[ccp4bb] Postdoctoral position at the University of Leeds

2016-12-22 Thread Adrian Goldman
.uk/FBSBM1056> To access Vacancy Management to view applications etc. use the link below: https://jobs.leeds.ac.uk/VM/Applications.aspx?jobId=6948 <https://jobs.leeds.ac.uk/VM/Applications.aspx?jobId=6948> I would be interested in seeing a diverse range of applicants! Adrian Goldman, P

[ccp4bb] Postdoc in Adrian Goldman's lab

2015-06-09 Thread Adrian Goldman
Molecular Biology. You will be supervised by Professor Adrian Goldman (SBMS), and the work will involve close collaboration with the University of Helsinki (Dr Henri Xhaard and Professor Seppo Meri) and with Drs. Roman Tuma and Sarah Harris at the University of Leeds. You will be a highly motivated

[ccp4bb] Symposium announcement Atoms2Disease symposium, Helsinki 10-12th June, Registration deadline approaching

2015-04-08 Thread Adrian Goldman
; Kurt Wüthrich, ETH Zurich Session speakers include: Riita Hari, Aalto; Edgar Kramer, Hamburg; Carlos Ibanez, Stockholm; Neil McDonald, Cancer Research, UK; Leo Sazanov, Cambridge; Ville Kaila, Munich; Adrian Goldman, Leeds; Ulrich Brandt, Nijmegen; Valerio Carelli, Bologna; Howy Jacobs

Re: [ccp4bb] Crystallization of a minority fraction monomers

2015-04-08 Thread Adrian Goldman
Without wishing to get into the terminology, and going back to the OP’s question: our crystal structures of factor H 19-20 would be a citeable example. In our hands, the wt 19-20 preferentially crystallises as a well-ordered D2 tetramer (cf Jokiranta et al 2006, EMBO J) that is completely

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

2015-04-01 Thread Adrian Goldman
no, and that’s why they all needed to be stored at Diamond in case future generations have better programs. And this applies also to those that have already been digested - I mean, processed. Adrian On 01 Apr 2015, at 12:03, Keller, Jacob kell...@janelia.hhmi.org wrote: Can anyone index

Re: [ccp4bb] Absence of contact between layers in a crystal

2015-02-06 Thread Adrian Goldman
Our recent membrane protein structure (4av3) doesn’t have much in the way of contacts either, as is characteristic of type 1 membrane protein crystals. Adrian On 06 Feb 2015, at 11:51, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote: Just to

Re: [ccp4bb] Absence of contact between layers in a crystal

2015-02-06 Thread Adrian Goldman
Well maybe some pressure should be put on Nature to retract the article, so that we can get the publication out of the PDB? It’s not good that it is there for the unwary. Adrian On 06 Feb 2015, at 11:44, Folmer Fredslund folm...@gmail.com wrote:

[ccp4bb] Research Fellow at the University of Leeds

2014-11-09 Thread Adrian Goldman
and physicists, and as part of the Astbury Centre for Structural Molecular Biology. You will be supervised by Professor Adrian Goldman (SBMS). You will be a highly motivated individual with a strong basis in all aspects of structural biology from expression to structure determination, and you

[ccp4bb] Postdoctoral position in structural studies of integral membrane pyrophosphatases

2014-07-12 Thread Adrian Goldman
. The applications (in English) should be sent to: Docent Taru Meri, P.O. Box 56, FIN-00014 UNIVERSITY OF HELSINKI, Finland or by email to taru.m...@helsinki.fi. The deadline for applications is 4 August 2014. For more information please contact Adrian Goldman, tel. +44 79 18951821; adrian.gold

Re: [ccp4bb] emergency substitute for RT loop cover?

2014-07-07 Thread Adrian Goldman
Why not draw out a pasteur pipette using a bunsen burner to the desired thinness? You’ll end up with something rather like an old-fashioned glass capillary. Adrian On 7 Jul 2014, at 17:52, Matthew Franklin mfrank...@nysbc.org wrote: Hi Frank - How about a gel loading pipet tip as a

Re: [ccp4bb] PyMol and Schrodinger

2014-04-23 Thread Adrian Goldman
Well as s/w improvements don't necessarily happen on a yearly basis, but people like being paid each year, I think the model is not unreasonable, as long as the cost is reasonable - which, for instance, the Adobe s/w isn't. As one can tell from the profit margins of s/w companies. So I do pay

[ccp4bb] Studentship in Crystallography and Parasitology

2014-04-23 Thread Adrian Goldman
and Muench at the addresses above. Adrian Goldman and Stephen Muench

[ccp4bb] Studentship in Crystallography and Parasitology

2014-04-23 Thread Adrian Goldman
and Muench at the addresses above. Adrian Goldman and Stephen Muench

[ccp4bb] Studentship in Crystallography and Parasitology

2014-04-16 Thread Adrian Goldman
. Informal enquiries can be addressed to both Goldman and Muench at the addresses above. Adrian Goldman and Stephen Muench

[ccp4bb] stereo monitors/MAC

2013-10-23 Thread Adrian Goldman
Hi, Having now had a chance (finally) to play with the Asus VG27A, I can say that (a) it works really well in stereo with both Coot and PyMol and (b) it is easier and nicer to use than the Zalmans. Though the technology is essentially the same (halving the vertical

[ccp4bb] stereo monitors/MAC (try 3!)

2013-10-23 Thread Adrian Goldman
Hi, (and apologies if ANYONE has seen this twice - CCP4BB rejected my first post as coming from an unknown (i.e. Leeds) address, and the second one because I had already posted from my Leeds address….) Here goes: Having now had a chance (finally) to play with the Asus

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

2013-10-10 Thread Adrian Goldman
…then the issue is to reduce the number of papers people publish: this is the central problem in the system: nobody reads them, nobody cites them, etc etc. There are papers out there - quite a number - that have no cites, meaning that even the authors weren't interested in them. A long time

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2013-09-09 Thread Adrian Goldman
Yes, my understanding too is that they all work at HD resolution, which is pretty unimpressive if you halve the vertical frequency. But that's what constitutes a cheap high-resolution screen this days. One can only wait and hope that people get into the 4K monitors, when life will become

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2013-09-08 Thread Adrian Goldman
)” Linda Olson bought the ASUSVG27AH - and it worked. hth, Adrian Adrian Goldman, Ph. D. | Leadership Chair in Membrane Biology| Astbury Centre for Structural Molecular Biology Astbury 6108b

[ccp4bb] somewhat off-topic: stereo on macs for building into density...

2013-07-03 Thread Adrian Goldman
Hi, I thought I'd pose my perennial question about 3D-stereo on Macs. There is the Zalman solution (not terribly good, and are they making monitors any more?) - are there other vendors doing the same thing? Maybe at higher resolutions?? In addition, is there any evidence

[ccp4bb] slightly off-topic: stereo visualisation on the MAC

2013-03-05 Thread Adrian Goldman
Hi, has anyone any joy with stereo visualisation on the mac? There's a 9/2012 note on the PyMOL page indicating that Zalman stereo no longer works on the MAC, which is certainly my experience: I don't seem t get stereo using Lion - not in Coot and not in PyMOL. Is it

Re: [ccp4bb] archival memory?

2012-12-12 Thread Adrian Goldman
I say write them out onto acid-free paper: should be good for at least 300 years without active management, if there is no fire. If that doesn't work, I believe babylonian clay tablets have an even longer expected life time…. Dale, I must say I am impressed… I gave up after the exabyte to DAT

Re: [ccp4bb] archival memory?

2012-12-12 Thread Adrian Goldman
Don't get your hopes up too high for ssd. I had one fail within 4 months of buying it - and the company's attitude was 'this sometimes happens'. Yum I think George is right - punched cards in two separate locations. (Hell any form of paper output will do - surely they'll have decent OCR in 100

Re: [ccp4bb] vitrification vs freezing

2012-11-16 Thread Adrian Goldman
Bernard Dixon is merely copying the great essay by George Orwell 'politics and the english language'. Its well worth a read. In it, Orwell lays out about six simple rules for writing good english prose. Three of them are: never use the passive voice. Always use the anglosaxon word instead

[ccp4bb] ResearchGate?

2012-10-30 Thread Adrian Goldman
. Adrian Goldman Adrian Goldman Institute of Biotechnology, University of Helsinki, Finland

Re: [ccp4bb] Ca or Zn

2012-10-30 Thread Adrian Goldman
This doesn't really give a useful answer. It tells you the overall composition, but there is no means of knowing whether the metal ions are equally present at all sites: some sites can favour Zn over Ca and vice versa. Flame spectroscopy also works but has the same issue - and both have the

Re: [ccp4bb] P321 space group reindex problem

2012-05-30 Thread Adrian Goldman
If the data sets are twinned, large differences between derivatives are to be expected unless the twin fraction is very, very low (1-2%). Given the above, I think nothing can be said until the data are all detwinned - and of course the correct axial interchange done. Adrian On 30 May 2012,

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-01 Thread Adrian Goldman
You can find all the principle investigators you want collecting datums ;) at the ESRF, as that is how the French spell it on the application form for beam time! (Unless it has _finally_ been corrected: haven't checked since I submitted my last BAG application in April.)

Re: [ccp4bb] Fwd: HR3699, Research Works Act

2012-02-16 Thread Adrian Goldman
I signed, and I think so. Further information can be found here: http://www.guardian.co.uk/science/2012/feb/02/academics-boycott-publisher-elsevier On 16 Feb 2012, at 11:41, Boaz Shaanan wrote: I initially thought that it had to do with a new Hampton Research thing. But can non-American

[ccp4bb] Stereo solutions on the MAC?

2012-01-08 Thread Adrian Goldman
Hi, Just curious if anyone has experience with stereo solutions on the MAC other than MacPro and stereographics glasses, or the Zalman monitors? Yes, the Zalman is cheap, and _ok_, but you lose half the horizontal resolution. If the monitor were 3600x2000 pixels, that wouldn't matter

Re: [ccp4bb] Mystery density

2011-12-01 Thread Adrian Goldman
We had a similar case in our Eib structure (2xzr), with large peaks on a 3-fold. We initially thought it was noise, but Andrei Lupas convinced us to look more carefully, and it turned out to be chloride ion. You could do an wavelength scan at a beamline looking for anomalous signal at the

Re: [ccp4bb] yellow crystals

2011-11-06 Thread Adrian Goldman
I agree: light yellow (straw-yellow) proteins often indicate metal-binding - it's typically iron III. Zn salts tend to be colourless, and the Mn-pink is too pale to be visible at protein (mM) concentrations. This can be determined by doing flame-spectroscopy, if you don't mind destroying your

[ccp4bb] Post-Doctoral Researcher – Institute of Biotechnology

2011-11-02 Thread Adrian Goldman
...@helsinki.fi. Closing date: Wednesday November 30th at 3.45pm EET. Adrian Goldman | Research Director and Professor,| Adjunct professor, Neuroscience Institute |Tel:358-(0)9-191 58923 Macromolecular X-ray Crystallography Group |FAX:358-(0

Re: [ccp4bb] Archiving Images for PDB Depositions

2011-10-31 Thread Adrian Goldman
I have no problem with this idea as an opt-in. However I loathe being forced to do things - for my own good or anyone else's. But unless I read the tenor of this discussion completely wrongly, opt-in is precisely what is not being proposed. Adrian Goldman Sent from my iPhone On 31 Oct

Re: [ccp4bb] raw data deposition

2011-10-27 Thread Adrian Goldman
fraction of the terabytes of frame data off the pilots is needed... Adrian Goldman Sent from my iPad On 27 Oct 2011, at 21:17, Ed Pozharski epozh...@umaryland.edu wrote: Dear Garib, I am afraid clarification is in order. Firstly, the results are available here https://docs.google.com

Re: [ccp4bb] raw data deposition

2011-10-27 Thread Adrian Goldman
an idea just because we think today that 640K is more memory than anyone will ever need On Oct 27, 2011, at 3:47 PM, Adrian Goldman wrote: 2) I agree with Susan. In a time of limited funding, is this the most important use of money?

Re: [ccp4bb] Linux vs MacOS for crystallographic software

2011-09-30 Thread Adrian Goldman
where my mouth is. Our last five purchases have been i7 iMacs. It seems like quite a nice amount of oomph for the money. Adrian Goldman Sent from my iPhone On 30 Sep 2011, at 19:46, Francis E Reyes francis.re...@colorado.edu wrote: Bill Thanks for focusing the thread to the original

[ccp4bb] Zalman displays and Macs?

2011-09-22 Thread Adrian Goldman
if one wants to do stereo on MACS... thanks for comment and advice... Adrian Goldman

Re: [ccp4bb] Zalman displays and Macs?

2011-09-22 Thread Adrian Goldman
on the zalman as much (as expected). HTH, Sabuj On Thu, Sep 22, 2011 at 8:22 AM, Sabuj Pattanayek sab...@gmail.com wrote: Am 22.09.11 11:58, schrieb Adrian Goldman: Hi, Anybody having problems with Zalmans and the newer macs? We can't get the MACS to even _recognise_ the existence

Re: [ccp4bb] Mac OSX 10.7 Lion

2011-09-19 Thread Adrian Goldman
Of course this has to be the case. I think most of us walk around with with mobile phones that have memory and processing power more powerful than all of the computers available before 1990. Some of the things that seem difficult in Lion and are nanny-state-ish such as automatic file

Re: [ccp4bb] Another paper structure retracted

2011-08-11 Thread Adrian Goldman
diligent about reviewing. Adrian Goldman On 12 Aug 2011, at 01:46, Phoebe Rice pr...@uchicago.edu wrote: Some people on this list seem to think that reviewers are on the whole lazy and irresponsible and in need of some sort of public ridicule. Please don't forget that reviewing manuscripts

Re: [ccp4bb] large R-Rfree difference in final structure

2011-07-13 Thread Adrian Goldman
In my experience, the most common cause of this is the locally correct, globally wrong issue. You could be in the wrong space group (i.e P21212 when you should be in P212121). Another possibility is missing some element of local symmetry. Is the packing in the unit cell appropriate or are

Re: [ccp4bb] Workshop on Soft X-ray Crystallography at the APS, May 4, 2011

2011-04-22 Thread Adrian Goldman
First line up 10^9 poohbears... Sent from my iPhone On 22 Apr 2011, at 19:58, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I think soft crystallography uses fuzzy logic--it's a comforting alternative to the usual SAD and MAD.

Re: [ccp4bb] where to buy stereo glasses for making stereo figures?

2011-03-30 Thread Adrian Goldman
Yes, but this is not how you do it. I assume you have a stereo image to start with generated from (eg) pymol. and you are trying to float the labels at the same z as specific atoms or objects. It is simple. Place the two labels for the two images at the same y value (y up, x across in my

Re: [ccp4bb] Stereo Microscope advice

2011-01-24 Thread Adrian Goldman
Just one comment on LEDs as we have them as part of an imaging system. While it is true that the LEDs themselves emit cool light, the associated electronics is hotter than I would have expected. FYI. Adrian Sent from my iPhone On 24 Jan 2011, at 19:24, Sampson, Jared jared.samp...@nyumc.org

[ccp4bb] Postdoctoral position in adhesin structural biology

2010-08-05 Thread Adrian Goldman
provides a richly collaborative environment for studying problems at the interfaces between cell, molecular, developmental and structural biology. For further information, please contact Professor Adrian Goldman, Institute of Biotechnology, University of Helsinki. Email: adrian.gold