Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
Sorry can't help it. The aggressive replies are mainly from senior PIs from US - friend in need is friend indeed. On Thu, Apr 23, 2015 at 2:20 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Well, with full respect to your sensitivities as far as your own person is concerned: if you play rough (and 5 exclamation marks qualify by commonly accepted email etiquette as incipient flame, at least), you need to be willing to take a few as well... Best, BR - Trigger warning --- This message may or may not contain references to issues of privilege and oppression in- cluding but not limited to enantiophobia, point classism, heteroatomism, transbondism, cisbonding, sizeism, curvature, references to color, alcohol, blood, small insects, cancer cells, and any combination thereof that may cause symptoms ranging from discomfort and anxiety to violent physical response in sensitive individuals and must therefore be labeled as potentially hazardous to your comfort and well-being. - Trigger warning --- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Misbah ud Din Ahmad *Sent:* Thursday, April 23, 2015 2:05 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers! I feel rather uncomfortable and cornered with the aggressive replies and phrases like throwing stones, public humiliation etc., which suggest that I have some personal enmity with the author. The structure is in the public domain and questions can be asked about it. I as a beginner in crystallography learn from each discussion on this board and such harsh and insinuating responses may, in future, deter people like me from posting any questions at all and learning refinement strategies like the one which Pavel outlined to improve such type of structures. Best Misbha On Thu, Apr 23, 2015 at 9:17 PM, Gert Vriend gerrit.vri...@radboudumc.nl wrote: At around 4.0 A resolution one normally cannot talk about accuracy. The density will at most locations not warrant any detailed interpretation. If, at 4.0 A resolution, you move atoms around a bit, you will not see significant changes in R/Rfree. So, you can do whatever you want, more or less. If the refinement puts great emphasis on the secondary structure (i.e. tries to force the Ramachandran plot, then you get a good Ramachandran plot, but if they put more weight of the fit to the density, you get a slightly lower R (and perhaps even Rfree) at the cost of the Ramachandran plot. And all of that is meaningless. At this resolution you have to check if the fold is likely to be correct. I superposed just any high(er) resolution domain with high sequence similarity at the corresponding 3bdn domain, and I take any bet that the fold of 3bdn is right (at least of the domain I looked at, and I extrapolate to the other domain). PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/) cannot improve this one, and WHAT_CHECK (http://swift.cmbi.ru.nl/gv/pdbreport/) throws its hands up in the air. At 4.0 A you should be happy with an indication of the fold (and with the fact that the authors probably went through great pains for you getting these coordinates close to where they should be). Gert
Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore
Sham is very right about the institute. Narayana Sthanam's illustrious former colleague Krishna Murthy who faked so many structures retracted quite a few papers was an alumnus of the institute. On Mon, Oct 29, 2012 at 12:21 PM, James Stroud xtald...@gmail.com wrote: The agism in the advertisement doesn't do the institute much credit. I'm inclined to believe Sham, given the Institutes stated policies: Applicants, preferably below 35 years James On Oct 29, 2012, at 11:28 AM, Narayana VL Sthanam wrote: Sham, who so ever you are, if you have such a long list of complaints, why don’t you put your name clearly and complain openly, instead of hiding behind some anonymous ‘SHAM’ name. What you write about IISc may be all true or it may be reflection of your frustration for not getting a job at IISc!*** * How do we know? So, grow a ‘spine’, if you have a complaint, say it like a man and do not hide behind and bad mouth others anonymously like spoiled child. You are not only throwing dirt on such a prestigious Indian institution, and also on many decent and capable scientists who do outstanding work and produce brilliant graduate students, some of which I was fortunate to have in my lab. ** ** Best Narayana Sthanam ** ** *--* *Narayana Sthanam,Ph D* *Professor of Structural Biology* *244 CBSE 1025 18th Street South* *Center for Biophysical Sciences and Engineering* *University of Alabama at Birmingham* *Birmingham, Al 35294* *Phone: 205 934 0119* *URL: **http://www.opt.uab.edu/narayanalab*https://mail.ad.uab.edu/owa/redir.aspx?C=80a7a9ef03ea46b58d648b78f13d4272URL=http%3a%2f%2fwww.opt.uab.edu%2fnarayanalab “Never let success go to your head, nor failure to your heart ” ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *U US *Sent:* Monday, October 29, 2012 12:03 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore ** ** Dear Friends, There is no need to apply to this position, we suggest. It is a PREDETERMINED SELECTION, i.e. candidate is fixed and this (advertisement, screening, selection board, selection and approval) is just the procedure. It does not matter whether you apply or not. If you apply and called for interview, then you have to waste your valuable time as well as huge travel money unless some Big Boss is fixing you to the post. Interestingly Indian Institute of Science recruits and carries faculties and trains them in such a way that it has become a epicentre of recruitment scams across India and it make rest of Indian Scientists/Faculties in their path of scams and CRIME. Students also inherit the character of their boss. They do not participate in any form of fair selection in the country. Almost all cases they select and load many times inferior candidates even though candidate was not seen by anybody or interviewed. Similarly they distribute various national awards among themselves and within their group. THEY ARE NOT ASHAMED AT ALL. This is just an attempt of WASTING HUGE PUBLIC MONEY by a bunch of crooks who are good for nothing but worst for everything. Sham ** ** -- Date: Mon, 29 Oct 2012 11:47:06 +0530 From: vikasnavra...@gmail.com Subject: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore To: CCP4BB@JISCMAIL.AC.UK Dear all Kindly make a note. Indian Institute of Science, Bangalore. ** ** Molecular Biophysics Unit (http://mbu.iisc.ernet.in/) ** ** Opening for Assistant Professor Positions. ** ** Applicants, preferably below 35 years, should have a Ph.D. with postdoctoral experience with an excellent publication record. ** ** We seek candidates in the general area of structural biology with an emphasis on understanding macromolecular systems at the molecular level. ** ** Applications with a detailed CV, research plan (not exceeding 3 pages) and names of at least 4 referees should be sent to chair...@mbu.iisc.ernet.in Best
[ccp4bb] resolution limit
Hello CCP4ers, In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. The water content is 68%. I loweredthe multiplicity to 4.1 by excluding few images but still the Rsym is 200 % and I/sigmaI 2.0. My rudimentary crystallography knowledge makes me believe it's quite Ok to use data upto 2.8 A and report the statistics. Could I request people's views. Thanks very much. Narayan
[ccp4bb] Bio Rad Econo system
Dear CCP4BB, Sorry for this off-topic question. However it would immensely help our not so greatly well-funded lab if people could share their experiences regarding Bio-Rad econo pump system. We are planning to buy the Bio Rad Econo system or the Bio Rad Bio Logic system. They are basically the same thing, but the Bio Logic is a bit fancier because it can be controlled by a windows pc. We will be using this for preparative protein purification on the order of 1 to 10 mg of purified protein. We require a method of for gradient formation for ion-exchange and hydrophobic interaction chromatography. Opinions on this system from other academic or commmericial sector scientists who have used this apparatus would be greatly appreciated. Thanks a lot. Narayan
