Re: [ccp4bb] somewhat off-topic :)

2020-04-28 Thread Thomas Cleveland
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

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

2018-09-29 Thread Thomas Cleveland
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

Re: [ccp4bb] Structure with missing density

2018-03-09 Thread Thomas Cleveland
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.

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

2017-08-21 Thread Thomas Cleveland
to 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

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

2017-02-16 Thread Thomas Cleveland
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 20899-6102

[ccp4bb] Fabricating hamilton syringe coupler for LCP preparation

2014-12-15 Thread Thomas Cleveland
removing it. Thanks, Thomas Cleveland

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

2014-12-15 Thread Thomas Cleveland
:09 AM, Thomas Cleveland wrote: Hi all, I'm trying to put together some homemade syringe couplers following the published instructions from the Caffrey group. I'm having a bit of trouble with this part: The stainless steel ferrule of the second needle is removed and placed

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

2014-05-20 Thread Thomas Cleveland
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

[ccp4bb] Reprocess data with new resolution cutoff?

2014-05-19 Thread Thomas Cleveland
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

Re: [ccp4bb] iMosflm bug?

2013-06-25 Thread Thomas Cleveland
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 this? When I go

Re: [ccp4bb] iMosflm bug? - SOLVED

2013-06-25 Thread Thomas Cleveland
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 everyone, Thanks

[ccp4bb] iMosflm bug?

2013-06-24 Thread Thomas Cleveland
://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland

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

2012-09-29 Thread Thomas Cleveland
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 stanev...@wisc.edu wrote:

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

2012-04-25 Thread Thomas Cleveland
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

Re: [ccp4bb] Linux vs MacOS for crystallographic software

2011-09-29 Thread Thomas Cleveland
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

Re: [ccp4bb] insect cell media

2010-06-08 Thread Thomas Cleveland
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 Biophysical

Re: [ccp4bb] problems with molprobity in coot

2010-04-10 Thread Thomas Cleveland
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 Paul

Re: [ccp4bb] problems with molprobity in coot

2009-10-12 Thread Thomas Cleveland
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

Re: [ccp4bb] problems with molprobity in coot

2009-10-12 Thread Thomas Cleveland
. Thanks again, Tom On Mon, Oct 12, 2009 at 1:54 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: Thomas Cleveland wrote: 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

[ccp4bb] problems with molprobity in coot

2009-10-11 Thread Thomas Cleveland
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)