hard to sort out later on. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] thanks god for pdbset
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Does 128A come before or after 128? Robbie, shouldn't it simply depend on which residue record comes first in the pdb file? Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Bug of GUI of ACORN?
Dear Jiawei, Thanks for spotting this and bringing it to our attention. It is a serious bug in the interface when using the default protocol for Acorn. When running Acorn to determine heavy atoms the default is to truncate the resolution to 3.5 Angstroms. However this default is there for all modes of operation and as it uses the same keyword for general resolution truncation it causes this issue. I'll send you a fix for it in a later email but we'll also provide this as an update in the next ccp4 auto update which will hopefully be the end of this week or early next week. (Note: to install the ccp4 auto updater please visit http://www.ccp4.ac.uk/download/update_manual.html). Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jwwang Sent: 05 December 2012 01:34 To: ccp4bb Subject: [ccp4bb] Bug of GUI of ACORN? Hi, In the GUI of ACORN, I use all the default setting, which should mean all observed reflections in the mtz file will be used for ab initio phasing. However, the command file output by GUI includes the keyword RESO 50 3.5. It's ridiculous that GUI has cut off the resolution to 3.5 A, which makes the ACORN running failed. If I set the full resolution in GUI with Use data from resolution range 50 1.2, the command file will include two RESO keyword --- RESO 50 1.2 RESO 50 3.5, which means resolution was still cut to the 3.5 A. Is it a bug in the GUI of ACORN? BTW, if you use the script to run ACORN, everything is fine. Best, Jiawei Wang -- Scanned by iCritical.
Re: [ccp4bb] thanks god for pdbset
Hi Ian, The 'standard' you describe below is more of a suggestion than a rule. The PDB does not enforce a numbering scheme which is particularly annoying when dealing with engineered proteins with linkers or domains of different proteins (they come with all sorts of numbering schemes). Of course, when you use the ATOM records and distance criteria you should be able to work out what is connected and where the gaps are. Unfortunately, this is not always properly implemented in software (I had a nice recent case with a gap in an insertion in a nucleic acid, that cause problems working out the connectivity). When dealing with ranges of residues, e.g. in TSL group descriptions, numbering issues with (or without) insertion codes can be a real pain because ranges can be somewhat ambiguous. In theory, it is easy and insertion codes (or other numbering issues) should not be a problem at all. In practice, as Ed pointed out, it is a big mess. Cheers, Robbie -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Wednesday, December 05, 2012 17:26 To: Robbie Joosten Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset I had always assumed that ASCII sort order was the standard so ' 128A' comes after ' 128 ' in the collating sequence, and indeed the PDB documentation seems to make it clear that it comes after, e.g. in the section describing the ATOM record: REFERENCE PROTEIN NUMBERINGHOMOLOGOUS PROTEIN NUMBERING --- -- 59 59 60 60 61 62 62 REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING --- --- 85 85 86 86 86A 86B 87 87 But does it actually matter if the insertion comes before? Surely the sequence is completely defined by the file order, regardless of the residue numbering, not by the alphanumeric sorting order? So if 86A comes immediately before 86 in the file then you must assume that 86A C is linked to 86 N (assuming of course that the bond length is sensible), if after then it's 86 C to 86A N. Cheers -- Ian On 5 December 2012 16:02, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, December 05, 2012 16:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] thanks god for pdbset The last time I tried the pdbset renumber command because of issues with insertion codes in certain programs, it failed to also renumber the LINK, SSBOND CISPEP records. Needless to say, thanking god (or even God) was not my first thought! (more along the lines of why can't software developers stick to the agreed standards?). I haven't tried it with the latest version, maybe it's fixed now. -- Ian On 5 December 2012 07:58, Francois Berenger beren...@riken.jp wrote: Especially the renumber command that changes residue insertion codes into an increment of the impacted residue numbers. Regards, F.
[ccp4bb] Postdoctoral position in the lab of Dr. Michael Marletta
The Marletta Lab at The Scripps Research Institute is looking for a postdoctoral fellow to study the structure and function of Heme- Nitric Oxide/Oxygen binding (H-NOX) domains, a family of gas sensing proteins that are prevalent in prokaryotes and higher eukaryotes. The ideal candidate will have excellent theoretical and practical knowledge in protein crystallization and structure determination of proteins by X-ray crystallography. Experience in sub-cloning, protein expression (bacterial and insect cell) and purification is also strongly desired. Interested individuals should submit a single PDF file to Mark Herzik (mher...@berkeley.edu) containing the following: curriculum vitae, a description of research experience, reference letters or contact information of references and a cover letter outlining interest in the position. Additional inquiries can be sent to Mark Herzik. Thanks, Mark Herzik Graduate Student Marletta Lab University of California, Berkeley
Re: [ccp4bb] thanks god for pdbset
Hi Peter, Thanks for the info. I'd better go check whether my code assumes insertion codes are not digits. Cheers, Robbie Date: Wed, 5 Dec 2012 17:57:58 + From: pkel...@globalphasing.com Subject: Re: [ccp4bb] thanks god for pdbset To: CCP4BB@JISCMAIL.AC.UK Hi Robbie, On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote: Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem. Properly used, the PDB exchange dictionary for mmCIF can indeed sort this out. In addition to the PDB-style residue number + insertion code, it has an item for the residue sequence number in the chain (running from 1 .. n). The relevant item names are: _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code and: _entity_poly_seq.num One thing to be careful of, is cases where the insertion code is a digit (which does happen sometimes). I have seen code many times where an assumption is made that the insertion code is not a digit, and this is assumption is used to separate the residue number from the insertion code (e.g. a user is asked to enter a residue number + insertion code as a single item). If the insertion code is a digit, this won't work. This is easy to handle in the fixed-width PDB format: 85 851 852 86 but if it gets written to mmCIF incorrectly as: loop_ _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code 85 . 851 . 852 . 86 . instead of the correct: loop_ _atom_site.pdbx_PDB_residue_no _atom_site.pdbx_PDB_ins_code 85 . 85 1 85 2 86 . it can be really hard to sort out later on. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] 4 year PhD studentship Imperial College London
I would like to call your attention to a BBSRC-funded PhD studentship in the lab of Doryen Bubeck at Imperial College London starting October 2013. Title: Complement-mediated pore formation The immune complement system in blood kills microbes by making ‘membrane-attack complex’ (MAC) pores in cell membranes. CD59 is a complement regulator that blocks MAC pore formation and protects hosts from bystander damage. Some microorganisms subvert the immune system by hijacking complement regulators to enhance infection. Intermedilysin (ILY) is bacterial toxin that engages CD59 to initiate membrane attachment, the first step in this toxin’s pore formation. The aim of this proposal is to understand a molecular mechanism underlying ILY pore formation and the role CD59 plays in the pathway. Specifically it uses an interdisciplinary approach, integrating structural biology and membrane biophysics, to characterize the assembly of ILY pores in a CD59-decorated liposome model system. This project is a 4 year BBSRC funded PhD studentship at Imperial College London to start October 2013, inclusive of a 1 year Masters in Research and a 3 month Professional Internship for PhDs (PIPS) placement. It is a collaboration between the labs of Doryen Bubeck (Division of Molecular Biosciences), Oscar Ces (Chemistry Department), and Xiaodong Zhang (Division of Molecular Biosciences). For more details on eligibility and how to apply please see: http://www3.imperial.ac.uk/bbsrcdoctoraltrainingpartnership References: Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin. Polekhina G, Giddings KS, Tweten RK, Parker MW. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):600-5. Mapping the intermedilysin-human CD59 receptor interface reveals a deep correspondence with the binding site on CD59 for complement binding proteins C8alpha and C9. Wickham SE, Hotze EM, Farrand AJ, Polekhina G, Nero TL, Tomlinson S, Parker MW, Tweten RK. J Biol Chem. 2011 Jun 10;286(23):20952-62. = Doryen Bubeck Lecturer in Structural Biology Imperial College London Division of Molecular Biosciences 602 Sir Ernst Chain Building South Kensington, London, SW7 2AZ (0) 207 594 2989 d.bub...@imperial.ac.uk =
