Re: [ccp4bb] Missing DNA density in Protein DNA complex structure

++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

that in pymol. So pymol developers, please consider yourselves wheedled ... ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu

[ccp4bb] atomic coloring for the color blind

color blind? thanks, Professor Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop

Re: [ccp4bb] TLS refinement refmac

EEK, it seems to me that anything called simply FP should be unadulterated FP. If the software modifies a column in some way, it should give it a new label, shouldn't it? ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University

Re: [ccp4bb] Twin or underestimation of symmetry

Check the pseudo-precession pics (0kl plane, etc). A rhombohedral crystal that is indexed as P6xx may have seemingly-bizarre systematic absences that could trick one into thinking its P63xx. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf

Re: [ccp4bb] Low 280 absorbance imidazole?

, and it goes easy on the budget as well. Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http

Re: [ccp4bb] structural search for homologs in pdb?

Hi Gloria, I've gotten useful results from these two threading / prediction servers: Raptorx and Phyre (for low homology, I found the original version works better than phyre2). Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology

[ccp4bb] FW: Departmental License for Pymol

; Robert Haselkorn; Geoffrey L. Greene; Sean Crosson; Nancy Schwartz; Joe Piccirilli; Tao Pan; Keith Moffat; David R. Kovar; Tobin R. Sosnick; Stephen C. Meredith M.D., Ph.D.; Phoebe A. Rice; Francisco Bezanilla; Marvin W. Makinen; Stephen Kent; Donald F. Steiner Md.; Benoit Roux; D Allan Drummond

[ccp4bb] Please Delete: FW: Departmental License for Pymol

MANY APOLOGIES the wrong address got auto-filled when I tried to forward this to my lab. Please delete. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http

Re: [ccp4bb] over-expression strategies

Something I recently learned from a friend: try changing the 4th base in the coding sequence to G (e.g. ATGGxx...) and the ribosome will like it better. We tried it recently on a frustrating construct and it worked like a charm. From: CCP4 bulletin board

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

of our paper about that structure was Flexible DNA bending ... Then again, at least somebody did look at the coordinates ;) Phoebe Rice PS - I recently participated in a e-life review and was quite impressed by the process. I think it cleared up several bits of confusion and pointed out where

Re: [ccp4bb] switching space group

If you're only changing the 2-fold axis along c to a 2-fold screw axis, you don't need to go back to the raw image files and reprocess them! Just tweak the header of the .sca file and carry on (and take notes on what you did). From: CCP4 bulletin board

Re: [ccp4bb] A question on protein microheterogenity for crystalization

It might be that the protein is innocent and the FPLC is guilty. If FPLC pump needs maintenance and is stuttering a bit when running at high pressure, the salt gradient won't be as smooth as you'd like. If you have an ionic strength detector, that trace will tell you. Otherwise, see if other

[ccp4bb] off-topic: bug busting

Some time ago, there was a nice discussion of cost-effective, wimpy protein-friendly ways to break open E. coli. We're thinking about replacing an aging sonicator. If people have a favorite gizmo, could they repeat that advice? thank you, Phoebe Rice

Re: [ccp4bb] coot problems to decrease R FREE

. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4 bulletin

Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore

. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp From: CCP4

[ccp4bb] off-topic: citations for GST dragging gunk into solution?

version (purified in a different lab) doesn't. thanks, Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu

Re: [ccp4bb] Superposing nucleic acids

of the glycosidic bond (note the atom number is different for pyrimidines vs. purines). The sublime thing about W:C pairing is that it keeps the orientation glycosidic bonds constant. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago

Re: [ccp4bb] Strange density in solvent channel and high Rfree

What happens if you solvent-flatten/flip/massage that map, but tell the software the solvent content much lower than what you think it is now? Maybe you'll find another copy of the molecule? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of

Re: [ccp4bb] Strange density in solvent channel and high Rfree

. Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp

Re: [ccp4bb] Strange density in solvent channel and high Rfree

for twinning or rotational pseudo-symmetry: the Rfree flags should be expanded by the xtal symmetry operators, not re-picked in the lower symmetry space group. Phoebe ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University

Re: [ccp4bb] plate crystal optimization

Among many possible reasons, the streaking could be caused mechanical stress to the thin plates during mounting. Have you tried those loops that look like miniature tennis rackets? Phoebe From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rakesh

Re: [ccp4bb] Puzzling Structure

Looks like a typo to me: if you change the CRYST space group record from P212121 to P21212, as the paper says it is, the packing problem goes away. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr

Re: [ccp4bb] Pseudo-translation problem

++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago 773 834 1723; pr...@uchicago.edumailto:pr...@uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp

Re: [ccp4bb] Can nucleoprotein complex inhibit EtBr binding?

! ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sudipta Bhattacharyya [sudiptabhattacharyya.iit...@gmail.com

[ccp4bb] Thymine methyl in coot

When trying to adjust the chi angles of a dT in coot 0.8.1, the methyl and its H's (which I called C5M to make phenix happy) rotate with the sugar, producing a rather base bizarre geometry.

Re: [ccp4bb] Thymine methyl in coot

are already more up-to-date! ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf

Re: [ccp4bb] Picking water molecules at 4A structure.

can't see nice density for side chains then you probably aren't really seeing density for waters either. ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

is problematic, please do let the community know! ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Interesting DNA contamination

for the ride during purification)? Good luck, Phoebe Rice ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu

Re: [ccp4bb] Protein precipitation

the metal affinity column. That seemed to help. Also, if you can get your protein to stick to the next column in whatever buffer it comes off the IMAC column in, there's no need to dialyze or concentration between columns - the faster you get it clean, the better. Good luck! Phoebe Rice

Re: [ccp4bb] Bad density for chains

Are you sure there really are 4 chains? 50% solvent may be average, but we've had crystals with closer to 80%. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Pooja Kesari [pkesar...@gmail.com] Sent: Tuesday, January 24, 2017 10:42 PM To:

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Excellent point. I've heard apocryphal stories of someone obtaining beautiful salt crystals (magnesium ammonium phosphate) by trying to crystallize an ATPase with ADP and Mg++ using (NH4)2SO4 as a precipitant. Wait long enough, and the ADP becomes ATP plus AMP, the ATPase takes the 3rd

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

Interesting way to look at it. But those loop residues are really in the crystal with an occupancy of 1, so wouldn't letting the B factor fly give a clearer description of what's in the crystal? Especially as many people know to color the structure by B factors to get a feel for which bits

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

I found that one can get RSRZ to go way down by loosening the geometry restraints. The result is a crappy structure and I don't recommend doing that, but it does get all the atoms crammed into some sort of density. RSRZ, in my most humble of opinions, seems like one of those statistics that is

Re: [ccp4bb] Two SGs in one droplet?

Back in my grad school days, we had crystals (of gamma delta resolvase large fragment) like that: at high protein concentrations, we'd get P6422 with 1/asymmetric unit, and at lower concentrations, C2221 with 3/asymmetric unit (with an imperfect ncs 2fold 60 degrees from the xtal fold, and very

Re: [ccp4bb] Ligand electron density

At long last, a brilliant theoretical framework for observations previously dismissed as mere discrepancies! This being Saturday, can the postulated time-dependent decay of previously observed observables also be applied to explain the apparent discrepancy in number of socks entering the wash

Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

Hi, Sometimes automated model building needs more manual intervention than one might expect, although it sounds like you've already carefully inspected the "good" regions. Could you use a model of the N-ter (from a homolog) simply to create a solvent envelope, then see if solvent flattening

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

For historical perspective: Molecular structure determination by electron microscopy of unstained crystalline specimens PNT Unwin, R Henderson - Journal of molecular biology, 1975 http://www.sciencedirect.com/science/article/pii/0022283675902120 From:

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

Thank you Bernard. I'd like to add that carving the density shown in a figure (especially without explicitly describing the carve radius used) is the moral equivalent of showing only 1mm of background above and below the band of interest in a western blot. Phoebe

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

We had a complex many years ago that could sometimes be convinced to crystallize by poking the drops (probably with a hair): if I remember correctly, both poking some of the skin into the drop and pulling some of the oily goo into more contact with the aqueous phase. Then again, that complex

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

ter. ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> Mobile DNA III: mobile elements are everywhere! http://www.asmscience.org/content/book/10.1128/

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

You might also be getting aggregation. If you do an old-fashioned EMSA ("gel shift") assay, does it hang up in the well? ++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:p

Re: [ccp4bb] Separating Monomers and Dimers

Sorry if this is an insulting question, but did you store it in enough glycerol to prevent it from freezing? Proteins don't like freeze/thaw cycles, especially slow ones. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jai mohan

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

In the distant past, we did get some additional phasing signal by a simplified version of the RIP concept based on the lability of the bromines in a 5-bromo-dU substituted DNA in an x-ray beam. We collected the peak anomalous signal first and fast, and then just kept collecting (we may

Re: [ccp4bb] Protein or DNA crystals

This is not at all conclusive, but one depressing thing is that DNA-only crystals are often hexagonal (like yours are). Can you reproduce them without the protein? ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicag

Re: [ccp4bb] Off topic: denaturing urea gels

Even though the protein should be denatured by all that urea, we find such gels sometimes look nicer if stop the reaction with SDS and protease K, and/or phenol extract the remains of the protein before loading the high-urea gel. ++ Phoebe A. Rice Dept

Re: [ccp4bb] Electron density in PDBe

different rotational states even if there's rough density for the planes of the bases? ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu https://voices.uchicago.edu/phoeberic

Re: [ccp4bb] secondary structure prediction

I'm fond of RaptorX ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> https://voices.uchicago.edu/phoebericelab/ From: CCP4 bull

[ccp4bb] teaching question: graphics for chromebook?

there already come up with a good solution – either an easy way to install pymol, or an alternative undergraduate-user-friendly, free macromolecular graphic program that will work for chromebook users. Thanks, Phoebe ~~~ Phoebe A. Rice Dept. of Biochem & Mol.

Re: [ccp4bb] According correct space group assignment...

How do your twinning statistics look? It could be that the real space group has lower symmetry (and thus more space for your G4 DNA). ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ 

Re: [ccp4bb] According correct space group assignment...

Sadly Rafal is right the unit cell dimensions don't make sense - either the space group is wrong or the contents have been digested before crystallization. The size of the overall unit cell is ~21 x 23 x 43. Given a (DNA-centric but close enough) view that a duplex is ~25A wide and there are

Re: [ccp4bb] does 12 A diffraction worth optimization

In addition to the other useful advice offered, I’d also suggest determining if the whole complex or just the DNA fits in the asymmetric unit. Particularly if the crystals are hexagonal rods or plates, you might have DNA-only crystals. ~~~ Phoebe A. Rice Dept

Re: [ccp4bb] Experimental phasing vs molecular replacement

(with exceptions of course). If you only have an existing structure for, say, half of what's in your asymmetric unit, SAD phases will be less biased than model phases from molecular replacement, even though both may be noisy. ~~~ Phoebe A. Rice Dept. of Biochem & Mol.

Re: [ccp4bb] translational NCS & twinning

. If you're desperate, and your weak spots are weak enough, it is worth a try! ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ On 1/10/19, 12:18 PM, "CCP4 bulletin board on behalf

Re: [ccp4bb] Purchasing slides with diffraction gratings for teaching diffraction

-1-Reptangles/dp/B00392NSQ4/ref=sr_1_2?ie=UTF8=1549988668=8-2=reptangles You can assemble an amazing array of symmetries with these things. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoeberic

Re: [ccp4bb] Ramachandran outliers

r server as a buffet of (often quite useful) suggestions for how to rebuild your refmac- or phenix- refined model. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board on beha

Re: [ccp4bb] naive question how to add GTP as a residue to a nucleic acid chain and refine!

At least last fall, the state of the art for getting your T7-transcribed RNA to start with a triphosphate in phenix was to add this file (edited for your chains, of course) through the gui (if you use the gui). Thanks to Deepak Koirala and Nigel Moriarty for help in working this out. *

[ccp4bb] Post-doc position

uchicago.edu> with their request. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ To unsubscribe from the

Re: [ccp4bb] ORCID being mandatory for PDB depositions

Very good point, and a good argument against the current trend of publications in the glossies including everything from mice to omics to structure all in one manuscript with one set of authors. Especially since it is being pointed out more vociferously these days (as it should be) that

Re: [ccp4bb] challenges in structural biology

e log of what kind(s) of density modification were applied? I get frustrated when other people's students can't tell me exactly what they've already tried, but it isn't always their fault. Best, Phoebe ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committ

Re: [ccp4bb] challenges in structural biology

cooperative interactions among multiple flexible partners. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board on behalf of John R Helliwell Reply-To: John R Helliwell

Re: [ccp4bb] difficult molecular replacement solution

function and shows nice packing. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board on behalf of Robert S Phillips Reply-To: Robert S Phillips Date: Wednesday, Nove

Re: [ccp4bb] microscope camera

With a little fiddling and patience, one can just point a cell phone camera down the eyepiece. It doesn’t produce the best pics, but works fine if you just want to stick a few in a notebook (or a grant …). From: CCP4 bulletin board on behalf of Sergei Strelkov Reply-To: Sergei Strelkov

Re: [ccp4bb] CCP4BB Digest - 27 Feb 2020 to 28 Feb 2020 (#2020-61)

While we're at it, it would also be a great improvement if the PDB would list nominal resolution in all 3 directions for structures with significantly anisotropic data. I'm never 100% sure what to do in those cases. Thanks, Phoebe ~~~ Phoebe A. Rice Dept

Re: [ccp4bb] What resolution - X-ray diffraction round this time

overstated resolution. ~~~~~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" wrote: Dear colleagues,

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

While there is some truth to that argument, the problem is that it is harder to achieve an international reputation in the first place while being routinely overlooked. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology h

Re: [ccp4bb] ITC Stoichiometry

two different surfaces of B, such that some number (< or = 6) of As could bridge two B hexamers … or the other way around … Mother Nature is inventive – best to get some experimental numbers! ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Co

Re: [ccp4bb] Paired refinement proves data quality goes beyond the spatial limits of the detector

This advance brings deep new meaning to crystallographic data having both a real and an imaginary component! On 3/31/20, 11:36 PM, "CCP4 bulletin board on behalf of Petr Kolenko" wrote: Dear colleagues, We, the developers of a program for paired refinement, have found a remarkable

[ccp4bb] Faculty position

Biochemistry and Biophysics Faculty at The University of Chicago The Department of Biochemistry and Molecular Biology at the University of Chicago invites applications for a faculty position, preferably at the assistant professor rank. We seek scientists studying macromolecular dynamics and

Re: [ccp4bb] taking information from a deposited structure

Each PDB entry now has a DOI which should make referencing that structure easier in your own publication. From: CCP4 bulletin board on behalf of Firdous Tarique Reply-To: Firdous Tarique Date: Wednesday, September 9, 2020 at 1:35 AM To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] taking

Re: [ccp4bb] [ccp4bb] Up-to-date 3D stereo solution

Ah yes, fond memories of that mirrored contraption! There were also wooden contraptions to strap on one's head with image-merging mirrors in them. We had fun lining up equal-height friends and merging them. But both of those did have the downside that getting engrossed in electron density

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

not get a fellowship. ~~~ Phoebe Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ On 1/20/21, 3:45 PM, "CCP4 bulletin board on behalf of Gerlind Sulzenbacher" wrote: Dear Markus, tha

Re: [ccp4bb] B-factors very high

Dear Silvia, While high Bs can be a sign that parts of your model are incorrect (and therefore some careful manual rebuilding may be required), for things like poorly-ordered surface loops, they can simply be truth. A point worth remembering for newbies: your goal is to produce the model

Re: [ccp4bb] Can twinning be seen in the diffraction pattern?

A side point, worth considering depending on your x-ray source: many years ago we threw out several crystals in a row for having split spots before we finally realized that the BEAM was split, not the crystals. Oops. ~~~ Phoebe A. Rice Dept. of Biochem & Mol.

Re: [ccp4bb] protein DNA complex structure and extension of DNA structure

I would try the tools on this site - http://web.x3dna.org/index.php/protein From: CCP4 bulletin board on behalf of "Srivastava, Dhiraj" Reply-To: "Srivastava, Dhiraj" Date: Monday, December 27, 2021 at 8:32 PM To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] protein DNA complex structure and

Re: [ccp4bb] Maps on mobile phones.

Oo that looks handy! And it reminds me to ask the community: if you wanted to do outreach to high schoolers and get them to, say, look at a DNA structure, is there a PyMol-like program that works on tablets? I see PyMol for ipad has been discontinued. Thanks, Phoebe From: CCP4 bulletin

[ccp4bb] FW: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

departments, one on each plan. Don’t assume logic. ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board on behalf of Hekstra, Doeke Romke Date: Sunday, October 15, 2023

Re: [ccp4bb] the structures of Nucleic acid

not -CH3) ~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/ From: CCP4 bulletin board on behalf of Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Date: Monday, September 18,

Re: [ccp4bb] problems in Rfree-flags when refining with REFMAC and processing with STARANISO

Why why why doesn’t REFMAC just write a new column – something like FOBS_mod? Shouldn’t it be a general rule that if you change something, you give it a different name? From: CCP4 bulletin board on behalf of Randy John Read Date: Wednesday, July 13, 2022 at 5:22 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Lower b-factors with increasing T

I guess the big question is what is the question that you’re trying to address from those numbers? I’d be nervous about making conclusions about trends in B factors from just 1 data set per temperature. As you probably know, the B factors will reflect static differences in atomic position

Re: [ccp4bb] Lower b-factors with increasing T

Apologies for the stupid post about freezing conditions last night – my brain was clearly very low on glucose when I read that list of temperatures! From: CCP4 bulletin board on behalf of Phoebe A. Rice Date: Wednesday, September 7, 2022 at 7:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re

Re: [ccp4bb] RNA's tertiary structure prediction ways with high accuracy

You might try this: https://seq2fun.dcmb.med.umich.edu/DeepFoldRNA/ I’m recommending it with the caveat that I’ve tested it on exactly 1 unpublished structure, and it did a really impressive but far from perfect job. From: CCP4 bulletin board on behalf of Abhilasha Thakur Date: Thursday,

Re: [ccp4bb] Future Diffraction Methods

Excellent idea. From: CCP4 bulletin board on behalf of Debanu Das Date: Saturday, December 24, 2022 at 5:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Future Diffraction Methods Consider merging with the Annual ACA meeting. The ACA meeting can also benefit from more X-ray diffraction

[ccp4bb] postdoctoral position

[Text Description automatically generated] Postdoctoral Position in the Rice Lab at the University of Chicago. Mechanism, Engineering, and Structural Biology of Large Serine Integrases A postdoctoral position is available immediately the laboratory of Dr. Phoebe Rice. Large serine integrases