[ccp4bb] EMBL Postdoc position available in structural neurobiology
Dear all, a three year postdoctoral position is available within the EIPOD (EMBL Interdisciplinary Postdocs) scheme in my group to study the role of the netrin receptor UNC5B in neuronal cell death. A more detailed description can be found here: http://www.embl.de/training/postdocs/08-eipod/application/04_2014_project_ideas/meijers.pdf The research will take place at the EMBL Hamburg Outstation in Germany, in collaboration with the group of Francesca Peri at EMBL Heidelberg. Candidates with a background in protein crystallography and affinity with cell biology are encouraged to apply. For more information on the EIPOD scheme, please visit: http://www.embl.de/training/postdocs/08-eipod/index.html A successful application will require a written motivation as to why this project is suitable, and candidates are therefore encouraged to contact me directly. The deadline for the application is 11th of September 2014. Best regards, Rob Meijers Group Leader EMBL Hamburg http://www.embl-hamburg.de/research/unit/meijers/contact/index.html
Re: [ccp4bb] wilson B in xds vs. truncate.
Hi Yarrow, XDS does the following: Data is divided into resolution shells and a straight line A - 2*B*SS is fitted to log(I), where SS = mean of (sin(THETA)/LAMBDA)**2 in shell I= mean reflection intensity in shell BO = (A - logI)/(2*SS) The value of B is reported (above the table) for all data, and additionally (in the table) for each resolution shell. best, Kay
Re: [ccp4bb] Problems about i
You may write Polish if you wish - it's case insensitive :-) Sent from my iPhone On 26 Aug 2014, at 21:37, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: hi Jacob You'd have to ask Phil Evans for the definitive answer, but my understanding is that it's a tribute to the developers of an integration and scaling package which isn't distributed by CCP4 (and which doesn't come from the MPI either). Harry -- 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 26 Aug 2014, at 19:44, Keller, Jacob kell...@janelia.hhmi.org wrote: I’ve chuckled at the “polish” nomenclature before, as I assumed this was a reference to certain software developers, but if so, shouldn’t it be “Polish?” Or does it mean polish, in the sense of shoe polish? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell Sent: Tuesday, August 26, 2014 2:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problems about i hi (1) provided the predictions match the spots (i.e. indexing etc has been successful) the best things to look at in the Integration task initially are the graphs - if they vary reasonably smoothly, and there are no big jumps then things have probably gone okay. (2) Really, the only way to reduce the mosaicity is to grow better crystals. Are you getting much larger values than with hkl2000? How many overlaps are you getting (both as the overall number and as a fraction of the whole?); there may be nothing wrong at all... (3) For everything apart from finding the heavy atom sub-structure with SHELXC/D/E, you want the MTZ file from ctruncate (so this is the one you want for molecular replacement). For SHELXC/D/E, you really want unmerged F^2 values which can be obtained by using the Aimless option output polish unmerged (as a processing option under Integration). HTH Harry -- 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 26 Aug 2014, at 16:51, 陈昂 angsc...@outlook.com wrote: Dear all： It is my first time to use IMOSFLM instead of HKL2000. Here are my problems. Hope you can help me. 1、what parameters can indicate the result quality of my imosflm? mosaicity ,anything else? 2、what can I do to reduce the mosaicity and decrease bad spots,resolution or the spot finding range? 3、after imosflm, I've got some MTZ maps such as original one and pointless one,aimless one, ctruncate one. Which one should I take to the next step?what steps do I need to take before molecular replacement and why? THANKS a lot Peter Chen
Re: [ccp4bb] wilson B in xds vs. truncate.
Hi, the original F W TRUNCATE broadly does the same as XDS, but as usual the devil's in the detail. A Wilson plot is usually far from a straight line, depending on the resolution of your data. This means that the parameters of the fit (intercept gradient) will depend on how the fit is weighted, e.g. are the low resolution data weighted more than the high res, and also how the data are binned, e.g. in ranges of equal steps of d*, or d*^2, or d*^3.. TRUNCATE weights each point in proportion to the number of reflexions in the bin (the sd(I) values are ignored for this purpose), so the fit should at least not depend on how the data are binned. Of course if you're using CTRUNCATE then that's another story ... We would need to see the actual data to get a better idea of the source of the discrepancy. Cheers -- Ian On 26 August 2014 22:26, Yarrow Madrona amadr...@uci.edu wrote: Hello CCP4 users. I noticed a discrepancy between the estimated wilson B reported by XDS and that reported by truncate. As far as I know XDSconv and truncate use the French and Wilson (K.S. Acta. Cryst. (1978), A34, 517-525.) method for converting to structure factors. However, the result below is from XDS before XDSconv. Does anyone know exactly how XDS is calculating the Wilson-B compared to truncate? XDS: WILSON LINE (using all data) : A= 7.372 B= 20.624 CORRELATION= 0.98 Truncate: Results Wilson plot: B = 11.375 intercept = 5.959 siga = 0.264 sigb = 0.053 scale factor on intensity = 387.0343
Re: [ccp4bb] Have everyone had a Scorpion Screen Builder or a Dragonfly screen optimizer?
Dear Joseph, We had the same question at the beginning of the year and we assisted to demos of the two machines. To me, the two liquid handlers are valid choices and the most appropriate one will ultimately depend on your specific needs as they have some differences. First of all, both liquid handlers have well-designed and intuitive software. They are easy to setup and use. The pipetting technology is however different. The Dragonfly uses disposable syringes with a piston directly in contact with the solution. With this technology, there is no need of liquid classes definition and the machine handles perfectly water, pure glycerol, 50% PEG 8k and higher MW PEGs as well as pure isopropanol (without droplet formation). The solutions are aspirated from disposable reservoirs you fill with the desired volume of chemical. The dragonfly has two possible configurations: with 5 or 10 syringes. The model with 5 syringes is upgradeable to 10 syringes. You can easily perform screens with more than 5 components with the 5-syringe model. The machine accepts any SBS format plate. We use the dragonfly to prepare the screens then use the Mosquito to prepare our crystallization trials. The Scorpion uses a positive displacement head to handle a wide range of fluid viscosities. Several liquid classes are predefined to adapt the pipetting speed to the viscosity of the solution. The Scorpion uses regular Tecan tips of different volumes (without graphene). It is designed to perform custom screens as well as to reformat commercial screens from 10 mL tubes to masterblock. At the time we tested the Scorpion, the screen reformatting part needed custom setup of the viscosity of all the solutions (to optimize the dispensing time) but Art Robbins was always clear they would help for that. The deck can adapt a great number of solutions as mentioned in a previous post. The Scorpion accepts SBS plates and I think it can or will accept Linbro plates. In terms of footprint, the two machines are compact. In our case, we decided to obtain the Dragonfly because it is very fast to dispense (around 6-7 minutes to prepare a 96 well plate with 5 components), very accurate (we usually dispense total volumes less than 80 uL) and there is no cross-contamination as the syringes are never in contact with the plate’s reservoir. The absence of liquid classes configuration increases the ease of use of the machine. The screen designer is very intuitive and it is extremely easy to divide a plate into sub-screens. The software that drives the Dragonfly is also instinctive allowing to minimal user training. The software is under continuous development. Hope this helps and again, the choice between these two machines will depend on your specific needs. Ludovic
Re: [ccp4bb] composite omit map
Further to Jurgen's comment, in the GUI comit is under 'Map and Mask Utilities', although if you want to run it in slow mode with refinement you'll have to use the script. On 26 August 2014 19:47, dusky dew duskyde...@gmail.com wrote: Can you people please tell me how to calculate a composite omit map in ccp4? Thanks Madhu -- EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm
[ccp4bb] Please post this message
Hi, I just subscribed to CCP4BB but I am trouble posting this message. Could you please upload this Job advertisement. Thanks much, Sudha *Postdoctoral Position in Structural Biology*, Department of Physiology and Biophysics at Case Western Reserve University, Cleveland OH Laboratory of Dr. Sudha Chakrapani ( https://physiology.case.edu/people/faculty/sudha-chakrapani/) We are looking for an outstanding and highly motivated candidate for a NIH-funded postdoctoral position to study structure and function of ligand-gated ion channels. Our laboratory employs cutting edge multidisciplinary approaches that include electrophysiology, electron paramagnetic resonance spectroscopy, fluorescence spectroscopy, X-ray crystallography, and a wide spectrum of biophysical techniques. The candidate should have a recent Ph.D. degree (in biochemistry, biophysics, structural biology or related area) with a strong publication record. In addition, the candidate is required to have substantial experience in molecular biology, protein expression and purification. Prior experience in ion channel research, X-ray crystallography or spectroscopy is desired. Competitive salary and fringe benefit will be provided. Please send a cover letter stating your scientific interests and goals, CV and contact information for 3 references to Sudha Chakrapani at sxc...@case.edu or sudha.chakrap...@case.edu *From:* JISCMAIL LISTSERV Server (16.0) [mailto:lists...@jiscmail.ac.uk lists...@jiscmail.ac.uk] *Sent:* Tuesday, August 26, 2014 9:24 AM *To:* sudha.chakrap...@case.edu *Subject:* Text of confirmation requests *CCP4BB* *CCP4 bulletin board* Your command: SUBSCRIBE CCP4BB Sudha Chakrapani requires confirmation. To confirm the execution of your command, simply click on the following link : *https://www.jiscmail.ac.uk/cgi-bin/webadmin?OK=603F641AL=CCP4BB* https://www.jiscmail.ac.uk/cgi-bin/webadmin?OK=603F641AL=CCP4BB Alternatively, if you have no WWW access, you can reply to this message and type ok (without the quotes) as the text of your message. Just use the word ok and do not retype the command. If you receive an error message, try sending a new message to *lists...@jiscmail.ac.uk* lists...@jiscmail.ac.uk and type ok 603F641A as the text of your message. Please note that your command will be cancelled automatically if LISTSERV does not receive your confirmation within 48h. After that time, you'll need to resend the command to get a new confirmation code. If you change your mind and decide that you do NOT want to confirm the command, simply discard this email and let the request expire on its own. *CCP4BB Home https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4BB*
[ccp4bb] Off topic post
Hi,Sorry this is off topic but I thought someone might know the answer, I used the "advanced search" option in the PDB and found 100 pdb hits, I can see them (small icons+ details) but I just want the names of the PDB's, as a list. I can't see an option to just get the list.Does anyone know how I could get the list names?Thank you,Patrick Free 3D Earth Screensaver Watch the Earth right on your desktop! Check it out at www.inbox.com/earth
[ccp4bb] FW: [ccp4bb] Please post this message
Hi, I just subscribed to CCP4BB but I am trouble posting this message. Could you please upload this Job advertisement. Thanks much, Sudha Postdoctoral Position in Structural Biology, Department of Physiology and Biophysics at Case Western Reserve University, Cleveland OH Laboratory of Dr. Sudha Chakrapani (https://physiology.case.edu/people/faculty/sudha-chakrapani/) We are looking for an outstanding and highly motivated candidate for a NIH-funded postdoctoral position to study structure and function of ligand-gated ion channels. Our laboratory employs cutting edge multidisciplinary approaches that include electrophysiology, electron paramagnetic resonance spectroscopy, fluorescence spectroscopy, X-ray crystallography, and a wide spectrum of biophysical techniques. The candidate should have a recent Ph.D. degree (in biochemistry, biophysics, structural biology or related area) with a strong publication record. In addition, the candidate is required to have substantial experience in molecular biology, protein _expression_ and purification. Prior experience in ion channel research, X-ray crystallography or spectroscopy is desired. Competitive salary and fringe benefit will be provided. Please send a cover letter stating your scientific interests and goals, CV and contact information for 3 references to Sudha Chakrapani at sxc...@case.edu or sudha.chakrap...@case.edu From: JISCMAIL LISTSERV Server (16.0) [mailto:lists...@jiscmail.ac.uk] Sent: Tuesday, August 26, 2014 9:24 AMTo: sudha.chakrap...@case.eduSubject: Text of confirmation requests CCP4BB CCP4 bulletin board Your command: SUBSCRIBE CCP4BB Sudha Chakrapani requires confirmation. To confirm the execution of your command, simply click on the following link : https://www.jiscmail.ac.uk/cgi-bin/webadmin?OK=603F641AL=CCP4BB Alternatively, if you have no WWW access, you can reply to this message and type "ok" (without the quotes) as the text of your message. Just use the word "ok" and do not retype the command. If you receive an error message, try sending a new message to lists...@jiscmail.ac.uk and type "ok 603F641A" as the text of your message. Please note that your command will be cancelled automatically if LISTSERV does not receive your confirmation within 48h. After that time, you'll need to resend the command to get a new confirmation code. If you change your mind and decide that you do NOT want to confirm the command, simply discard this email and let the request expire on its own. CCP4BB Home Free 3D Marine Aquarium Screensaver Watch dolphins, sharks orcas on your desktop! Check it out at www.inbox.com/marineaquarium
Re: [ccp4bb] Off topic post
Hi Patrick, If you need only IDs, [Reports]-[List selected IDs] is what you want. You can also create tables by [Reports]-[Customizable table] and download it in CSV format. http://www.rcsb.org/pdb/staticHelp.do?p=help/tabularHelp.html Best regards, Takanori Nakane On 2014-08-27 14:32, PC wrote: Hi, Sorry this is off topic but I thought someone might know the answer, I used the advanced search option in the PDB and found 100 pdb hits, I can see them (small icons+ details) but I just want the names of the PDB's, as a list. I can't see an option to just get the list. Does anyone know how I could get the list names? Thank you, Patrick - [1] FREE 3D EARTH SCREENSAVER Watch the Earth right on your desktop! Check it out at www.inbox.com/earth [1] Links: -- [1] http://www.inbox.com/earth
[ccp4bb] AW: [ccp4bb] Off topic post
Dear Patrick If you go to the Rutgers website (www.rcsb.orghttp://www.rcsb.org) and do a search, there will be a reports pull-down menu on the right in the area just above the list of entry summaries. Here you can select just the IDs, but also a customizable table, where you could select e.g. the IDs and titles, which a find very useful. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von PC Gesendet: Mittwoch, 27. August 2014 15:32 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Off topic post Hi, Sorry this is off topic but I thought someone might know the answer, I used the advanced search option in the PDB and found 100 pdb hits, I can see them (small icons+ details) but I just want the names of the PDB's, as a list. I can't see an option to just get the list. Does anyone know how I could get the list names? Thank you, Patrick http://www.inbox.com/earth[3D Earth Screensaver Preview]http://www.inbox.com/earthhttp://www.inbox.com/earth Free 3D Earth Screensaver Watch the Earth right on your desktop! Check it out at www.inbox.com/earthhttp://www.inbox.com/earth
[ccp4bb] Postdoctoral Position in Structural Biology
*Postdoctoral Position in Structural Biology*, Department of Physiology and Biophysics at Case Western Reserve University, Cleveland OH Laboratory of Dr. Sudha Chakrapani ( https://physiology.case.edu/people/faculty/sudha-chakrapani/) We are looking for an outstanding and highly motivated candidate for a NIH-funded postdoctoral position to study structure and function of ligand-gated ion channels. Our laboratory employs cutting edge multidisciplinary approaches that include electrophysiology, electron paramagnetic resonance spectroscopy, fluorescence spectroscopy, X-ray crystallography, and a wide spectrum of biophysical techniques. The candidate should have a recent Ph.D. degree (in biochemistry, biophysics, structural biology or related area) with a strong publication record. In addition, the candidate is required to have substantial experience in molecular biology, protein expression and purification. Prior experience in ion channel research, X-ray crystallography or spectroscopy is desired. Competitive salary and fringe benefit will be provided. Please send a cover letter stating your scientific interests and goals, CV and contact information for 3 references to Sudha Chakrapani at sxc...@case.edu or sudha.chakrap...@case.edu
[ccp4bb] Save the dates for the first DLS/CCP4 data analysis workshop
PhD students, postdocs and early career scientists, Please consider applying for the first joint DLS/CCP4 workshop on MX data analysis, this December. This workshop is styled on the highly successful APS/CCP4 summer schools and offers the opportunity for you to work alongside leaders in the field of MX on data from your own crystals. For more details please check here: http://www.ccp4.ac.uk/schools/DLS-2014/ A further announcement will be made when the application pages are ready. Best wishes on behalf of the organisers, -- David Waterman (CCP4)
[ccp4bb] ATP library file in REFMAC
I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The ideal distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report. BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] ATP library file in REFMAC
Hi Bernie, This is an issue that the REFMAC developers and the PDB are aware of (at least at the EBI site) and that we have also encountered in a recent deposition. The problem is that there is indeed a discrepancy between the stereochemistry for ATP and ADP as defined in the CCP4 monomer libraries and that defined by Mogul that the PDB now uses for its validation report. As both REFMAC and PHENIX make use of the CCP4 monomer library, this will affect the majority of depositions with the PDB, but will only have been picked up since PDB introduced their new validation software. I therefore suspect that almost all PDB entries for ATP/ADP would fail the new validation test. There is a working group being set up (funded by CCP4 I believe) to address issues of errors in the CCP4 monomer library, and this will, in time, sort out these issues. It think that a significant number of other ligand library entries may also contain errors. Best wishes, Andrew On 27 Aug 2014, at 16:12, Bernard D Santarsiero b...@uic.edu wrote: I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The ideal distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report. BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] ATP library file in REFMAC
Cant you edit the ATP.cif on your computer to have the correct expected bond length? Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 8/27/2014 4:12 PM, Bernard D Santarsiero wrote: I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The ideal distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report. BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] ATP library file in REFMAC
Down load the MOGUL coordinates and use some program - PRODRG LIBCHECK ELBOW to make a new dictionary.. Then check it! You can assign that dictionary as LIBIN and the new ATP will have precedence over the wrong one. Eleanor On 27 August 2014 18:25, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Cant you edit the ATP.cif on your computer to have the correct expected bond length? Best, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 8/27/2014 4:12 PM, Bernard D Santarsiero wrote: I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The ideal distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report. BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
[ccp4bb] Lattice Translocation Disorder Correction
Dear CCPers, Is there an existing script or program for implementing the intensity corrections for trans-located lattices in macromolecular crystals as described in Wang et al (2004)?. Any input or sharing will be immensely helpful. Thanks a lot, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*
Re: [ccp4bb] ATP library file in REFMAC
Or use Grade: http://grade.globalphasing.org/cgi-bin/grade/server.cgi which gives the correct bond length. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernard D Santarsiero [b...@uic.edu] Sent: Wednesday, August 27, 2014 6:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ATP library file in REFMAC I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The ideal distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report. BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMJ
Re: [ccp4bb] Lattice Translocation Disorder Correction
Dear Arko, my first port of call would be the man himself: jimin.wang AT yale.edu Andreas On 27/08/2014 7:12, Arka Chakraborty wrote: Dear CCPers, Is there an existing script or program for implementing the intensity corrections for trans-located lattices in macromolecular crystals as described in Wang et al (2004)?. Any input or sharing will be immensely helpful. Thanks a lot, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)*/ /*BARCELONA, SPAIN*/ / -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
[ccp4bb] ATP library file in REFMAC - Part II
I appreciate all of the comments and suggestions on how to locate a better CIF file for ATP. I adopted the suggestion of Boaz, and generated a new ATP.cif file, and refined one of my structures. The validation server still uses substantially different target bond lengths and angles, so there is better agreement, but I still get flags. Both bond length and angles target values are more realistic than what was used in the REFMAC ATP.cif file, but I still find fault with the target values. For example, the bond lengths and angles around PB, the beta P atom, range from 104.4-108.7deg in the grade file, and are unrealistic since they are all less than the tetrahedral angle. The CIF also targets one P-O as a single and the other as formally a double bond, but most crystallographic studies indicate at least some delocalization over both internal oxygen atoms, and a slight compression of that angle. The validation server has an ideal target value of 101.66deg which is surely contracted from a more reasonable value near 105deg. One approach that would be useful is to consider refinement on special groups, like phosphate, with structural parameters, instead of actual target bond lengths and angles, so R1 for the two PB-O1B and PB-O2B distances, and R2 for the two PB-O3A and PB-O3B distances, and pairs of angle restraints incorporating a complete delocalization model. See, for example, Murray-Rust, Burgi, and Dunitz, J. Am. Chem. Soc., 97, 921 (1975), or Tamasi at al., The Open Crystallography Journal, 3, 1 (2010). This could be used to directly address questions about delocalization and hydrolytic capacity, rather than trying to determine then from bond lengths. Bernie On Wed, August 27, 2014 2:05 pm, Boaz Shaanan wrote: Or use Grade: http://grade.globalphasing.org/cgi-bin/grade/server.cgi which gives the correct bond length. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernard D Santarsiero [b...@uic.edu] Sent: Wednesday, August 27, 2014 6:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ATP library file in REFMAC I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The quot;idealquot; distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report.BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie --
Re: [ccp4bb] ATP library file in REFMAC - Part II
L On Aug 27, 2014 5:12 PM, Santarsiero, Bernard D. b...@uic.edu wrote: I appreciate all of the comments and suggestions on how to locate a better CIF file for ATP. I adopted the suggestion of Boaz, and generated a new ATP.cif file, and refined one of my structures. The validation server still uses substantially different target bond lengths and angles, so there is better agreement, but I still get flags. Both bond length and angles target values are more realistic than what was used in the REFMAC ATP.cif file, but I still find fault with the target values. For example, the bond lengths and angles around PB, the beta P atom, range from 104.4-108.7deg in the grade file, and are unrealistic since they are all less than the tetrahedral angle. The CIF also targets one P-O as a single and the other as formally a double bond, but most crystallographic studies indicate at least some delocalization over both internal oxygen atoms, and a slight compression of that angle. The validation server has an ideal target value of 101.66deg which is surely contracted from a more reasonable value near 105deg. One approach that would be useful is to consider refinement on special groups, like phosphate, with structural parameters, instead of actual target bond lengths and angles, so R1 for the two PB-O1B and PB-O2B distances, and R2 for the two PB-O3A and PB-O3B distances, and pairs of angle restraints incorporating a complete delocalization model. See, for example, Murray-Rust, Burgi, and Dunitz, J. Am. Chem. Soc., 97, 921 (1975), or Tamasi at al., The Open Crystallography Journal, 3, 1 (2010). This could be used to directly address questions about delocalization and hydrolytic capacity, rather than trying to determine then from bond lengths. Bernie On Wed, August 27, 2014 2:05 pm, Boaz Shaanan wrote: Or use Grade: http://grade.globalphasing.org/cgi-bin/grade/server.cgi which gives the correct bond length. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernard D Santarsiero [b...@uic.edu] Sent: Wednesday, August 27, 2014 6:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ATP library file in REFMAC I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon submission to Acta for publication, the wwPDB validation report was run. Several things were flagged, including the C4-C5 bond in the adenosine moiety as being too long. It generally refines to 1.46-1.47A. The quot;idealquot; distance in the validation report is 1.38A, and the upon review of the ATP.cif file in the REFMAC library, the target distance is 1.49A (and listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond length as 1.404A. Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of my structures and re-run the validation report.BTW, I also looked at the PDB_REDO structure report for my structure, and can't reproduce the Rcryst and Rfree values with the same model. Bernie --
[ccp4bb] Advices on experimental phasing
Hi, I would like to seek some advices on experimental phasing. I have datasets of the following: 1. Around 4-6 datasets per crystal collected at sulfur edge. There's no anomalous signal but I used one of the best dataset collected as the native dataset (nat2). 2. Peak (aupeak) and inflexion (auinf) for a gold derivative 3. Peak for a hg derivative (hgE3pk) 4. One native dataset Here's the scaleit summary for the different datasets Table: The Rfactor Riso |F_nat2 FP_hgE3pk F_aupeakF_auinf F_nat2 |0.380 0.239 0.239 FP_hgE3pk |0.380 0.388 0.379 F_aupeak |0.239 0.388 0.126 F_auinf|0.239 0.379 0.126 Table: Normal Probability for acentric data Normal Prob. |F_nat2 FP_hgE3pk F_aupeakF_auinf F_nat2 |3.112 4.661 5.057 FP_hgE3pk |3.112 2.803 2.777 F_aupeak |4.661 2.803 2.120 F_auinf|5.057 2.777 2.120 Table: Normal Probability for Centric data Normal Prob. |F_nat2 FP_hgE3pk F_aupeakF_auinf F_nat2 |2.688 3.127 3.091 FP_hgE3pk |2.688 1.966 2.017 F_aupeak |3.127 1.966 1.288 F_auinf|3.091 2.017 1.288 Table: Anomalous Differences ( FPHi+ v. FPHi-) Anom difference |nref_cent Prob_cent nref_acent Prob_acent Rfactor -- F(+)_hgE3pk v F(-)_hgE3pk|361 0.346 15380.732 0.209 F_aupeak(+) v F_aupeak(-)|353 0.020 15521.094 0.104 F_auinf(+) v F_auinf(-) |557 0.024 29491.200 0.105 Sulfur SAD with the datasets collected at the sulfur edges was not successful. - There are 14 S in the 309 amino acids long protein. - These datasets range from 2.5A to 3A. - No anomalous signal can be detected even (all the CCanom 0.1 across all the resolution shells) SAD with the Hg peak datasets wasn't successful too - Unable to find the positions of the Hg atoms with shelxd/phenix hyss But! I was able to find 3 au atoms using shelxD using the SIRAS (SAD/MAD did not work) protocol with aupeak (resolution to 4A) and nat2 (resolution to 2.5A). - shelxE built about 2/3 of the model with nice (but disconnected) helices. - After density modification, the map improved with obvious solvent edges. However, after rounds of refinement using refmac, the Rfree remains 0.5. - Autobuilding using arp/warp and phenix autobuild did not complete the model. In fact, only 1/3 of protein was build as loops. - I attempted to build the rest of the model and connect the helices manually using coot but there's a lot of ambiguous electron densities extending in two different directions. I can't really comprehend it. It is so near yet so far. Is the structure really solved? If it's solved, is there anything that I could do to build the model? Can I make use of the other datasets that I have to help improve the phases? Really hope to hear from you soon! Many thanks in advance!! Cheers, Kelly
[ccp4bb] An opening for a post-doctoral position in structural biology, Bangalore, India
At National Institute of Mental Health and Neuro Sciences (NIMANS), a post-doctoral / Research Associate position is available in our Structural Biology Lab. The candidate should have a Ph. D with substantial research experience in protein biochemistry. Research experience in protein crystallography is also preferable. Interested candidates may send their recent CV to: B. Padmanabhan, Ph. D Additional Professor, Department of Biophysics, NIMHANS, Bangalore, India. Email: balapa...@gmail.com
Re: [ccp4bb] ATP library file in REFMAC - Part II
On 27/08/14 23:11, Santarsiero, Bernard D. wrote: I appreciate all of the comments and suggestions on how to locate a better CIF file for ATP. I adopted the suggestion of Boaz, and generated a new ATP.cif file, and refined one of my structures. Grade is what I would have recommended, FWIW. The validation server still uses substantially different target bond lengths and angles, to that in the dictionary from grade? so there is better agreement, but I still get flags. Both bond length and angles target values are more realistic than what was used in the REFMAC ATP.cif file, but I still find fault with the target values. For example, the bond lengths and angles around PB, the beta P atom, range from 104.4-108.7deg in the grade file, and are unrealistic since they are all less than the tetrahedral angle. The angles of the terminal phosphate oxygens (O1G, O2G, O3G) to the ester oxygen are less than ideal-tetrahedral because the internal angles of the terminal phosphate oxygens are greater than ideal-tetrahedral. I'd bet that the dictionary from grade reflects that. The CIF also targets one P-O as a single and the other as formally a double bond, It is quite usual for different dictionary generators to specify the bond orders (types) of delocalized groups differently. If the bond *lengths* are based on the bond types then that's a more substantial problem. Is that what you meant? but most crystallographic studies indicate at least some delocalization over both internal oxygen atoms, and a slight compression of that angle. The validation server has an ideal target value of 101.66deg which is surely contracted from a more reasonable value near 105deg. Interesting - that is quite different to what I see (if we are talking about the same thing (I am looking at the O1B-PB-O2B angle - is that what you meant?)). Paul.
