Re: [ccp4bb] Combating disinformation in science and other areas

in the 20th and 21st centuries, not eons ago. So, my humble request: Can we stick to crystallography and allied fields of structure determination on this e-mail list, and not digress into divisive politics, please? Respectfully submitted, Daniel Daniel M. Himmel, Ph. D. Principal, Himmel

Re: [ccp4bb] Autoinduction Medium

Another recommendation: Increase the concentration of your pH buffer, if possible, for better results (possibly a larger yield). I agree that some components, especially the sugars, should not be autoclaved and should be filtered instead. Daniel Daniel M. Himmel, Ph. D. Principal

Re: [ccp4bb] High Temperature Factors with TLS

(such as sulfate instead of phosphate)? Daniel ___ Daniel M. Himmel, Ph. D. Principal, Himmel Sci Med Com, LLC E-mail: danielmhim...@gmail.com URL : https://www.HimmelSciMedCom.com On Wed, Aug 2, 2023 at 10:42 AM Thomas, Leonard M. wrote: > Hello All, > >

Re: [ccp4bb] Alexey Vagin

, Daniel M. Himmel On Sun, Mar 26, 2023 at 3:21 PM Roberto Steiner < 2497b6493202-dmarc-requ...@jiscmail.ac.uk> wrote: > Very very sad to hear this. I have some great memories of our time > together in York several of which involve molecular replacement problems, > Fortran77

Re: [ccp4bb] Energy minimization and explicit solvent model

The Schrodinger software suite may also have a module that you can use (https://www.schrodinger.com/platform#product-list-collapse). You can contact technical help for advice. Daniel On Wed, Jun 24, 2020 at 7:54 PM Andre LB Ambrosio wrote: > Dear Sorin, many thanks for this. Very useful. > >

Re: [ccp4bb] New phasing approach

That's fascinating! Can such an interferometer actually be constructed for an X-ray beam line or is this still in the realm of the theoretical possible? Daniel ___ Daniel M. Himmel, Ph. D. E-mail: danielmhim...@gmail.com On Tue, Mar 31, 2020 at 10:01 PM Bernhard Rupp wrote

Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

al biology and allied sciences in the CCP4 list, please. Respectfully, Daniel M. Himmel > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [OT] Structure-related pun needed urgently

You're welcome to boo this one down, but how about something like, "With a some coaxing, a protein can be X-cited to expose its structure." I think that's poor, but maybe it's a starting point. -Daniel On Thu, Aug 15, 2019 at 7:42 AM Gerard DVD Kleywegt wrote: > Dear CCP4BB-ers, > > Once

[ccp4bb] Fwd: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

-- Forwarded message - From: Daniel M. Himmel, Ph. D. Date: Mon, Aug 5, 2019 at 12:45 PM Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ To: Pentagonal phosphate geometry would be a transition state, except that three oxygens

Re: [ccp4bb] Importance of temperature during initial crystallization screening

crystallization at higher temperatures). Daniel M. Himmel, Ph. D. E-mail : danielmhim...@gmail.com URL : http://www.DanielMhimmel.com/index_Xtal.html <http://www.danielmhimmel.com/index_Xtal.html> On Thu, Aug 1, 2019 at 5:24 AM Sergei Strelkov wrote: > Dear all, > > > I wondere

Re: [ccp4bb] Michael Rossmann (1930-2019)

During the few years that I had the opportunity to work with Michael Rossmann, I found him to be not only a great scientist but a fine and humble gentleman, who will be missed. -Daniel On Tue, May 14, 2019 at 9:13 PM Hasan, Syed Saif wrote: > Dear Colleagues, > > > It is with profound

Re: [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

Fisher Scientific makes 22 inch square plastic cover slips, which are labeled "Fisherbrand Unbreakable Cover Slips". I and my colleagues have used them for over 15 years instead of siliconized glass coverslips. Just dip each one in ethanol to clean before use, dry with an air blower, and use it

Re: [ccp4bb] high B factor

t). Use MolProbity to help in identifying errors > >> and clashes. > >> If a few rounds of simulated annealing and model building don't improve > >> things, try some > >> refinement in CCP4 Refmac. PDB_REDO, which uses Refmac, can also help > >> give you al

Re: [ccp4bb] high B factor

By the way, I would recommend running simulated annealing with each composite omit map you generate to help in overcoming model bias. -Daniel On Sat, Nov 10, 2018 at 9:31 PM Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > Anandhi, > > Assuming the data redu

Re: [ccp4bb] high B factor

ther model and then correct the geometry in Coot. If B-factors don't come down no matter what you do, you could be in the wrong space group or have problems with the original data that need to be addressed. I hope this helps. Daniel _______ Daniel M. Himmel, Ph. D. URL: http://www.DanielM

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

esult from weak overall attractions between the protons in the nucleus of one atom and the electron cloud of another atom and therefore increase as the atomic number of the atoms increase. -Daniel On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: >

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

gt; for the formation of the interface. > > > Sheila > > > > -- > *De:* Daniel M. Himmel, Ph. D. > *Enviado:* terça-feira, 18 de setembro de 2018 15:10 > *Para:* sheila_bore...@hotmail.com > *Cc:* CCP4BB@jiscmail.ac.uk > *Assunto:* R

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

Sorry. I may have been unclear. H-bonds are actually a subset of dipole interactions. On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > By the way, distinguishing between dipole and ionic (salt bridge) > interactions could > be a

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

By the way, distinguishing between dipole and ionic (salt bridge) interactions could be a slippery slope, because which one you have sometimes depends on the protonation state of the protein(s), which is pH dependent. -Daniel On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. < danielm

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

Sheila, Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions are often collectively called electrostatic interactions. Note that dipole interactions involve partial charges. If you want to exclude dipole interactions, you have say so specifically in your manuscript.

Re: [ccp4bb] crystals that dont diffract :( :(

Dear JL, Years ago, this was a common problem when I was crystallizing myosin constructs for my doctoral work. Some of the most beautiful crystals I got showed little or no diffraction. Often this occurs when there is a very large water content in the asymmetric unit and in proteins that have a

Re: [ccp4bb] Normalization of B-factors

Just be careful when drawing conclusions from B-factors. If you look at the mathematical way that a B-factor modifies a structure factor, you can see that as a B-factor's numerical value increases, the corresponding structure factor's contribution to a calculated diffraction pattern is reduced.

Re: [ccp4bb] 3D stereo and pymol

If I may jump in, I wonder if there are any hardware configurations (monitor, 3D glasses, graphics cards, etc.) that allow 3D graphics with a MacIntosh OSX platform. -Daniel On Wed, Jan 3, 2018 at 4:42 AM, Wim Burmeister wrote: > I answer a bit late, but I repost a

Re: [ccp4bb] What's happened over the last five years with high-throughput protein crystallization screening?

I skimmed your paper, and overall it looks like a good overview of high-throughput protein crystallization. However, I was surprised that no mention was made of Formulatrix Rock Maker software, which is an excellent computer-aided graphical tool for designing crystallization screens rapidly.

Re: [ccp4bb] determining the point group and the space group

stal with know unit-cell parameters. (these are XFEL > data so indexing wouldn't give the point and space groups). I checked the > PDB, but no luck the PDB structures have the different space group > assigned, no definitive answer > hopefully, somebody can point me in the right dire

Re: [ccp4bb] determining the point group and the space group

Gihan, The best way, in my opinion, to choose a suitable (and correct) space group is to combine your own understanding and knowledge with the available software tools. I’ve never indexed XFEL data, so I don’t know if this data can be sampled and run through hkl2000/3000 or Mosflm to get some

Re: [ccp4bb] ?lsqkab?

Have you tried using the CNS script rmsd.inp? You can explicitly list the atoms to superimpose and set "coord_fit=true;". -Daniel On Mon, Apr 16, 2018 at 3:30 PM, Carter, Charlie wrote: > I think I’ve asked this question before and I was pointed in a number of >

Re: [ccp4bb] B-factor standardization

Oliviero, We published a paper in 2003 in which we normalized B-factors to do a comparison of relative mobility or flexibility. The reference is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon we used for Bave of the protein is . In our case, to be conservative in our

Re: [ccp4bb] Strange Diffraction pattern! Protein/DNA complex or DNA alone crystal?

(or try combination of PEG 400 and PEG 200), or vary the MPD concentration. Good luck. I hope this helps. -Daniel [image: RnNZfQn2o2xpggJQqefCOervMbPIci5mujDPJnvl43kv6Rtxjyh5gHN_JKVzeU-aaGz3pePFgxfoAAtZJZNx8mveVTc-11j98EfuAJVcumUenA=s0-d-e1-ft.gif]Daniel M. Himmel, Ph

Re: [ccp4bb] Unknown density

Oops. I meant to say that Ca2+ usually has seven coordinating atoms. Mg2+ usually has six. Sorry for the error. -Daniel On Wed, Mar 7, 2018 at 2:27 PM, Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > Rajesh, > > Ca2+ usually is coordinated by five atoms, where

Re: [ccp4bb] Unknown density

Rajesh, Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is coordinated by six. I've seen that a lot in structures that I've determined. -Daniel On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You just calculate a anom

[ccp4bb] Fwd: [ccp4bb] suggestions on a microscope for Crystallography

-- Forwarded message -- From: Daniel M. Himmel, Ph. D. <danielmhim...@gmail.com> Date: Wed, Mar 7, 2018 at 12:23 AM Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography To: Chandramohan Kattamuri <kattamuricha...@yahoo.com> My best experience wa

[ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

I'm looking for some computer hardware advice. I have a MacBook Pro with a "Retina" screen and an Intel HD Graphics 4000 1536 MB graphics card, running OS X 10.11.16 ("El Capitan"), and I would like to view structures in 3-D in Coot. Which computer monitors and which 3-D glasses brands would

Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

about what type of structural element is always ordered. I hope this helps. -Daniel ____ Daniel M. Himmel, Ph. D. On Tue, Nov 28, 2017 at 9:44 AM, vincent Chaptal <vincent.chap...@ibcp.fr> wrote: > Hi, > > I've been searching but can't find what I am looking for so I thought I

Re: [ccp4bb] normalization of B-factor values from different crystal structures

conformations of the protein, and I had to look at a variety of crystal structures to do the comparison and demonstrate a possible trend. I hope this helps. -Daniel M. Himmel