[ccp4bb] Post-doctoral position available
Dear All, A postdoctoral position is available in my lab to study the interactions of zinc-dependent (metallo) beta-lactamases with beta-lactam substrates and candidate inhibitors using both rapid kinetics and X-ray crystallography. The position will be offered for one year in the first instance but with a strong possibility of renewal. Details of the post and application procedure are available at: http://www.bris.ac.uk/boris/jobs/feeds/ads?ID=112771 or by informal enquiry to me. Please note that, if interested, you will need to apply online through the link above. Best wishes Jim Spencer -- Dr. James Spencer, Lecturer in Microbiology School of Cellular and Molecular Medicine Medical Sciences Building University of Bristol University Walk Bristol BS8 1TD jim.spen...@bristol.ac.uk http://www.bristol.ac.uk/cellmolmed/staff/spencer.html -- Tel: (44) (0) 117 331 2084 Fax: (44) (0) 117 331 2091
Re: [ccp4bb] Question on Symmetry Axis Notation Convention
Ethan Merritt merr...@u.washington.edu writes:
On Thursday, June 14, 2012 12:06:13 pm James Stroud wrote:
Hello All,
I would like to discuss symmetry axes, but I'm not sure what the
notation convention is. For example, I'd like to say something about
a 2(1) along the x-axis, but the phrase the 2(1) symmetry axis
along x is a bit cumbersome to repeat many times or to put in a
table. So I'd like a shorthand, maybe something like x(2_1) (where
the preceding _ means that the 1 is subscript. Another way I
like is x_{2(1)} (where the curly braces mean that all of 2(1)
is subscript).
Does anyone know what the convention is or if there is one?
One would think that this document would have the answer:
http://www.iucr.org/resources/commissions/crystallographic-nomenclature/symel
But it's too cryptic for me.
I'd go with the full expression in the text.
For table entries, I'd want something shorter.
International Tables for Crystallography, Vol A defines the glyph used to
indicate
2_1 screws in the space group diagrams (a solid oval with two flagella).
But finding a font to print it in your table could be challenging.
There is a cryst.mf font for TeX if that helps.
http://www.tex.ac.uk/CTAN/fonts/cryst/
This font (by Ulrich Müller) is available in many formats on the IUCr
web site:
http://www.iucr.org/resources/symmetry-font
I can't find these symbols in the Unicode character tables.
Perhaps the IUCr should propose to have Unicode code points assigned for
the standard set of crystallographic symmetry elements.
That has occurred to me too! As far as I know, no proposal has yet been
made.
--
Ian ◎
Re: [ccp4bb] FFT for map variance
Frank, This has features in common with my proposal at the 2011 CCP4SW to use rho_obs / SU(rho_diff) as a model reliability (or precision) metric (now implemented in EDSTATS). This should not be confused with my proposed accuracy metric which uses a chi-square test based on the values of rho_diff / SU(rho_diff). The main difference between the precision metric proposed in this paper (i.e. presumably rho_obs / SU(rho_obs)) and mine is that I use SU(rho_diff) in place of SU(rho_obs) because it's much easier to get the former from a QQ plot of rho_diff (making the not unreasonable assumption that if only random errors are present then rho_diff has a normal error distribution). I also tried to compute SU(rho_obs) directly but the results I got didn't look right so I didn't pursue it. Of course dividing rho_obs by the SU is the easy bit: determining the SU values in the first place is the hard part (as I said, I've tried!), and I guess that is what this paper is all about. If they have a good way of getting SU(rho_obs) by FFT then that's great - I can use it in EDSTATS! Ideally I think COOT should implement the whole package of e.d. metrics (RSR, RSCC as well as the ones described above) so people can decide for themselves what works best. I haven't actually been able to read their paper yet so I can't answer these questions. I have to go through our individual reprint ordering service which takes 4-5 days to get it, so hopefully I'll have more info next week. Cheers -- Ian On 14 June 2012 19:34, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Proposition: what the paper below describes (map variance) would be rather useful to access routinely (e.g. in coot etc), given that it describes how to calculate by FFT. Discuss. (No, I've not read any of it carefully.) Acta Cryst. (2012). A68, 464-469 [ doi:10.1107/S0108767312015772 ] A practical study of the electron-density-map variance C. Giacovazzo and A. Mazzone An algorithm is described for the calculation of the variance of the electron density via fast Fourier transform. The main features of the ratio electron density/standard deviation are described; it is shown that such a ratio may be considered a useful criterion for estimating, on an absolute scale, the quality of an electron-density map, no matter the quality of the model and the data resolution. In some way, it is a good estimate of the confidence one should have in the reliability of the proposed structure. The ratio was tested both for observed and for difference Fourier syntheses, in order to control the usefulness of the criterion for the most popular maps in crystallography.
Re: [ccp4bb] Off topic about application of detergent on non-membrane protein crystallization
beta lactamase cymal 6 and see this reference Guan, R.-J., Wang, M., Liu, X.-Q, Wang, D.-C. Optimization of soluble protein crystallization with detergentshttp://www.sciencedirect.com/science?_ob=ArticleURL_udi=B6TJ6-43J6VF9-17_user=10_coverDate=09%2F30%2F2001_rdoc=1_fmt=high_orig=search_sort=d_docanchor=view=c_acct=C50221_version=1_urlVersion=0_userid=10md5=b2d7f909136aa6fa3dcd5c7d9b596e37 Journal of Crystal Growth 231 (2001) 273-279 pius On Thu, Jun 14, 2012 at 10:35 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I wonder if anyone has successful experience on using detergent to crystallize non-membrane protein. Based on what criteria to choose detergent to help solubilize and crystallize your non-membrane protein. Thanks for any input or comments. Best regards, Donghui -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] error popup with imosflm 1.0.6 despite valid executable MOSFLM_EXEC for mosflm 7.0.8
Hi folks This problem arises because I inadvertently included the versions of MOSFLM_EXEC that require X11 libraries in the iMosflm distribution (for Linux only - Macs and Windows were okay) - iMosflm doesn't need these. I've put fixed binaries on the Mosflm download site for Linux - http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/pre-built/mosflm_linux_32_noX11.zip and http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/pre-built/mosflm_linux_64_noX11.zip If you haven't had this problem you don't need to download the new copies. On 15 Jun 2012, at 16:10, hari jayaram wrote: Hi, I just installed imosflm 1.0.6 and the associated mosflm 7.0.8. I can run the mosflm executable by itself . Yet when imosflm starts it gives me an error popup iMosflm cannot run /home/hari/imosflm_download/1.06/imosflm/bin/mosflm. And then gives me the output from the running of the mosflm executable BFONT COLOR=#FF000:/...etc I have chmod-ed +x the MOSFLM_EXEC mosflm and it runs quite well on the shell. I also have an older imosflm and mosflm that work..any ideas why I get the error popup . I have a feeling its something that bleeding through my .bashrc file because it complains that some Postgres library is not there in the path further down after it gives the header from the mosflm executable output. This postgres error msg may be coming from something else being sourced. Help in troubleshooting will be greatly appreciated I am attaching a screenshot. Thanks for your help Hari imosflm-1.0.6-wrror-popup.png Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Off topic about application of detergent on non-membrane protein crystallization
Hi Donghui, Yes. Crystals for restriction enzyme Bsob I were ugly and did not diffract well without detergent and were beautiful with good diffraction in presence of OBG. You can find it in the publication. We did not find any detergent molecules in the structure. Now, when to try such things... I am not sure I have a good answer. This protein was perfectly soluble in regular buffer without detergent. Detergent is just one of the things to try to improve crystals and it makes sense to try the cheapest detergent first. Hope this helps a little. Mark -Original Message- From: wu donghui wdh0...@gmail.com To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Fri, Jun 15, 2012 9:03 am Subject: [ccp4bb] Off topic about application of detergent on non-membrane protein crystallization Dear all, I wonder if anyone has successful experience on using detergent to crystallize non-membrane protein. Based on what criteria to choose detergent to help solubilize and crystallize your non-membrane protein. Thanks for any input or comments. Best regards, Donghui
Re: [ccp4bb] Off topic about application of detergent on non-membrane protein crystallization
Donghui, There is detergent screen from Hampton: http://hamptonresearch.com/product_detail.aspx?cid=1sid=39pid=31 We set up detergent screen for crystal conditions we'd like to improve: 200nl(buffer) + 200nl(protein) + 40nl(detergent). Occasionally (very occasionally) it works, but don't put to much hope on it. Vitali On Thu, Jun 14, 2012 at 9:35 PM, wu donghui wdh0...@gmail.com wrote: Dear all, I wonder if anyone has successful experience on using detergent to crystallize non-membrane protein. Based on what criteria to choose detergent to help solubilize and crystallize your non-membrane protein. Thanks for any input or comments. Best regards, Donghui
[ccp4bb] Fw: [ccp4bb] Question on Symmetry Axis Notation Convention
The standard notation is 21 axis parallel to [100]?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
From: James Stroud xtald...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 14 June 2012, 20:06
Subject: [ccp4bb] Question on Symmetry Axis Notation Convention
Hello All,
I would like to discuss symmetry axes, but I'm not sure what the notation
convention is. For example, I'd like to say something about a 2(1) along the
x-axis, but the phrase the 2(1) symmetry axis along x is a bit cumbersome to
repeat many times or to put in a table. So I'd like a shorthand, maybe
something like x(2_1) (where the preceding _ means that the 1 is
subscript. Another way I like is x_{2(1)} (where the curly braces mean that
all of 2(1) is subscript).
Does anyone know what the convention is or if there is one?
Thanks in advance for any help.
James
