Re: [ccp4bb] solving difficult protein structure

If the I/sigI and CC1/2 that you quote are for the outer resolution shell of your data, you can use data to a higher resolution limit. It may still be tricky, and rebuilding will be worse; as Eleanor says you'll probably be better off growing a better crystal. Good luck! -- Kevin Jude, PhD (he

Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts

DMSO is a good solvent for superglue and won't dissolve your loops. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Mon, Nov 16

Re: [ccp4bb] Space group/Unit cell

don't believe you have salt crystals, you probably need to do some mass spec to figure out what species in your drop. Best of luck Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279

Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

and aimless masked that result for me. Thanks to those who responded for the help and for the chance to dive into the International Tables. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279

Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

Medicine > Morsani College of Medicine > *University** of South Florida* > Schonbrunn lab, Moffitt Cancer Center > Tampa, FL > E-mail: reza...@yahoo.com, rez...@usf.edu > Phone: +1-954-937-8487 > ORCID: https://orcid.org/-0002-0424-127X > LinkedIn: https://www.linkedin.

[ccp4bb] aimless outputs mean intensities for friedel pairs

Hi all, I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via pointless and aimless. Everything looks good through pointless, as far as I understand: xds reports significant anomalous correlation in CORRECT.LP Inspection of the mtz output from pointless shows that (+) and (-)

Re: [ccp4bb] tNCS incompatible with cell dimensions

Thanks everybody for your replies. I am having another look at my data in P1 and will post an update and summary to the list. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive

Re: [ccp4bb] tNCS incompatible with cell dimensions

-- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Fri, May 31, 2019 at 1:35 PM Diana Tomchick < diana.tomch...@utsouthwestern.

[ccp4bb] tNCS incompatible with cell dimensions

e I believe that my model is good (or at least the correct shape, based on SAXS), I wonder if I'm misinterpreting my crystallographic data. Any insights into how to approach this problem would be much appreciated. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medi

Re: [ccp4bb] crystal contacts and biologically relevant contacts

the biological unit, as well as what you know from biochemical studies (not to mention the position of CDRH3, etc). The easiest way to make the change, IMHO, is to open your molecule in Coot, center on the appropriate symmetry mate, and use Extensions>Modelling>Symm Shift Reference Chain Here. -- Kevi

Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

time I use STARaniso. Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Wed, Sep 26, 2018 at 11:34 AM Kevin Jude

[ccp4bb] preparing ellipsoidally truncated data for PDB deposition

cif before and am not sure what column names are permissible, nor what would be recognizable to other users or software. I'm interested to hear the thoughts and experiences of the community on this. Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hugh

Re: [ccp4bb] microdiffraction data assembly method

Hi Charles, a couple of years ago a colleague and I put together a perl script based on this paper. It worked pretty well in our hands. I'd be happy to share it with you if you'd like. Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical

Re: [ccp4bb] ATP analog

; best > > Adriana > -- Kevin Jude, PhD Research Specialist, Garcia Lab Departments of Molecular & Cellular Physiology and Structural Biology Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

Re: [ccp4bb] Some problems in data processing

ts will be appreciated! > > Best Regards, > > -- Kevin Jude, PhD Research Specialist, Garcia Lab Departments of Molecular & Cellular Physiology and Structural Biology Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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

al3.html . Can you please share > your experience with us? > > Thanks for your help. > > Joseph Ho > -- Kevin Jude, PhD Research Specialist, Garcia Lab Departments of Molecular & Cellular Physiology and Structural Biology Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

Re: [ccp4bb] Completely Off-Topic

I am actually a big fan of using KGlu solutions for protein purification and have found it to be compatible with both IEX and DNA binding (for replication proteins) at concentrations that NaCl does not support. On Thu, Jan 12, 2017 at 2:14 AM, Jon R Sayers wrote: >

Re: [ccp4bb] Could this be a complex crystal? or only RNA crystal? or micromolecular？

In this case, calculating Matthews coefficients / solvent fractions for different possible complexes will be helpful. http://www.ccp4.ac.uk/html/matthews_coef.html In the general case, without solving the structure I would dissolve the crystals and run them on an SDS-PAGE gel, then silver stain

Re: [ccp4bb] distorted NRQ in JLigand 1.0.40

. Does it work normally now? Best regards Andrey On 26 May 2015, at 18:36, Kevin Jude wrote: Dear colleagues, I'm having an issue with a particular ligand in JLigand 1.0.40. When I load NRQ, the topology is correct but the bond lengths and angles are highly distorted, making

[ccp4bb] distorted NRQ in JLigand 1.0.40

: patch level 6.5.008 Program: refmac5; version 5.8.0107 --- LIBCHECK --- /Vers 5.2.00 ; 12.12.2011/ dictionary version 5.44 Best wishes Kevin Jude

Re: [ccp4bb] Fwd: [ccp4bb] adjusting bad Ramachandran angles

opening too large a can of worms. Basically though, beauty and truth are not synonymous, whether or not we regard protein crystallography as a video game where the person with the lowest R-factor wins. best wishes to all! Jeremy the Pedant Begin forwarded message: *From: *Kevin Jude kj

Re: [ccp4bb] adjusting bad Ramachandran angles

I think the Ramachandranplot should be used in the refinement and rebuilding process - a Ramachandran outlier is a flag that that region of the model needs a closer look, and the fix may be more complicated than simply rotating a peptide. Maybe a C-beta is pointing the wrong way, maybe there is a

Re: [ccp4bb] Collecting Spread-Out Molecules

In coot: ExtensionsModellingSymm Shift Reference Chain Here Quick, but not automatic. On Wed, Feb 11, 2015 at 7:07 PM, Keller, Jacob kell...@janelia.hhmi.org wrote: Dear Crystallographers, I've encountered this many times, and fixed it a different way each time, but my molecules are all

[ccp4bb] cluster Ta6Br12 in phaser

pdb file with the HA sites to bypass this error. We're using phaser from ccp4-6.3.0 distributed by sbgrid. Any help will be much appreciated, Kevin Jude

Re: [ccp4bb] off topic - legacy hardware help needed

Note that you'll need a crossover rather than a straight through serial cable and probably a DB25 to DS9 adaptor, but once you get your hands on the cable this is a straightforward solution. kmj On Wed, Jan 23, 2013 at 5:49 PM, Johan Hattne jhat...@lbl.gov wrote: On 23 Jan 2013, at 16:07, Dave

Re: [ccp4bb] ssDNA self-aneal

I would bring up the DNA in TM buffer (10 mM Tris, 5 mM MgCl2) or similar and anneal under dilute conditions to favor hairpin formation over dsDNA. Fast cooling will also favor hairpin formation, so you may try heating to 95° and then cooling on ice, or using a short gradient on a thermocycler.

Re: [ccp4bb] pdb file deposition

Probably, you have built water molecules that are associated with symmetry-related macromolecules rather than the host molecule. Turn symmetry on, check the nearest neighbors of the offending waters, and move the waters close to the host molecule if appropriate. I believe you can do this with

Re: [ccp4bb] SHELXL refinement

I haven't had the good fortune of using SHELXL in a few years, but I seem to recall that you need to make sure that you don't have an END statement preceding your newly added waters. Check this after each cycle of SHELXWAT. best wishes kmj On Fri, Feb 12, 2010 at 1:45 PM, Ajit Datta

Re: [ccp4bb] Detection of DNA in protein complex crystals

Note that, despite the claim otherwise in Kettenberger and Cramer, SYBR Gold does stain at least some proteins, so be sure to run the appropriate controls. kmj On Tue, Jun 23, 2009 at 11:52 AM, Allyn Schoeffler asch...@berkeley.eduwrote: Dear Nick, If you have access to a fluorescent

Re: [ccp4bb] Crystal vacuum cleaner

As an undergrad late in the last century, I used a micromanipulator, quartz capillaries, and a device similar to a patch pipet (manually operated via a screw) to do just this. It was just about the time that nylon loops were coming into wide use, though, and I gladly abandoned he capillary

Re: [ccp4bb] correct atom name

I'm not sure what name phenix or ccp4 like, but looking in $CNS_TOPPAR/dna-rna.top, I see this line: ATOM C5A TYPE=CC3E CHARGE=0.00END so CNS likes C5A. If you want CNS to play well with other programs, just change that line in your topology file to ATOM C7TYPE=CC3E

Re: [ccp4bb] Spooky, moving crystals

I've seen haunted crystals before - the culprit was indeed with the mounting of the pins in their bases (I was re-using some pins and apparently the adhesive had cracked or otherwise failed). Fortunately I never leave home without a tube of Duco cement and was able to correct the problem in

Re: [ccp4bb] crystallisation

PEG 3350 can also provide some cryoprotection; 22% PEG 3350 with 5% glycerol has proved a good cryoprotectant in my hands. kmj Phoebe Rice wrote: If you have high [DTT] in your buffer, you might be catalyzing the addition of dimethyl arsenic (from the cacodylate) to some of your cysteines?

Re: [ccp4bb] protein degraded when setting xtal?

If your protein is autolyzing, you may need to crystallize it in the presence of an inhibitor. In the case of trypsin, I have crystallized in the presence of benzamidine, then removed the inhibitor by dialysis after crystallization. kmj Ngo Duc Tri wrote: Dear CCP4 experts, I'm working on

Re: [ccp4bb] detecting RNA from possible protein-RNA complex crystals

You could stain your crystals directly with Sybr Gold, which will fluoresce upon binding nucleic acids, or you can visualize both protein and RNA on a silver-stained SDS-PAGE gel. Kevin Rongjin Guan wrote: Dear All I am trying to co-crystallize a protein and dsRNA complex, and looking for

Re: [ccp4bb] Filament lifetime on Rigaku Micromax007

I use a multimeter from Radioshack (catalog number 22-812) that can record this data on a PC via a serial connection. Presumably by now there is a similar device with a USB connection. Publishing the resulting text file on the web would be effortless on a *nix machine, but I'm not sure how to do