[ccp4bb] PhDs in BioDesign Engineering at Imperial College CDT

Dear all, There are 11 PhD projects available at the Imperial College/Manchester/UCL EPSRC CDT on Biodesign Engineering. Some of these projects might appeal to structurally inclined students. https://www.imperial.ac.uk/synthetic-biology/cdt-biodesign-engineering/available-projects/ Deadline 26t

[ccp4bb] PhD available

Dear all, I have a PhD available, deadline 12th March, on the structural biology of nitrogenase oxygen protection. Please email me if you are interested. Normal UKRI funding rules apply. https://www.imperial.ac.uk/life-sciences/postgraduate/research/phd-opportunities/ best wishes James Bio

[ccp4bb] EPSRC PhD at Imperial College in protein design

Dear all, I have a EPSRC-funded PhD in protein design for October 2018. Please forward to structurally-oriented Masters or just-finished undergraduate students. https://www.findaphd.com/search/ProjectDetails.aspx?PJID=99441 https://www.imperial.ac.uk/life-sciences/postgraduate/research/phd-oppo

Re: [ccp4bb] Validity of Ion Sites in PDB

Dear all, It is well known that you can look at anomalous difference maps to see heavier atoms - although I think not enough people do it. One technique that I think is powerful, but under-used is to calculate element-specific maps by taking the difference of anomalous difference data from ju

[ccp4bb] PhD positions at Imperial College, UK

Dear all, Imperial college currently has some PhD studentships available through a BBSRC DTP. http://www3.imperial.ac.uk/bbsrcdoctoraltrainingpartnership/phdprojects The mode of action of the cereal mildew RNAse-like effectors Structural Basis of Calvin Cycle Regulation Pesticide effects on be

[ccp4bb] Problems in scaling up expression

Dear All. A question on protein expression. We have been doing small scale test expressions in 15ml of terrific broth+kanamycin using E.coli KRX cells in falcon tubes. On reaching OD600 of ~0.6 we induced with rhamnose+IPTG and expressed for 4 hours at 37 C. There is a big band corresponding to o

Re: [ccp4bb] How to identify unknow heavy atom??

Dear All, re identifying metals, It's possible to calculate crystallographic element-specific anomalous difference maps if you can collect data on either side of the absorption edge. I have used this successfully for Sr, Zn and Mn. http://www.ncbi.nlm.nih.gov/pubmed/15858259 I have a set of

Re: [ccp4bb] off-topic:a dataset from a polluted sample

Dear Tianlong, You have probably crystallized a contaminant. You can check to see if your unit cell has been seen before in the pdb with this service from Robert Esnouf at Srubi, http://www.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi or apply to do a "wide search" whole pdb molecular replac

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

>I think there is a misconception floating around that processing your >data with "anomalous turned on" will somehow degrade the quality of >"normal" intensity data. I can think of very few circumstances when I would NOT want anomalous data, yet for many data processing pipelines, it is the defa

Re: [ccp4bb] SAD data is enough

Dear Debajyoti, It is likely that you have crystallized a contaminant in your preparation. You can put the unit cell into BALBES which will tell you if the PDB has seen it before. Another thing is to submit your polyalanine trace to DALI to see if the fold is recognised. James -- Dr. James

Re: [ccp4bb] saxs on xtals

Dear Anna, I once modified CNS to refine two solvent regions of ferritin, one inside and one outside the shell. Perhaps this can be done in Phenix now. If you want to locate magnetite particles in this way, you should collect data to as low a resolution as you can (may need to move backstop),

Re: [ccp4bb] Neutron data collection

>Wow, neutrons are pretty cool! No radiation damage--and time >resolution? Actually, as calculated by Richard Henderson in 1995, there is non-negligible radiation damage from neutrons due to infrequent but energetic nuclear reactions. The reason that radiation damage by neutrons is not observed

[ccp4bb] PDRA job opportunity

Dear all, see below for a PDRA opportunity at Imperial college to work on the structural basis of Photosystem II assembly and repair. James http://www.jobs.ac.uk/job/ADC906/research-associate/ Research Associate Imperial College London - Faculty of Natural Sciences, Division of Molecular

Re: [ccp4bb] Sequence Alignment Question

Re sequence alignment, For those TeXnically inclined, TeXshade produces beautiful alignment figures. (Steep TeX learning curve, I have an example script if anyone wants one). http://www.ctan.org/pkg/texshade James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Bio

Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases

Dear all, The following paper describes 'element specific maps', calculated by collecting data immediately above and below an absorption edge. http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html I have used this technique, and it works very well. If anyone is interested I have a s

Re: [ccp4bb] How to detect the concentration of detergent?

Dear Y B Lin, Measuring detergent has been discussed before on this list - one way is to do thin-layer-chromatography against a set of standards. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg12915.html >A strategy for identification and quantification of > detergents frequently used in

Re: [ccp4bb] Reverse Translatase

>So, let's say instead these adaptors recognize 2 amino acids at a time >(still probably not robust enough). Then, one would need 2^20 >adaptors, already a far greater number of gene products than that >present in any genome than I know of... Surely only 20^2, which is 400? A lot, but managabl

[ccp4bb] FW: [ccp4bb] Is there any easy to convert a colume in mtz file (say fom) into a fixed value?

>Is there any easy to convert a colume in mtz file (say fom) into a fixed >value? I tried to convert to ascii first, but mtz2various only takes 1 >single FP colume (unfortunately I have 2). Thanks! Can't think why you might want to do this, but sftools will do it. shellscript: #!/bin/bash sftoo

Re: [ccp4bb] Common protein crystallization contaminants

best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: Chris Ulens [chris.ul...@med.kuleuven.be] Sent: Friday, June 11, 2010 12:56 PM To: Murray, J

[ccp4bb] common protein crystallization contaminants

Dear All, I was wondering if anyone has compiled a list of common proteins that can co-purify from E. coli preps (and yeast etc), and crystallize instead of the protein of interest. If list members send me individual examples I will compile a summary for the bulletin board. best wishes James

Re: [ccp4bb] Displaying repeats in a amino acid sequence

Dear Klaus, You could make a dot-plot of the sequence against itself. Repeats will show up as diagonal lines parallel to the main diagonal. http://emboss.sourceforge.net/apps/cvs/emboss/apps/dotmatcher.html best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division on

Re: [ccp4bb] Alignment software

>I’m trying to prepare an alignment figure of 2 proteins that highlight >conserved and similar residues and probably secondary structures; I will >greatly >appreciate it if anybody can recommend a software that I can use. >Thanks, Mohd For those who like TeX, TeXshade is incredibly powerful, an

Re: [ccp4bb] When can I say the refinement is done?

Can we have a moratorium on plugs for books please? James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behal

[ccp4bb] rotamer nomenclature question

Dear All, A non-CCP4 question: In proteins (and RNA), the term "rotamer" is used to refer to a specific conformer (or class of conformers), found in structures. According to IUPAC (http://goldbook.iupac.org/R05407.html), the term should only apply to rotation around a single bond, which is no

Re: [ccp4bb] low B factor for water

Dear all, > When I refined one of my structures in refmac and cns, I found some water > molecules having low B factor (i.e < 10). If no one else has suggested it calculate an anomalous difference map, these are very powerful, and can reveal very small f'' with good data. James Dr. James Mur

Re: [ccp4bb] FreeR flag value swap

Dear Petra, the following shell script should do the job. best wishes James #!/bin/bash input=input.mtz oldfreer=FREE newfreer=NEWFREE sftools <

Re: [ccp4bb] Volume calculation of a crevice

Dear Enrique, VOIDOO does what you want. http://xray.bmc.uu.se/usf/voidoo_man.html Other similar programs are CAVENV in the CCP4 suite, and CAVER (http://loschmidt.chemi.muni.cz/caver/), which finds tunnels, and gives you tunnel radii. best wishes James Dr. James Murray Biochemistry Buildi

Re: [ccp4bb] How to replace 2.45M K/Na phosphate buffer - 2

Dear Claudia, >These crystals dissolve in several cryoprotectant solutions and survive only >in malonic acid, with which they give diffraction at 7-8 A. You do not mention what the room temperature diffraction is like. If you have not tested it already, you should do so - even without malonat

Re: [ccp4bb] Is anomalous signal a different wavelength?

Dear All, While we are talking about X-ray scattering, I have another question. If an X-ray is elastically scattered from an electron at an angle theta, its energy is the same is the incoming X-ray. However, the momentum is not the same, as it now has a component in a perpendicular direction

Re: [ccp4bb] Molecular Replacement of a Known Anomalous Substructure

Dear All, The authors of the following paper used molecular replacement of the substructure to locate the heavy atoms. The known 11-fold symmetry meant that the heavy atoms had to be in a circle - molecular replacement with circles of different radii did the trick. Antson et al. Nature, Vol