[ccp4bb] PostDoctoral researcher in Protein Interaction Engineering, Birkbeck College, London UK
Dear all, apologies for the slightly off-topic advertisement. We have an opening for a post-doctoral position at Birkbeck College focusing on Protein interaction engineering. This is part of the EU funded project MOSRBI (European Molecular-Scale Biophysics Research Infrastructure https://www.mosbri.eu/ <https://www.mosbri.eu/>) which involves several structural biology and biophysics Laboratories across Europe. Description of the job and further details about the post can be found here: https://cis7.bbk.ac.uk/vacancy/postdoctoral-researcher-in-protein-interaction-engineering-456021.html Application deadline is on the 3rd of October -- Dr. Nikos Pinotsis Protein Crystallography and Biophysics Centre Institute of Structural and Molecular Biology Department of Biological Sciences, Room B16b Birkbeck College Malet Street London WC1E 7HX Direct: +44 (0)20 3926 3507 Office: +44 (0)207 631 6458 Mobile: +44 (0)792 384 3593 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] postdoctoral position at Birkbeck/UCL
The Marechal group is looking to recruit a postdoctoral researcher to study the structure and function of the mitochondrial respiratory complex IV (cytochrome c oxidase). The position is funded for 3 years and it is immediately available. Deadline for applications is the 14th of May 2020. Details and on-line application can be found in the following link: https://cis7.bbk.ac.uk/vacancy/postdoctoral-research-associate-417932.html More information about our research can be found in our recent publications: Marechal et al PNAS 2020 PMID:32291342 Hartley et al PNAS 2020 PMID: 32291341 Hartley et al Nat Struct Mol Biol 2019 PMID: 30598554 For informal enquires please contact Dr Amandine Maréchal (a.marechal @ ucl.ac.uk). -- Dr. Nikos Pinotsis Protein Crystallography and Biophysics Centre Institute of Structural and Molecular Biology Department of Biological Sciences, Room B16b Birkbeck College Malet Street London WC1E 7HX T: +44 (0)207 631 6458 M: +44 (0)792 384 3593 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] ccp4/coot on macOSSierra
Hi Ehmke, for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This set up works for me (including pymol etc) good luck Nikos Dr. Nikos Pinotsis Institute of Structural and Molecular Biology Department of Biological Sciences, 3rd Floor, R313 Birkbeck College Malet Street London WC1E 7HX T: +44 (0)207 631 6827 F: +44 (0)207 631 6803 M: +44 (0)792 384 3593 On 06/04/2017 09:59, POHL, EHMKE wrote: Dear ccp4 community, I would appreciate any suggestions how to get the ccp4 interfaces (ccp4 and ccp4i2) and coot running on the new MacBook Pro under macOS Sierra 10.12.3. control. I have already tried different Xquartz version with no success thanks so much Ehmke
Re: [ccp4bb] [OT] which column to use in SLS/MALS instruments
Hi Sebastiano, we have used both silica based and superdex columns and we found the second as a better option for general usage. Most of our proteins are on basic buffer and about 50% of them stick on the silica based column. On the other side a superdex 200 10/30 from GE performed quite well, we got quite accurate results for both a ~250kDa hexameric enzyme as also for a 0.3 mg/ml injection of an insulin sample. Eventually I think depends on the applications you prefer to have. cheers Nikos Dr Nikos Pinotsis Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43-1-4277-52224 On 03/08/2011 02:03 PM, Sebastiano Pasqualato wrote: Dear all, I was wondering if somebody could help me out by suggesting the "best" column to be used in a Static Light Scattering (I guess it would be the same for a Multi Angle Light Scattering) instrument. We were suggested using a silica-based column, with very high separation properties, but it seems that these columns are highly sensitive to (even slightly) basic pH's. Even running the column in PBS, it looks like injecting samples at pH 8.0 ruins the column resin, making it unusable. On the other hand, GE Healthcare columns would require a huge amount of material to be loaded. What are you guys using in your instruments? Thanks a lot in advance for the feedback, best, ciao Sebastiano
Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time
Hi Darren, Sunbird from mozilla is accessible in any computer running linux and windows connected to the home network (I guess it should be compatible with other OS systems as well) and it's free. The problem is that it's getting slow depending how many instruments you have for booking. To address however booking in speculative manner is more complicated than a simple electronic booking system. cheers Nikos Dr Nikos Pinotsis Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43-1-4277-52224 On 02/16/2011 01:25 PM, Darren Hart wrote: Hello, Since we are now part of the "Facebook Generation" (or at least 10% of the planet is), it seems there must be a better way of distributing time on our various Aktas to an institute of scientists than our current system which involves a race for the paper booking sheet every Thursday morning. Inevitably people book in a speculative manner and time slots are not always used due to problems in preparative steps etc. Bits of paper in different buildings make it difficult to see who booked what and when. Has anyone successfully implemented an electronic system, perhaps shared through the "cloud", that allows real time booking in a manner that can be revised easily and has worked well? An electronic calendar (Google..) would partially address this, but it seems some sort of social networking site/tool might be better for negotiating instrument time, swapping timeslots, reallocating unused time if the sample prep fails. Any suggestions would be greatly appreciated. If governments can be toppled through Facebook, I'm sure we can book our Aktas in a better way! Darren -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** www.embl.fr/research/unit/hart/index.html <http://www.embl.fr/research/unit/hart/index.html> For funded access to ESPRIT construct screening via EU FP7 PCUBE: http://tinyurl.com/ydnrwg4 Email: h...@embl.fr <mailto:h...@embl.fr> Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **
Re: [ccp4bb] protein dimensions
quite straightforward with moleman2 and the command stat On Wed, September 8, 2010 19:37, Brett, Thomas wrote: > Hi all: > Is there program or utility out there that will give maximum protein > dimensions (length and width) from the pdb file? I'm sure there is, just > curious what people use. > Thanks, > -Tom > >
Re: [ccp4bb] phenix.refine and refmac
Dear Yang, it would be better if you could provide more details about your refinement strategies. As I can see from your results you might have used the default values in phenix giving you finally very low rmsd values. Refmac by default is not using so tight restraints and even if you used tight restraints in refmac the difference between R and Rfree might be much lower than the 7% in Phenix. I am guessing that the values that you are reporting have to do also with the weight values each program uses and how you are define them. Also have you used TLS in any of the two programs? regards Nikos - Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 - yang li wrote: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface
Hi, apart from the ccp4 "contact" it's also worth checking the following servers: pisa: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html protein-protein interaction server: http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html Cheers Nikos Xiaoyi Deng wrote: > Dear all: > > I used moleman2 to calculate the contacts between chain A and B. Can > anyone suggest a program to calculate the contacts between the > interface of dimer-dimer? > > Thank you, > > Xiaoyi > > Graduate student > University of Nebraska Medical center > > -- *** Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] ***
Re: [ccp4bb] Cannot running NTA to purify the protein having His-tag?
- Original Message - From: "Juergen Bosch" <[EMAIL PROTECTED]> To: Sent: Wednesday, 28 February, 2007 8:18 PM Subject: Re: [ccp4bb] Cannot running NTA to purify the protein having His-tag? Ngo Duc Tri wrote: Dear CCP4 users, I'm purifying a kind of protease having His-tag. The protein is expressed in insect cells and broken by sonication. I used NTA resin to purify this protein. Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl. Buffer B is 50mM phosphate buffer pH 7.5, 300 mM NaCl and 300 mM Imidazole. However, all proteins cannot bind to NTA resin. My protein is eluted in Flow-through. I also check the NTA resin with the control His-tag. The western blot also shows that my protein has His-tag. Do you have any ideas about my problem? I'm really appreciate all of your advices how to solve this. Thank you very much! My best regards, TriNgo Sungkyunkwan University You His tag is most likely inaccessible, can you easily change the tag from e.g the N-terminus to the C-terminus ? Or if you have a structural homolog you could add the His tag into a loop, which is exposed. Alternatively you can purify your protein under denaturing conditions using 8 M urea and refold it if you dare :-) Juergen Or try a partial unfold of your protein by including 1-3 M Urea in your buffer A Nikos ***** Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] *
Re: [ccp4bb] Question about glove boxes for protein crystallization
Dear Mathews, we were successful in crystallizing two ferredoxins under strict anaerobic conditions using the much cheaper solution of a glove bag and filling it with argon. I guess that in both cases (box and bag) the thickness of the gloves is a problem especially if you are dealing with cover slides. The glove bag occupies also much less space however its major problem was the very bad visualization of the inner space and finally we added a plexiglas window on the bag. Needless to say how essential is not to forget anything outside the bag/box before starting the crystallization set up. Finally you can also consider the possibility to use a crystallization robot. In some of them it is possible to create anaerobic conditions using argon. good luck Nikos * Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] * - Original Message - From: "Mathews, Irimpan" <[EMAIL PROTECTED]> To: Sent: Friday, 23 February, 2007 3:03 AM Subject: [ccp4bb] Question about glove boxes for protein crystallization Dear Friends, Sorry for the non CCP4 question. We are planning to purchase a small glove box to setup crystallization trays under anaerobic conditions. If you have used glove boxes for crystallization, would you please give me some idea? We are thinking of getting the 815 series from Plas-labs (link below). http://www.plas-labs.com/ Thank you very much, Mathews Ps: If others are interested, I will post a summary.
Re: [ccp4bb] omit map on OMIT ccp4 program
Dear Taiana, thy the updated info according to the new sfcheck style in: http://www.ysbl.york.ac.uk/~alexei/sfcheck.html or simply type "sfcheck -h" What worked for me recently (and also described in the link above) was simply typing sfcheck -f mydata.mtz -m mymodel.pdb -omit 2 -map you will get an omit "sfcheck_ext.map" in ccp4 format good lack Nikos ***** Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] * - Original Message - From: Taiana Oliveira To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 05 February, 2007 2:52 PM Subject: [ccp4bb] omit map on OMIT ccp4 program Hi everyone!! Does anybody have a example script for OMIT? The script link present on http://www.ccp4.ac.uk/html/omit.html leads to nowhere... I really appreciate your help! Sincerely, -- Taianá Maia de Oliveira Laboratório de Moléculas Biologicamente Ativas - Biomol-lab Departamento de Bioquímica e Biologia Molecular Univesidade Federal do Ceará Campus do Pici, s/n Bloco 907 Caixa Postal 6043 60.455-970, Fortaleza-Ce, Brasil tel/fax: +55 85 33669818
Re: [ccp4bb] OMIT MAP
Dear Bruno, you can use sfcheck. More information on http://www.ccp4.ac.uk/dist/html/sfcheck.html Regards N. * Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] * - Original Message - From: Bruno Matias To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 01 February, 2007 3:19 PM Subject: [ccp4bb] OMIT MAP Hi, Does anyone know how calculate omit maps in CCP4? I tried to find Omit in CCP4 program list, but I did not find it. I am using CCP4 Program Suite 6.0.1.
