[ccp4bb] comfortable OS X level

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to

Re: [ccp4bb] [phenixbb] comfortable OS X level

I’ve not had any problems; the current version is 10.2.5, so it’s pretty stable now. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

Re: [ccp4bb] Conserved water

Easiest way is to line up molecule pairs or chain pairs in COOT and see if there are equivalent waters. If the number of waters is too large to inspect manually, save the superposed structures to disk, grep out the waters from each into a separate files, and use a program like

Re: [ccp4bb] Problems with an exonuclease

I've found that washing my IB's with B-PER helps dramatically to get rid of any impurities. https://www.thermofisher.com/order/catalog/product/78248 Nicole Thomas University of Wisconsin, Madison Gellman Group On Wed, Jun 7, 2017 at 11:27 AM, Jon R Sayers wrote: >

Re: [ccp4bb] Problems with an exonuclease

I missed the Triton - that will be it! On 7 June 2017 at 15:46, Bonsor, Daniel wrote: > It will either be two things. DNA or residual Triton-X-100. When you say, > cleaned the IBs, do you mean you sonicated the IBs, or just resuspended the > pellet and then

Re: [ccp4bb] [phenixbb] comfortable OS X level

10.2 ? That OS is 15 years old. > On Jun 7, 2017, at 8:27 AM, Diana Tomchick > wrote: > > I’ve not had any problems; the current version is 10.2.5, so it’s pretty > stable now. > > Diana > > ** > Diana R.

Re: [ccp4bb] [phenixbb] comfortable OS X level

Hahahaha, that was a typo, I meant to write 10.12.5 Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816

Re: [ccp4bb] [phenixbb] comfortable OS X level

REFMAC and COOT seem fine on my iMac running 10.12.5 On 7 June 2017 at 17:28, Diana Tomchick wrote: > Hahahaha, that was a typo, I meant to write > > 10.12.5 > > Diana > > ** > Diana R. Tomchick > Professor >

Re: [ccp4bb] Conserved water

Many years ago I wrote code to label waters with a code related to the residue/atom they were Hbonded to , so then you could check whether all OH TYR 227 in each chain had an associated water.. But it used non-standard water naming .. Easiest way is to line up molecule pairs or chain pairs in

[ccp4bb] MoRDa update

Dear All Morda at ccp4online has been updated. The structure solution program is improved and database is extended . The update is also available for existing local Morda installations and can be installed from command line: change to installation directory (by default MoRDa_DB) and type

Re: [ccp4bb] Problems with an exonuclease

Yes, washing IB with 10 % BPER  twice with sonication makes our IB (from various proteins) very clean before denaturation with 6M guanidine hydrochloride and further processing. Smita  On Wednesday, June 7, 2017 12:03 PM, Nicole Thomas wrote: I've found that

Re: [ccp4bb] Problems with an exonuclease

Several further notes after contemplation, lunch and a slow day. If the protein is His-tagged, you could stick the unfolded protein to Ni-Resin and extensively wash with 8M Urea to remove DNA/Triton-X-100, elute, and then refold. This may be easier than multiple sonications/centrifugations. Or

Re: [ccp4bb] post-doctoral position and PhD position structural biology of ion channels

A post-doctoral position and PhD position are available at the laboratory of Structural Neurobiology, KU Leuven Belgium. The lab website is available at http://www.xtal.be. The research in our laboratory is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our method

[ccp4bb] CryoEM Postdoctoral position at the Wellcome Centre for Cell biology, Edinburgh, UK

A postdoctoral position is available in Jeyapraksh (JP) Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of Edinburgh. The JP lab (http://jeyaprakash.bio.ed.ac.uk) aims to understand the structural level mechanistic details of processes

Re: [ccp4bb] Conserved water

Thanks everyone for the tips. Actually, I need this information to improve my analysis on drug/protein interaction. Best regards:) Gerardo A. Libreros Universidade de São Paulo Laboratório de Biologia Estrutural Aplicada Sent from my iPhone > On 7 Jun 2017, at 18:34, Jared Sampson

Re: [ccp4bb] Problems with an exonuclease

On 06/07/2017 10:46 AM, Bonsor, Daniel wrote: It will either be two things. DNA or residual Triton-X-100. Actually Triton X-100 absorbs more at 280 than 260 - in fact the hydroxyphenyl in TX-100 looks remarkably like tyrosine in RNase A. I long ago gave up hope of resolving triton from

[ccp4bb] CryoEM postdoctoral position at the Well one Centre for Cell Biology, Edinburgh, UK

A postdoctoral position is available in Jeyapraksh (JP) Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of Edinburgh. The JP lab (http://jeyaprakash.bio.ed.ac.uk) aims to understand the structural level mechanistic details of processes

Re: [ccp4bb] Conserved water

How about WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design? Ben On 7 Jun 2017, at 07:59, Eleanor Dodson wrote: Many years ago I wrote code to label waters with a code related to the residue/atom they were

Re: [ccp4bb] Problems with an exonuclease

Probably nucleic acids. Increase the number or volume of washes and improve the washing of your inclusion bodies. Instead of sonication, we use a Polytron homogenizer to resuspend the IBs pellet during washing. This is faster and easier. Incorporate an additional chromatography step such as

[ccp4bb] AutoSol invalid MTZ column_types error

Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best,

Re: [ccp4bb] Problems with an exonuclease

Dear Mohammad, If your protein is purified from insoluble material there could be some DNA in there though if it were stoichiometric your 26 would be >> than your 280, as the former has a much higher extinction co-efficient. A ratio of 2 is could be RNA contamination. I'd also check the mass spec

[ccp4bb] Problems with an exonuclease

Dear all, I am working with an exonuclease by refolding it from inclusion bodies (IBs). I tried various constructs and hosts, but couldn't get it in soluble form. I lyse my cells using a cell disruptor and after solubilizing IBs with urea, I refold the protein by rapid dilution and get an

Re: [ccp4bb] Problems with an exonuclease

It will either be two things. DNA or residual Triton-X-100. When you say, cleaned the IBs, do you mean you sonicated the IBs, or just resuspended the pellet and then centrifuged again? If the latter, try sonication. I wash my IBs at least 4 times with the following buffers; 1. 20mM Tris, 500mM