[ccp4bb] Expression of large proteins in E. coli

if anyone out there has some magical trick they wouldn't mind sharing. Thanks in advance, Nick - Nicholas R. Silvaggi, Ph.D. University of Wisconsin-Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer Street Milwaukee, WI 53211 Phon

[ccp4bb] Post-doctoral position in structural enzymology at the University of Wisconsin-Milwaukee

Post-doctoral position in structural enzymology A post-doctoral position will be available starting July 1, 2010 in the group of Dr. Nicholas R. Silvaggi at the University of Wisconsin-Milwaukee. Our lab uses X-ray crystallography, steady-state enzyme kinetics, and complimentary biochemical

[ccp4bb] RFP for Small Molecule Discovery - AIMS Awards Deadline is October 28th

ttp://bit.ly/32mb1Ax> Flyer: http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Flyer-Fall-2019_updated-1.pdf <http://bit.ly/2VOF69N> Best regards, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ --

[ccp4bb] Deadline Extended to December 9th

ise.com/wp-content/uploads/2019/11/Request-for-Proposal-RFP-Fall-2019-Extended-Deadline.pdf?utm_source=CCP4BB&utm_medium=Email&utm_campaign=AIMS%205&utm_term=Deadline%20Extended&utm_content=RFP> Please don't hesitate to reach out to me directly if you have any questio

[ccp4bb] Submission deadline next Monday!

.ly/32EeoTK> Best regards, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information conta

[ccp4bb] Lectureship vacancy at Bristol

*** Posted on behalf of Leo Brady, please contact him with any queries (contact details included below) *** Dear all, Please could I draw your attention to a lectureship/readership recently advertised here in Bristol. We are hoping to appoint a new faculty member with interests that overlap

[ccp4bb] Mysterious density

1.5sigma. Thanks in advance. Nick

[ccp4bb] Detection of DNA in protein complex crystals

advance. Nick

[ccp4bb] protein interaction and solubility

Hi, Does anyone know of a protein which can interact with several different proteins independently and whose solubility can be improved by binding to its interacting partner, maybe by co-expression or mixing the two and then concentrating? I am not looking for cases where one protein is inter

[ccp4bb] RFP for Drug Discovery - In Silico Small Molecule Screening Awards

to reach out with any questions. You can contact me directly at n...@atomwise.com. Best, Nick -- Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational pu

[ccp4bb] Drug Discovery RFP Application Deadline Approaching - Early Applicant Awards Due Monday!

rogram, and hundreds of projects are already underway at institutions around the world. Our team is incredibly excited to provide this opportunity to the global research community, and I encourage you, your colleagues, and your collaborators to apply! Kind regards, Nick Nick DeHaan, MsE *Partnerin

[ccp4bb] Autoscale in HKL2000

density modification is better, but to run the final refinement with full dataset instead because refinement also treats unisotropicity? Best, Nick Huang

[ccp4bb] How long does it take crank 2 (refmac step) to run?

tput. Does anybody know if it is normal or there is an error? Thanks, Nick Huang Hauptman-Woodward Institute

Re: [ccp4bb] How long does it take crank 2 (refmac step) to run?

Hi Gabriel, My datasize is very small with a very low resolution. Was there an error output when your refmac process didn't converge? I started a SAD process along as you suggested and will see what is going to happen. Thanks NIck >>>>>> Hi Nick, In my experience, this i

Re: [ccp4bb] About NCS and inhibitors

Yes, it is very common. I solved two of them at 2-3 A resolution and saw my colleague had one with 1.4 A resolution (can't remember the name of the protein). Please see references J Med Chem. 2010 Jul 22;53(14):5229-39. doi: 10.1021/jm100377f. Complexes of bacterial nicotinate mononucleotide aden

[ccp4bb] Research assistant position for Schistosomiasis drug discovery pilot project

be addressed to nick.furn...@lshtm.ac.uk<mailto:nick.furn...@lshtm.ac.uk> . Best wishes, Nick -- Dr Nicholas Furnham Associate Professor Department of Infection Biology London School of Hygiene & Tropical Medicine Keppel Street, WC1E 7HT, United Kingdom — Tel: 0207 958 8374 W

[ccp4bb] Creating local/specific B-factor restraints in refmac

first chain A resi 308 alte A atom N second chain A resi 308 alte D atom N value 0.0 sigma 10.0 type 1 == such that the restraint can be imposed locally, between specific atoms? Thanks, Nick —> Nicholas Pearce Post-doctoral Researcher Universiteit Utrecht

Re: [ccp4bb] Unknown electron density

or enough prior information to restrain a modelling approach — i.e. you could build a model that fit the density, but you could never determine if it was “correct”. I would probably just leave that bit un-modelled. Thanks, Nick — Nick (Nicholas) Pearce Post-doctoral Researcher L

Re: [ccp4bb] Unknown electron density

ay it safe and model nothing — the conservative approach. Thanks, Nick ————— Nick (Nicholas) Pearce Post-doctoral Researcher Lab of Piet Gros Crystal & Structural Chemistry Group Universiteit Utrecht > On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri > wrote: > >

Re: [ccp4bb] Refining alt. confs for only part of a ligand

Conformer A atoms don’t “see” conformer B atoms so as far as the program is concerned the B conformer only has the last ring. You should set all confA atoms not in the last ring to blank conformers. So: last ring - A +B conformers rest of ligand - no conformer Thanks, Nick

[ccp4bb] JOB POSTING: Membrane protein structural biology in Cambridge, UK

Posted on behalf of Vassilis Koronakis: Dear structural biologists, We have an opportunity for a postdoctoral researcher in my lab in the School of Biological Sciences, Department of Pathology, University of Cambridge, UK. The successful applicant will continue our work on  bacterial multidru

Re: [ccp4bb] Trouble Visualizing tRNA on Urea-PAGE – Seeking Advice

tRNA should be very easy to see. I suggest to buy cheap yeast tRNA as control and test different concentrations and different dyes until you can see it on the gel. I am not sure about SybrGold. It is a tricky dye and may take a long time to get in. Filter and excitation both need optimization. If

[ccp4bb] Abstract deadline is 28th April for Diffraction Methods in Structural Biology GRS

Dear BB, There are five more days until the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be co

[ccp4bb] Abstract deadline is TOMORROW for Diffraction Methods in Structural Biology GRS

Dear BB, Tomorrow is the abstract deadline for the Gordon Research Seminar in Diffraction Methods 2018 at Bates College, Maine (28-29th July 2018). Applications/abstracts received after this date (28th April) will still be able to attend and present posters, but will not be considered for oral

Re: [ccp4bb] Pandda problems

, but on Monday you should be able to update your ccp4 to the newest update and then update your version of pandda using pip, following the instructions on the website (https://pandda.bitbucket.io). If that doesn’t work on Monday, let me know if you have any more problems. Thanks, Nick On 25

Re: [ccp4bb] AW: [ccp4bb] Pandda problems

I agree completely for error messages regarding errors that the user can fix. However that is not the case with this error, which was an “unexpected” error — perhaps I will add a “contact developer” message to those errors to make this clear. Thanks, Nick On 25 May 2018, at 16:22

Re: [ccp4bb] PanDDA error revisiting old run

Hi, Yes, it is the case that newer pandda version may not be compatible with old pandda analyses. You’ll have to downgrade to the version you used originally. Thanks, Nick > On 20 Jun 2018, at 12:17, Chris Richardson wrote: > > One of our group has been using the newly updat

Re: [ccp4bb] Normalization of B-factors

Merritt points out in one of the replies.) Nick Nicholas Pearce, PhD, Post-doctoral Researcher, University of Utrecht On 9 Aug 2018, at 11:54, Santhosh Gatreddy mailto:santhoshgl2...@gmail.com>> wrote: Hi all, I have to compare the B-factors of three of my ligand bound structures

Re: [ccp4bb] unmodeled blobs

ic data and the local chemical environment”. You don’t need to model every single blob in the crystal — only model the clearly resolved ones, or the ones for which you can construct a “sensible" model. Nick On 18 Jan 2019, at 12:03, Satvik Kumar mailto:kumarsatvi...@gmail.com>> wro

Re: [ccp4bb] visualising anis B factors

in pymol you can just type “as ellipsoids”. On 23 Jan 2019, at 16:17, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Is there any easy way to do this? Coot? ccp4mg? Eleanor Dodson T

[ccp4bb] fix b-factors/coordinates during refinement

Hi all, Is it possible to fix the B-factors/coordinates of a model in refinement with REFMAC? It’s trivial to do so in phenix.refine (strategy=…), but I can’t find an equivalent command line flag in refmac… Thanks, Nick Post-doctoral Fellow, Crystal and Structural Chemistry, Utrecht

Re: [ccp4bb] fix b-factors/coordinates during refinement

But no way to fix to a set of refined/parametrised Bfactors and refine? (That’s the one I wanted most). I.e. “refi coordsonly”. Thanks, Nick On 20 Feb 2019, at 12:47, Jon Agirre mailto:jon.agi...@york.ac.uk>> wrote: Hi Nick, you can refine B-factors while leaving coordinates untouc

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

manuscript submission rather than asking for them if a reviewer requests it — I don’t think that’s a big ask. Thanks, Nick > On 23 Jul 2019, at 09:52, "melanie.voll...@diamond.ac.uk" > > Dear John, > > > Yes, I think the PDB should be stricter. The PDB is i

[ccp4bb] protein web viewer that shows ADPs

. Thanks, Nick To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Open position - data management in biophysics

Academia, one of the only careers where _success_ is rewarded with perpetual impending employment every two+ years. Nick On 22 Jan 2021, at 08:25, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: It is

Re: [ccp4bb] Open position - data management in biophysics

Meant to write “perpetual impending unemployment”. Thanks, Nick On 22 Jan 2021, at 11:02, Jan Dohnalek wrote:  On Fri, Jan 22, 2021 at 10:54 AM Pearce, N.M. (Nick) mailto:n.m.pea...@uu.nl>> wrote: Academia, one of the only careers where _success_ is rewarded with perpetual imp

Re: [ccp4bb] Open position - data management in biophysics

ated, they should absolutely be applauded for that. After all, as Frank said, we do this for the science, and it shouldn’t need to include personal sacrifice. Nick On 22 Jan 2021, at 11:18, Pearce, N.M. (Nick) mailto:n.m.pea...@uu.nl>> wrote: Meant to write “perpetual impending unempl

Re: [ccp4bb] unknown density

f you recontour the Polder map to a higher contour you should be able to get the two maps to look basically the same. Nick On 23 Mar 2021, at 09:36, Sam Tang mailto:samtys0...@gmail.com>> wrote: Dear colleagues Thanks a lot for the comments. I echo that this pentagon-like density may like

[ccp4bb] Abstracts for IUCr SARS-CoV-2 methods session

s session, and 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Ni

[ccp4bb] Deadline today -- IUCr SARS-CoV-2 special symposia.

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural

Re: [ccp4bb] Unmodeled density

Is it on a symmetry axis? If so it could be the superposition of two molecules (a molecule and a copy of itself). On 26 May 2021, at 15:08, leo john mailto:ljohn16012...@gmail.com>> wrote: Hi Group Can you please suggest what this unmodeled blob can be (see appended picture)? I have Malonate, B

Re: [ccp4bb] Analysis of NMR ensembles

If you want something comparable to B-factors don’t forget to put the MSF in the B-factor column, not the RMSF. Will change the scaling of the tube radius considerably! Nick On 27 May 2021, at 11:16, Harry Powell - CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk<mailto:193323

Re: [ccp4bb] Overlapping ligand electron density

It’s definitely possible to have a superposition of states: https://www.ncbi.nlm.nih.gov/m/pubmed/28291761/ You need to use alternate conformers to generate the different states of the crystal. Thanks, Nick On 13 Dec 2017, at 20:12, Matthew Bratkowski mailto:mab...@cornell.edu>>

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Could you expand a bit on what you mean by a “putative” systematic absence? (e.g. why only the lowest order hkl?) On 5 Apr 2018, at 19:39, James Holton mailto:jmhol...@slac.stanford.edu>> wrote: You need to be careful with the exact space group at the particular stage in your pipeline here.

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

f any reindexing occurs. Thanks, Nick On 6 Apr 2018, at 02:02, James Holton mailto:jmhol...@slac.stanford.edu>> wrote: I say "putative" because I don't know what your space group is. In P212121 the reflection h,k,l = 0,0,1 is absent, but in P222 it is not absent. So, if your unit