[ccp4bb] PDB Upload
Dear all,uploading a PDB I am ERROR: 2 atoms in lines (10536, 10670) have same coordinates: -1.977 101.862 34.009. If these records are for the same atom of the same residue, the redundant coordinates should be either removed or combined. If these records are for different atoms assigned alternate conformations, please add their alternate conformation indicators at column 17. Deepak Chand Research Fellow (SRF) Structure Biology Group National Chemical Laboratory Pune 411008 Maharashtra, India (+91)020-25902212, Mob No. 9021766452
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Dear all, I am uploading a PDB and after executing upload option along with mtz file several errors pop-up which is mentioned below.. where 10536 Serial no. correspond to the water molecule and 10670 S. No. doesn't exist in the PDB. ERROR: 2 atoms in lines (10536, 10670) have same coordinates: -1.977 101.862 34.009. If these records are for the same atom of the same residue, the redundant coordinates should be either removed or combined. If these records are for different atoms assigned alternate conformations, please add their alternate conformation indicators at column 17. how Can I solve the problem? Thank you Deepak chand Deepak Chand Research Fellow (SRF) Structure Biology Group National Chemical Laboratory Pune 411008 Maharashtra, India (+91)020-25902212, Mob No. 9021766452
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Dear Deepak Chand, (in my understanding) the error message tells you very detailed and clearly how to resolve the problem. Maybe you could explain a little which part of it you don't understand? You could open the PDB file with a text editor and take a look at the mentioned lines. Regards, Tim On 09/02/2014 08:36 AM, Deepak Chand wrote: Dear all, I am uploading a PDB and after executing upload option along with mtz file several errors pop-up which is mentioned below.. where 10536 Serial no. correspond to the water molecule and 10670 S. No. doesn't exist in the PDB. ERROR: 2 atoms in lines (10536, 10670) have same coordinates: -1.977 101.862 34.009. If these records are for the same atom of the same residue, the redundant coordinates should be either removed or combined. If these records are for different atoms assigned alternate conformations, please add their alternate conformation indicators at column 17. how Can I solve the problem? Thank you Deepak chand Deepak Chand Research Fellow (SRF) Structure Biology Group National Chemical Laboratory Pune 411008 Maharashtra, India (+91)020-25902212, Mob No. 9021766452 -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
[ccp4bb] Off-Topic_Instruct Biennial Structural Biology Registrations open
Instruct Biennial Structural Biology Registrations open The second Instruct Biennial Structural Biology Meeting at Convitto Della Calza, Florence, Italy 20-22 May 2015 will showcase integrative structural biology and its impact on biological research. The program includes sessions that represent recent advances on structural biology toward cellular biology, emerging methods and technologies and results of biomedical importance. Confirmed speakers are: John Womersley (ESFRI, STFC), Wah Chiu (Baylor), Patrick Cramer (Ludwig-Maximilians-Universität München), Marc Baldus (Utrecht University), Teresa Carlomagno (EMBL Heidelberg), Sriram Subramaniam (NIH), Edward Arnold (Rutgers), Helena Käck (Astrazeneca) and Anne-Claude Gavin (EMBL). A session will focus on Instruct in the wider context of integrated European infrastructures. Eero Vuorio, Director of Biocenter Finland (BBMRI) and David Stuart (Instruct director, University of Oxford) have confirmed their participation to speak in this session. Young scientists who want to know where structural biology is and where it is going are especially encouraged to attend. Upcoming submission opportunities/deadlines include: Abstract submission: March 15 Registration closing: April 1 Student fellowships: March 15 We look forward to seeing you in Florence, register at www.structuralbiology.eu/update/biennial/ The Instruct Operations Team Dr Claudia Alen Amaro Scientific Project Manager Instruct: An Integrated Structural Biology Infrastructure for Europe, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK Tel: +44 1865 287808 email: clau...@strubi.ox.ac.uk Follow us on twitter @instructhub
[ccp4bb] PhD student position available at Department of Drug Design and Pharmacology, University of Copenhagen
If you are interested please follow the link: http://employment.ku.dk/phd/?show=683707 Best regards Michael Gajhede Michael Gajhede Professor Faculty of Health and Medical Sciences Biostructural Research University of Copenhagen Jagtvej 162 2100 Copnhagen Ø Denmark TEL +45 35336000 DIR +45 35336407 m...@sund.ku.dkmailto:m...@sund.ku.dk www.ku.dkhttp://www.ku.dk/ [Description: Description: Description: Description: Description: Description: SUND_bomaerke_UK]
[ccp4bb] Help with importing density fit bar plots from Coot
Hi, Density fit analysis in Coot plots the real space R-factor for each residue. Is it possible to import these values for each residue? Thank You, Amit
Re: [ccp4bb] Help with importing density fit bar plots from Coot
Dear Amit, I am not aware of an easy way to do this using Coot. However, if you run the Comprehensive validation tool in Phenix, it will generate a similar real-space correlation plot automatically, and the raw data for that plot can be exported (there is an option to save results to file). Alternatively, the Map correlation tool, under Map and mask utilities in CCP4i will perform a similar function (and I believe there is also an option in SFCHECK to do the same). Cheers, Oliver.
Re: [ccp4bb] Help with importing density fit bar plots from Coot
On 02/09/14 15:06, amit sharma wrote: Density fit analysis in Coot plots the real space R-factor for each residue. Is it possible to import these values for each residue? And this time to the right list (sorry)... If you are using the coot package, you can use density-score-by-residue to get these numbers as text. Paul.
[ccp4bb] Question 2/2: Internal deletions of construct
Hi all, I am expressing a construct in e. coli (BL21-CodonPlus(DE3)-*RIL*) that corresponds to a truncated form of a lower eukaryotic protein. I inherited this construct (though I did do some additional SDM), but DNA sequencing of the insert confirms it is as expected. Without protease inhibitors, if I perform SEC immediately after Ni-NTA purification, all protein comes out in the void volume; however, if I leave it at 4oC for ~24h or more, a second lower molecular weight band corresponding to a possible tetramer appears (with subsequent decrease in the void volme peak); longer incubation times don't change the relative peak heights. In the presence of protease inhibitors, this lower molecular weight peak doesn't appear. Aha - proteolysis I thought - but read on! SDS-PAGE shows both peaks correspond to the expected construct size, and at least without without protease inhibitors, a 7.5% acryl/bis gel shows there are 3 tightly clustered bands in the teteramer peak. This is again consistent with proteolysis - but continue reading. A western blot (anti-His) shows that in addition to this cluster, some very high molecular weight bands (which are barely visible in the coomassie- stained SDS PAGE gel) light up like a Christmas tree. I originally put this down to being a false positive, but a totally different protein made from the same e. coli stock and same purification protocol doesn't produce this, so I'm starting to have doubts (maybe co-purification of e. coli proteins, but pretty unlikely). Obviously I was pretty sure that the 3 bands observed in the SDS-page gel were the result of N-terminal proteolysis (the His-tag is at the C-terminus and I still see binding to Ni-NTA); however, after mass spec analysis it appears that they are the result of short stretches of internal deletions that vary between the 3 (one of the bands showed any N- or C-terminal deletions). My question: Could this heterogeneity in expression be brought about by mis-reading the RNA template? If so, why is there a time dependence in the SEC chromatograms? Would a synthetic gene minimizing local secondary structure likely solve my problems? Also, any suggestions on the Western blot result would be appreciated (if it's not a false positive, the best explanation I can come up with is co-purification of large, weakly bound e coli proteins that are recognized by the anti-His antibody). Thanks for your help!
[ccp4bb] Question 1/2: Ethanol-tight seals for 96-well racks
Hi all, I'm looking for a suitable SBS footprint plate that has 96 wells and can be sealed (and resealed), one column (8 wells) at a time, using a system that won't allow volatile organic solvents to escape or dissolve the seal. Racks will be stored at -20oC, so that is a consideration too. I've used Micronic racked tubes with individual caps before, but they only come in a minimum of 10-packs, are expensive, and the caps are fiddly to use. Does anyone have any recommendations? Thanks.
Re: [ccp4bb] mtz map data
Well, it is sort of a catch-22. If you already know what the signal looks like, then you're already done. But being close is better than being far away. The Wiener filter itself is described in the Undisputed Source of All Human Knowledge here: http://en.wikipedia.org/wiki/Wiener_filter As for a well-defined measure of the goodness of a filter, the best metric is to compare the result of the filtration to a known right answer. If you don't know the right answer, then the next best thing is to make one up that is as close as possible to what you believe the right answer should look like, add to that your best guess of the kind of noise you are dealing with, and then try different filters on your fake data to divine the best way to recover the uncorrupted signal. Then you can blindly apply that best filter to the real data. After all, the only difference between signal and noise is that you find the signal interesting. Your detector doesn't know the difference. To separate the two you may find that you need to learn as much about the noise as you do about the signal, and that is what the concept of optimal filtering is all about. HTH -James Holton MAD Scientist On 8/29/2014 2:57 PM, Keller, Jacob wrote: That is, the optimum noise filter is generally the same shape as the signal of interest ... Has this been proven, or it just common sense? And if the filter is the same shape as the signal, why does one need the signal at all? I guess I don't know precisely what you mean, but anyway, I like the concept, which seems to have a sort of Bayesian aroma to it. I'd also be interested to know of a well-defined and useful measure of the goodness of a filter. Good weekend, Jacob Keller
Re: [ccp4bb] Felix Frolow has passed away
Sad news indeed. Felix was my PhD mentor (together with Yosef Gilboa, who alas is also no longer with us - another bright light extinguished before his time). He was one of the few true old-school structural biologists; someone who was not afraid to ask the tough questions and who had the persistence and the strength of will to work hard (and to push others) until answers emerged. He was very fond of the maxim 'extraordinary results require extraordinary proof' (which at the time was something of a challenge for me as I was young and impatient) -- as time passes, I see the wisdom of this approach come true over and over again. As opposed to the more standard lecturing style Felix always taught his students to learn - to earn the knowledge through one's own work - and because of this he was a fantastic teacher and a true master in his field. Even though Felix is gone, the reflections of his light in other people's lives shall live on. He was, and forever remains, my friend. I will miss him dearly. Artem
[ccp4bb] paper
please can you send me this paper... i can not subscribe it from my lab... *Acta Cryst.* (2014). F*70*, 1296-1302[ doi:10.1107/S2053230X14014381 http://dx.doi.org/10.1107/S2053230X14014381 ]
