Re: [ccp4bb] beryllium chloride

2019-04-01 Thread Daniel Anderson
Is this for standard crystals? I think people used to use "basic beryllium acetate" for that application. A quick Google search got me nowhere. -Dan On 4/1/19 2:07 PM, Alexandra Deaconescu wrote: Hello, Is anyone aware of a company that sells Beryllium chloride in the US? Sigma does not ca

Re: [ccp4bb] Asn/Gln - pi-stacking prevalence

2018-11-13 Thread Daniel Anderson
While working on PDB entries 1F0N and 1F0P, I aligned the side-chain dipoles of 4 asparagines with the side-chain dipoles of tryptophans (ring nitrogen is slightly negative, the rest of the 5-membered ring is slightly positive). Aligning dipoles simultaneously optimized hydrogen bonding for the

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

2014-12-15 Thread Daniel Anderson
correction: www.hamiltoncompany.com addition: The compression fittings at least used to be available from us.vwr.com part number 89187-0002. On 12/15/2014 11:48 AM, Daniel Anderson wrote: Here's my addition to Jim Fairman's reply: You could use a pair of RN compressio

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

2014-12-15 Thread Daniel Anderson
Here's my addition to Jim Fairman's reply: You could use a pair of RN compression fittings (www.hamilton 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., Da

Re: [ccp4bb] dynapro DLS cuvettes

2014-08-14 Thread Daniel Anderson
At hellma-analytics dot com, the closest match seems to be catalog number 176-353-15-40, but, that's an HPLC flow cell. Daniel Anderson wrote: Hello, Gloria and everybody, I'm typing most of this reply from memory. When I tried to buy one, my recollection was that it was avail

Re: [ccp4bb] dynapro DLS cuvettes

2014-08-14 Thread Daniel Anderson
Hello, Gloria and everybody, I'm typing most of this reply from memory. When I tried to buy one, my recollection was that it was available from Hellma, but I couldn't (and still can't) find my Hellma paper catalog, and for some reason I did not find the Hellma web site when I wanted to buy a

Re: [ccp4bb] Akta vs HPLC

2012-05-29 Thread Daniel Anderson
Hi, Ho, Your question has a lot of variables. "HPLC" columns should not be used on the Akta within my field of view because the Akta within my field of view does not have gradual pump acceleration and deceleration. "HPLC" columns can be damaged by sudden changes in pressure or composition.

Re: [ccp4bb] MALLS analysis question

2011-02-18 Thread Daniel Anderson
In the Wyatt light scatter training class, they told us to set the alignment parameters ONLY with a monodisperse peak, such as the monomer peak from "monomeric BSA", formerly Sigma Chemical A-1900. The BSA alignment parameters are then manually typed as inputs for the scientifically interesting

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread Daniel Anderson
The journal was Molecular Physics (1987) Vol 62(2), 451-459. (my brain librates when I type) Daniel Anderson wrote: Maybe you should look at: "Rotation barriers in crystals from atomic displacement parameters" Emily Maverick and Jack Dunitz (1987) Vol 62(2), 451-459. They reporte

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread Daniel Anderson
Maybe you should look at: "Rotation barriers in crystals from atomic displacement parameters" Emily Maverick and Jack Dunitz (1987) Vol 62(2), 451-459. They reported that the libration amplitude of one part of a crystalline small molecule relative to another part is strongly correlated to bond

Re: [ccp4bb] Trouble running dm

2010-11-12 Thread Daniel Anderson
AVER DOMAIN 1 should be followed by ROTA MATRIX and TRAN. What does "NCS 2 1" do? Is that in the documentation? I never saw that before, and I don't see it now in blah/ccp4-6.1.3/doc/dm.doc . If you intend to refine the NCS matrices, the instructions for that should be on the same line with "AV

Re: [ccp4bb] embarrassingly simple MAD phasing question

2010-10-13 Thread Daniel Anderson
The Fa" vector is always a 90 degree left turn from the Fa vector. For a centrosymmetric heavy atom substructure such as 1 mercury site in P21, the Fa" vector would point straight up or down. hope that helps, Citizen Dan William Scott wrote: Hi Citizens: Try not to laugh. I have an embar

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

2010-07-15 Thread Daniel Anderson
Refinement with rigid-base TLS parameterization has been previously explored: Holbrook, Dickerson, Kim (1985) Acta Cryst B41, 255-262. (the photocopy is located in the pile of dust that I maintain adjacent to my desk) Ethan Merritt wrote: On Thursday 15 July 2010, Huw Jenkins wrote: Hi,

Re: [ccp4bb] X-Ray films

2010-04-15 Thread Daniel Anderson
(What is in the Hollywood district other than tourists looking for "Hollywood"?) I have a silly anecdote that does not answer Harry's question: It must have been 1995 or 1996, the Beckman sales representative appeared at my desk on a Friday afternoon without an appointment, but carrying a bri

Re: [ccp4bb] cryoEM maps out of scale for docking experiments

2009-08-07 Thread Daniel Anderson
eliver maps with the wrong size. Sincerely, Filip Van Petegem -- ******* Daniel Anderson, Ph.D. Email: d...@mbi.ucla.edu Phone: 310-206-3642 Fax: 310-206-3914 Howard Hughes Medical Institute at University of California Los Angeles Lab: Paul Boyer Hall Room

Re: [ccp4bb] Program to fill unitcell randomly

2008-12-01 Thread Daniel Anderson
very deep, and the answer depends strongly on the intended application. -- *** Daniel Anderson, Ph.D. Email: [EMAIL PROTECTED] Phone: 310-206-3642 Fax: 310-206-3914 Howard Hughes Medical Institute at University of California Los Angeles Lab: Paul Boyer Hall Room 219 For US Postal Servi

Re: [ccp4bb] Broken Masks

2008-03-18 Thread Daniel Anderson
COOT and CCP4mg ? -- ******* Daniel Anderson, Ph.D. Email: [EMAIL PROTECTED] Phone: 310-206-3642 Fax: 310-206-3914 Howard Hughes Medical Institute at University of California Los Angeles Lab: Paul Boyer Hall Room 219 For US Postal Service and 2-dimensional, use: Box 951662 MRL5-748 Los Angeles, CA 90095-1662

Re: [ccp4bb] Bio-rad DuoFlow

2007-02-14 Thread Daniel Anderson
It still seems to me strange that Bio-Rad would build a machine that can reach pressures suitable for reverse-phase chromatography, but then not include software control for gradual pump acceleration. I tried to communicate to BioRad corporate suits that many HPLC columns are too fragile for abrupt

Re: [ccp4bb] Bio-rad DuoFlow

2007-02-14 Thread Daniel Anderson
That was cryptic. My point was that the BioRad pumps are very reliable given some basic care. Its users quickly learn how to use it, as mentioned previously. On Wed, 14 Feb 2007, Daniel Anderson wrote: > My direct experience is with the old "HR" pumps, but my remarks apply t

Re: [ccp4bb] Bio-rad DuoFlow

2007-02-14 Thread Daniel Anderson
My direct experience is with the old "HR" pumps, but my remarks apply to the newer "DuoFlow". On Day Zero, I disassemble the pump heads in the order specified in the manual. I re-assemble with grease on the threads, thus preventing expensive repairs due to corrosion of the bolts caused by salty bu

Re: [ccp4bb] AKTA prime

2007-02-13 Thread Daniel Anderson
Are you sure that you want AKTA anything? They are so expensive. We have had good service from the old style ("HR") Bio-Rad Bio-Logic chromatography systems. The new ones are called "DuoFlow". -Dan On Tue, 13 Feb 2007, Frank Lee wrote: > > Dear all, > > I need to decide between buying an AKTA p

Re: [ccp4bb] "B" in B-factor

2007-01-24 Thread Daniel Anderson
An IUCr nomenclature committee once recommended eradication of the "B-factor". Trueblood, et al. Acta Cryst (1996) A52, 770-781. Whether or not the factor of 8 pi squared can be eradicated, the publication is worth reading because it discusses what is modeled by Ueq (times 8 pi squared = B), and it