[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:

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

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

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

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

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

[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

[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

[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.

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

[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.

[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

[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

[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

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

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

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

[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

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:

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

[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

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

[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

[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

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.