Re: [ccp4bb] somewhat off-topic :)

Hi, There are tons of these listed on eBay, many in very good condition or even unused. I used to get them there all the time. Best On Tue, Apr 28, 2020 at 8:51 AM Artem Evdokimov wrote: > CCP4 friends, > > Sorry for the somewhat off-topic post! > > For many years I've been a fan of the Pharma

Re: [ccp4bb] R-merge is too high !!

I once had a problem that seemed to manifest itself similarly to what you describe. It turned out to be a misindexing of the diffraction origin by +/- 1 due to a slightly incorrect beam center. You can use the pointless "centre" option to do a search for the correct center. There's an example of th

Re: [ccp4bb] Structure with missing density

Hi, Long crystallization times and irreproducibility together with missing residues points strongly to some slow proteolysis in your crystal drops that eventually generated a crystallizable fragment. A lot of people actually do this on purpose by adding proteases to generate stable fragments. Here

Re: [ccp4bb] Protein quantitaion based on extiction coefficient versus peptide bond

experimentally determine accurate extinction coefficients is the Edelhoch method. You can read about it here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143013/pdf/8563639.pdf -Tom --- Thomas Cleveland NIST Center for Neutron Research Gaithersburg, MD On Sun, Aug 20, 2017 at

Re: [ccp4bb] off topic: Alternatives to GE HiTrap columns

ndous amounts of time in one case, where I no longer had to concentrate/dialyze liters worth of media but could just filter it and shoot it through a column. -Tom ----- Thomas Cleveland, Ph.D. NIST Center for Neutron Research 100 Bureau Dr. MS 6102 Gaithersburg, MD 20899-610

Re: [ccp4bb] Fabricating hamilton syringe coupler for LCP preparation

dot com part >> number 55751-01) and a segment of HPLC tubing. HPLC tubing within my field >> of view can have an inside diameter as small as 0.005 inch. >> >> hope that helps, Happy Merry, etc., >>Dan >> >> >> On 12/15/2014 11:09 AM, Thomas Cleve

[ccp4bb] Fabricating hamilton syringe coupler for LCP preparation

d I'm having trouble removing it. Thanks, Thomas Cleveland

Re: [ccp4bb] Reprocess data with new resolution cutoff?

Hi everyone, Thanks for all your input. I will consider processing and depositing the data out to 2.35 A, but refining only against data up to 2.55 A. Just to give a little more information, and make sure what I'm doing is reasonable, I am attaching below the table of statistics vs. resolution f

[ccp4bb] Reprocess data with new resolution cutoff?

Hi all, This is a basic question and I'm sure the answer is widely known, but I'm having trouble finding it. I'm working on my first structure. I have a dataset that I processed in XDS with a resolution cutoff of 2.35 A, although the data are extremely weak-to-nonexistent at that resolution limi

Re: [ccp4bb] iMosflm bug? - SOLVED

nfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi xfs xfstt (ttf-mscorefonts-installer was already installed by default) Everything is working fine now. Thanks again. -Thomas On Tue, Jun 25, 2013 at 10:23 AM, Thomas Cleveland < thomas.clevel...@gmail.com> wrote: > Hi everyo

Re: [ccp4bb] iMosflm bug?

ry, I could drag the lower right corner to make the window *smaller*, but it would not let me make it any bigger. Reginald, I'll take a look at that. Thanks, Thomas On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland < thomas.clevel...@gmail.com> wrote: > Has anyone else encountered

[ccp4bb] iMosflm bug?

ks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland

Re: [ccp4bb] Poor baculovirus stability at 4C?

Hi, I agree with others here. We produce virus in homemade ISFM and supplement with 2% serum, then store at 4 C protected from light. We don't titer. I have noticed no difference in expression over 1-2 years. -Tom Cleveland On Sep 27, 2012 8:19 PM, "Vitali Stanevich" wrote: Alexander, We p

Re: [ccp4bb] minimum protein concentration for NI-NTA column

Jerry, In my experience with GE's HiTrap Chelating HP columns (which use the tridentate IDA linkage, rather than the tetradentate NTA), capture is usually quite good as long as the protein is well behaved and the tag isn't occluded. It is definitely possible to capture proteins at the level of 0.

Re: [ccp4bb] Linux vs MacOS for crystallographic software

Hi, I have been extremely happy with the latest Ubuntu release, on both a Toshiba tablet (the touch screen worked right out of the box) and on a desktop with the proprietary NVIDIA driver. I haven't had to update, so I don't know what happens with the NVIDIA driver in that case, but I can tell yo

Re: [ccp4bb] insect cell media

10 L prep of liquid media. Note that these prices include institutional discounts for some components that may or may not apply to you. I can send you our protocols if you are interested. -Tom --- Thomas Cleveland Leahy Lab Biophysics & Biophys

Re: [ccp4bb] problems with molprobity in coot

Rongjin, It does look like you have the same problem I did. I was never totally able to figure it out completely. First of all, it was only a problem with some PDB files and not others. Modifying generic_objects.py (i.e., change the line "if (reduce_status):" to "if (True):" ) as suggested by P

Re: [ccp4bb] problems with molprobity in coot

ing "probe"? Otherwise, I might try to just work around this by modifying the Coot source to ignore the return value of "reduce." Thanks again, Tom On Mon, Oct 12, 2009 at 1:54 PM, Paul Emsley wrote: > Thomas Cleveland wrote: >> >> Bernhard, >> >> I h

Re: [ccp4bb] problems with molprobity in coot

Bernhard, I have tried this using several versions of coot. I tried it first in the coot that came packaged with ccp4 (Coot 0.5.2). I then tried WinCoot-0.6-pre-1-revision-2411, which is one of the later revisions of 0.6-pre, just to see if a more recent version would work. As far as I can tell

[ccp4bb] problems with molprobity in coot

6076 hydrogens"). However, at the very end, I get the message "BL WARNING:: reduce didnt run ok, so stop here!" It seems like probe never runs. Does anyone know how to solve this? Thanks, Thomas Cleveland (graduate student, Johns Hopkins University)