[ccp4bb] Postdoctoral Fellowship at the NIH – Structural Biology of Microtubule Modification Enzymes

Dear All, I am looking for a talented scientist to join my lab as a postdoctoral fellow to work on the structure and mechanism of tubulin modification enzymes (please see details below). Many thanks, Antonina *Postdoctoral Fellowship at the NIH – Structural Biology * A postdoctoral fellow po

[ccp4bb] About protein aggregation～！

Hi, Recentely,we determined a monomer protein structure which looks like an dimer in solution via size-exclusion chromatography and SAXS, have you guys met such a situation before? or some references, Thank you for your reading Best wishes,

Re: [ccp4bb] 1st NJUST/CCP4 Crystallography School Announcement

Dear Eva I checked the application information on the Web page and can only find the information below: Thank you for your interest in the 2015 CCP4/APS Summer School. The application system for the 2015 school is now closed. The 2016 workshop will be advertised towards the end of 2015. Best Ro

[ccp4bb] POSTDOC FELLOW POSITION

A postdoctoral position is available for highly motivated applicant in the field of chemokine receptor (GPCR) structural biology that includes complexes with chemokines and small molecule ligands. Applicants should have experience with membrane protein biochemistry, GPCR expression, purification

[ccp4bb] 1st NJUST/CCP4 Crystallography School Announcement

Dear All, We are pleased to announce the first CCP4 Chinese crystallographic school at Nanjing University of Science and Technology (NJUST), in the city of Nanjing, China. All details can be found at http://www.ccp4.ac.uk/schools/china-2015/index.php Title:"NJUST/CCP4 school: From data proc

Re: [ccp4bb] reference needed for "TRUNCATE NO" equation.

Derivation but no reference except truncate is in BMC page 330 sidebar. Probably read the source code or some prog. ref…. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jonathan Cooper Sent: Tuesday, May 26, 2015 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] r

[ccp4bb] Segmentation fault in Pirate cmakereference

Dear CCP4 community, I am running the "make Pirate reference file" utility through CCP4i using downloaded coordinates and data. It consistently fails with: #CCP4I TERMINATION STATUS 0 "child killed: segmentation violation" #CCP4I TERMINATION TIME 26 May 2015 17:41:21 #CCP4I MESSAGE Task failed

Re: [ccp4bb] Hi

On 26/05/15 14:41, vijay srivastava wrote: Dear All, I want to superpose the nucleotide form one GTPase on to the nucleotide of other GTPase in order to study the interaction in the nucleotide binding pocket. I tried to superpose but it is superposing on the basis of secondary structure as a r

Re: [ccp4bb] Fwd: HETATM (.pdb) vs. ATOM (cif) records for modified nucleotides

Dear Xiang-Jun Lu, the part of the mmCIF file comes from a loop "_atom_site.group_PDB". According to the mmCIF dictionary, " The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose." I r

[ccp4bb] Position for recent MS or PhD

A position is open for a motivated scientist in biochemistry or a related field with a recent MS or PhD degree. The successful candidate will clone, express and purify proteins from a variety of expression systems for structural studies using x-ray crystallography and NMR. Excellent communicatio

Re: [ccp4bb] Off-topic: Request for DNA

Synthesize your gene: [advertisement on] https://www.idtdna.com [/advertisment off] Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street

[ccp4bb] Off-topic: Request for DNA

Dear all I am looking for a small amount of Aquifex aeolicus DNA or cell pellet for PCR. Unfortunately neither ATCC nor DSMZ holds this bacterium. Thanks.

[ccp4bb] Crystallography Symposium, 17th July 2015, Life Sciences Building, Lecture Theatre 3, University of Liverpool

Dear all, A symposium at the University of Liverpool has been organized to celebrate the achievements of Lipson and Beevers in the presence of a number of members of Lipson's family. The event, which will take place on 17 July 2015, is free to attend. Speakers include Eleanor Dodson, Mike Glaz

[ccp4bb] distorted NRQ in JLigand 1.0.40

Dear colleagues, I'm having an issue with a particular ligand in JLigand 1.0.40. When I load NRQ, the topology is correct but the bond lengths and angles are highly distorted, making it uninterpretable to my eye. A screenshot is viewable at https://www.dropbox.com/s/44nmmc96899o3uo/NRQ.tiff?dl=0.

[ccp4bb] Fwd: HETATM (.pdb) vs. ATOM (cif) records for modified nucleotides

Recently, I came across and was a bit surprised by the different assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format. Using PDB entry 1ehz (the crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution) as an example, 1MA58 in .pdb has atomic coordin

Re: [ccp4bb] Hi

Pymol -> pairwise align wizard -> done - Cosmic Cats approve of this message On Tue, May 26, 2015 at 11:44 AM, Zhijie Li wrote: > Hi Vijay, > > I am not sure if I understand you correctly. If you want to align by the > two nucleotide in two GTPase structures, you can simply do it in COOT usin

Re: [ccp4bb] Hi

Hi Vijay, I am not sure if I understand you correctly. If you want to align by the two nucleotide in two GTPase structures, you can simply do it in COOT using the “LSQ superpose” function. You need to fill in the chain id and residue number only for the nucleotide and choose “all atoms”. Unless

Re: [ccp4bb] Hi

Hi Vijay, In addition to the suggestions you've already received, the pair_fit command in PyMol is also an easy way to align based on specific atoms. You could use the C-alphas of relevant active site residues, or atoms of the ligand itself, for example. Just be mindful of the bias introduced base

Re: [ccp4bb] Auto-proteolysis

Hi Mohammad, I'm not sure anyone here can give you absolute answers, because we don't know enough about your system, but there's 3 things you might want to explore: 1. Contaminating proteases, even at tiny amounts, could lead to appreciable cleavage of your protein over the length of a crystalliz

Re: [ccp4bb] Auto-proteolysis

Extraordinary conclusions require extraordinary proof, yes? If you are completely convinced (!) that auto-proteolysis is possible (meaning that the enzyme you're studying is at least a proteinase in potentia, and also you have utterly ruled out contamination by host proteases) then the next step i

[ccp4bb] BioSAXS beamline scientist vacancy at Diamond

Dear All, Apologies for slightly off topic post but can I draw your attention to the following vacancy at Diamond. Regards Gwyndaf Job Reference & Title DIA1033/CH – Beamline Scientist BIOSAXS B21 Type of post

Re: [ccp4bb] Auto-proteolysis

Hi, How certain are you that what you see is the result of auto-proteolysis and not proteolysis  by a contaminating protease? Have you used protease inhibitors (of all sorts) during purification?            Boaz     Boaz Shaanan, Ph.D. Dept. of Life

[ccp4bb] reference needed for "TRUNCATE NO" equation.

Dear all I have been asked by Randy for a reference for the following equation which appears in Sherwood & Cooper: http://www.ucl.ac.uk/~rmhajc0/truncate_no.jpg ... or in text form:  sigma(F) = sqrt(I + sigma(I)) - sqrt(I) It is the equation which TRUNCATE uses to calculate sigma(|F|) if the use

Re: [ccp4bb] Hi

I would suggest biopython. http://combichem.blogspot.com/2013/08/aligning-pdb-structures-with-biopython.html On Tue, May 26, 2015 at 10:25 AM, Dimitry Rodionov wrote: > Dear Vijay, > > Your problem sounds like a job for LigAlign: > http://www.pymolwiki.org/index.php/LigAlign > > Regards, > Dm

Re: [ccp4bb] Hi

Dear Vijay, Your problem sounds like a job for LigAlign: http://www.pymolwiki.org/index.php/LigAlign Regards, Dmitry On Tue, May 26, 2015 at 8:42 AM vijay srivastava wrote: > Dear All, > > I want to superpose the nucleotide form one GTPase on to the nucleotide of > other GTPase in order to

Re: [ccp4bb] Hi

Hi vijay, I think the pymol-based program “legalign” will do what you want: http://compbio.cs.toronto.edu/ligalign/ Hope this can help, Marco > Il giorno 26/mag/2015, alle ore 05:41, vijay srivastava > ha scritto: > > Dear All, > > I want to supe

Re: [ccp4bb] Hi

I am not absolutly certain to understand the steps that you followed. But if it doesn't work with the nucleotid as "reference" and "target", maybe if you face two GTPase, you can find some conserve residues in the binding pocket. In this cas, you can use these residues as ref. and target. To be

[ccp4bb] FW: [3dem] Citing Structures

Letter send on the behalf of Dr. Les Loew: Dear Crystallography Community, The Biophysical Journal (BJ) and the Biophysical Society leadership recently published a joint Editorial entitled “Reproducibility of Research in Biophysics

Re: [ccp4bb] Hi

Dear Vijay, Have you try to use superpose in ccp4 ? In superpose it's possible to select exactly what you want (atoms, residues...) . In your case if you use only the atoms or the nucleotids that you want to be superpose, it could be ok. Hope to help. Nicolas __

[ccp4bb] Hi

Dear All, I want to superpose the nucleotide form one GTPase on to the nucleotide of other GTPase in order to study the interaction in the nucleotide binding pocket. I tried to superpose but it is superposing on the basis of secondary structure as aresult both the nucleotides from two structutr

[ccp4bb] Post doctoral position in kinetic structural biology

Dear ccp4bb, I have a post-doc position available in my lab (see below) and would be grateful if this advert could be passed on to suitable candidates. Thanks, Mike SENIOR RESEARCH OFFICER (PDRA) - 18 months. Ref RE815 Location School of Biological Sciences, Unive

[ccp4bb] PhD call at the Free University of Bolzano, Faculty of Science and Technology

Dear All, I would like to bring to your attention the public call for PhDs at the Faculty of Science and Technology of the Free University of Bolzano. Two projects on the structural and functional characterization of proteins involved in the pathogenicity of Erwinia amylovora, the agent respon