[ccp4bb] A faculty position in the Department of Biophysics, NIMHANS, Bangalore, India

2017-06-27 Thread Padmanabhan B
A vacancy for a Faculty Position (Assistant Professor) in the Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, INDIA. Candidates who have research experience in membrane protein crystallography and Cryo-EM are encouraged to apply. Here is

[ccp4bb] project scientist position in structural biology at the NIH in Bethesda, Maryland

2017-06-27 Thread Antonina Roll-Mecak
DESCRIPTION The Roll-Mecak lab at the National Institutes of Health in Bethesda, Maryland is seeking to hire an expert researcher in the area of structural biology with emphasis on X-ray crystallography or electron microscopy of large multi-subunit complexes. Candidates should have expertise in s

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Relevant to this discussion, the 2018 ACA meeting in Toronto will have a session on "Best practices for building, refining, and analyzing ligands in macromolecular structures” co-chaired by Anna Gardberg and Kurt Krause. I expect this session will include case studies of structures that went w

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Trevor, I can share our recent experience correcting the record about a misplaced ligand binding site. It represents one possible way to deal with erroneous structures. Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited by another group in 2006 suggested that the NAD

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.
Trevor, I can share our recent experience correcting the record about a misplaced ligand binding site. It represents one possible way to deal with erroneous structures. Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited by another group in 2006 suggested that the NAD

[ccp4bb] Postdoctoral Position available, IHV of University of Maryland, Baltimore, MD

2017-06-27 Thread Pazgier, Marzena
A postdoctoral position is available immediately to participate in an inter-disciplinary research program on structural immunology at the Institute of Human Virology of School of Medicine, University of Maryland, Baltimore, MD. Candidates are expected to work on ongoing research projects in stru

Re: [ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread Phoebe A. Rice
Sorry if this is an insulting question, but did you store it in enough glycerol to prevent it from freezing? Proteins don't like freeze/thaw cycles, especially slow ones. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jai mohan [0cab66323371

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Constance Jeffery
Hi Trevor, I think you should also email the authors of the key paper in your field that you mention. They should be told that the structure they used to create the model of the mechanism was incorrectly interpreted and should have the opportunity to write a correction to their paper. Best re

[ccp4bb] My apologies to the PDB-REDO team

2017-06-27 Thread Philippe BENAS
Dear all, I realized I didn't properly aknowledge the team who made PDB REDO. So let me please correct my mistake by citing here the PDB REDO references (as found on the PDB REDO website) and providing a list of interesting papers to all : - Joosten RP, Long F, Murshudov GN, Perrakis A. Th

Re: [ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread Debasish Kumar Ghosh
Dear Jaimohan, With high amount of purified protein (like obtained in recombinant expression) they are likely to form higher oligomers if they have intrinsic property of association. With time the content of oligomers do increase. In SDS-PAGE even, you will see a faint band of oligomer. This is

Re: [ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread Satya
Hello Jaimohan, Is it SDS-PAGE gel or Native PAGE gel ?. Theoretically SDS-PAGE is supposed to show monomers and Native PAGE oligomers On Tue, Jun 27, 2017 at 8:27 AM jai mohan < 0cab66323371-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > I am working on a Red Fluorescent Protei

Re: [ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread Keller, Jacob
Are you boiling your samples? Seems funny that under SDS PAGE there should be dimers, unless there is a disulfide link. If so, reducing agents (DTT, TCEP, BME) should take care of this. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Smith Liu Sent: Tuesday, June 27, 2

Re: [ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread Smith Liu
it was not stable for frozen storage. if necessary,using protein fresh without frozen 发自网易邮箱大师 在2017年06月27日 20:22,jai mohan 写道: Dear all, I am working on a Red Fluorescent Protein (His-Tag) molecular weight around 27kDa. After purification I ran a SDS page, the band at 27kDa confirms the mono

[ccp4bb] Separating Monomers and Dimers

2017-06-27 Thread jai mohan
Dear all,I am working on a Red FluorescentProtein (His-Tag) molecular weight around 27kDa. After purification I ran a SDSpage, the band at 27kDa confirms the monomer. The protein was stored at -20C, aweek later again I ran a gel, this time I saw another new band between 50-60kDa, it confirmsthe

[ccp4bb] EMBL-EBI user survey

2017-06-27 Thread Gerard DVD Kleywegt
Dear colleagues, EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand usage of its resources (there are several dozen, including UniProt, Ensembl, ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you to forward this request within your departmen

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
I think the PDB (and Gerard DVD) got the answer with their quite new validation report provided for each entry.On the other hand PDBredo (Tassos & Co) is an excellent tool to compare a currently deposited structure and its reprocessed version (although it doesn't tell about the phasing). Best,Ph

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
Dear Bernhard, I totally agree with you and it was absolutely the meaning of my first email while thinking the used F were coming from Adrian's data. And by the way of the second as well. This being said what about groups that publish always poor structures ? Ins't it in some way dishonest ? Be

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Goldman, Adrian
I agree: I don’t think this is fraud, and was never even suggesting it. If it were fraud, _I_ at least would back-transform my structure so that there weren’t horrible red and green blobs all over the place…! I think it’s just sloppy - and the question remains, as posed by the original poster:

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Bernhard Rupp
I beg to differ. You are not pulling a murthy simply by depositing a poor or even wrong structure. Although the borderline beteeen sloppy work (and selfdeception) and reckless misleading of others can be floating, real cases of fraud and fabrication are almost exceptionally rare. Best, br On Jun

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Philippe BENAS
Dear Adrian, OK, I understand. You might be perfectly right. Moreover as I wrote it is difficult to tell something from a single mono view picture.And as you are pointing out their Ramachadran plots doe not look good at all. So they are poor crystallographers. But the question that remains is to

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Pietro Roversi
On the subject of withdrawal of entries from the PDB, I just flag up another interesting aspect. Four years ago I was Visiting Fellow in a colleague's lab, and in the course of the year I determined, refined and deposited 4 good structures, authored by me and my colleagues who were part of the

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Frank von Delft
What tiny fraction of the gazillions it would cost to store all the raw data, would be enough to arrange the training courses needed to get the ballooning population of practitioners up to speed, he mused idly. On 27/06/2017 09:21, Goldman, Adrian wrote: That’s quite something. To me, this t

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Goldman, Adrian
That’s quite something. To me, this thread raises another issue: I see a lot of comments about extracting the last little bit from every byte of data collected - but that’s not our main problem. Our main problem appears to be shoddily-done refinement of data that are in fact perfectly decent (

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread benjamin bax
Hi Trevor, Some of my colleagues came across a misinterpreted structure published in Acta D., a couple of years ago. They raised the issue with the editors of Acta D., who were most helpful in getting the issue sorted out. My impression is that the journals are the responsible for the papers

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Dale Tronrud
It can't hurt to try to work with the author, and it's the only way to get the current PDB file out of the database. If you don't get the response you want you can still go ahead and look for a venue to publish your own interpretation. Having a paper to go with the model is not only a requi

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tristan Croll
Note that in most cases a structure may only be obsoleted with the written agreement of a senior author. From experience it's by far the best approach to work together with the original authors on a correction, in any case. Goodwill is an important thing. If you wish, you can go it alone and de