[ccp4bb] Postdoctoral position available at University of Texas Southwestern Medical Center

This message is posted for Eric Olson, Ph.D. (Chair of Molecular Biology), who is looking for a postdoctoral fellow to join his lab to work on a novel membrane protein (first described in Nature, in press). See project description below and if interested please contact him at: Email:

Re: [ccp4bb] Control the crystallization process in the presence of small volatile organic molecules

Another thing to try when cryoprotecting any crystals grown at room temp using a volatile precipitant is to first transfer the crystal tray to 4 degrees, then quickly add a cold aliquot of a viscous cryoprotectant to the drop. Evaporation is considerably slower at 4 degrees, and I prefer to

[ccp4bb] Question about Phoenix crystallization robot

BACKGROUND: Recently we acquired an Art Robbins Phoenix crystallization robot. This instrument is in a shared environment, accessible to labs with projects that range from small, well-behaved soluble cytosolic proteins to large complexes and integral membrane proteins. Many of our users

Re: [ccp4bb] font size CCP4i

I don't know, I kind of liked the larger font size. I thought it was an improvement. Maybe that's because I'm getting older and need new glasses... Diana On May 23, 2008, at 7:47 AM, Kristof Van Hecke wrote: Dear all, I recently installed the CCP4 Program Suite 6.0.2., together with

Re: [ccp4bb] is it Ok to freeze

Every small molecule dataset I collected as a graduate student in chemistry back in the mid to late 1980's was at 100K. I never had to worry about crystal slippage during collection, organic solvent evaporation, air oxidation of the sample (organometallic metal clusters) or secondary

Re: [ccp4bb] Na Acetate Buffer volatility

One important consideration with acetate buffer is volatility. All the care in the world to painstakingly reproduce the pH of the buffer will not help you if store your acetate buffer for long periods of time in a container that doesn't minimize evaporation (so all of you out there trying

Re: [ccp4bb] off-topic: Enzymology textbook recommendations?

I have a copy of that textbook, and I like it. I had the privilege to sit in on Perry Frey's lectures at the University of Wisconsin, and the text is as clear and informative as his lectures. Plus it's easier to read than my old lecture notes (and more up-to-date). Diana On Sep 11, 2008,

Re: [ccp4bb] Quick-soak

Or you could try crystallizing the protein in the presence of KI or NaI, and collect some in-house SAD data. You could also try to boost the concentration and number of ordered halide sites by quick soaking the crystals with a higher concentration of the iodide salt. In my limited

Re: [ccp4bb] protein crystallography universe

Does this mean that you are now King of the protein crystallography universe? I am confident that you will be a kind and benevolent ruler, Diana On Oct 14, 2008, at 2:47 PM, Paul Swepston wrote: Folks: While attending the ICSG meeting in Oxford last month it struck me that there might

[ccp4bb] Faculty position in Structural Biology at UT Southwestern Medical Center

Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting and tackle biological problems in a comprehensive way. We use a multitude of experimental approaches

Re: [ccp4bb] microseeding SeMet drops with native xtal seeds

See the following publication for an interesting method to resolve pseudo-merohedral twinning in SeMet crystals: Cansizoglu, A. E. and Chook, Y. M. (2007) Conformational heterogeneity of Karyopherinβ2 is segmental. Structure, 15(11):1431-1441. In an effort to obtain single selenomethionine

Re: [ccp4bb] Structures determined: breakdown of methods

On Jan 17, 2011, at 11:46 AM, James Holton wrote: I am willing to bet that the earliest no method entries (particularly the ones that lack a REMark 200 record) were probably MIR, since that was the obvious method to solve a structure for some time. Modern NULL entries seem to be mostly

Re: [ccp4bb] Another paper structure retracted

A quick glance at the header of the PDB file shows that there is one glaring discrepancy between it and the table in the paper that hasn't been mentioned yet in this forum. The data completeness (for data collection) reported in the paper is 95.7%, but in the header of the PDB file (actually,

Re: [ccp4bb] Check PDB file for missing atoms

The RCSB PDB Validation server will also report this info for you. Diana ** Diana R. Tomchick Associate Professor Department of Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214B Dallas, TX 75390-8816

[ccp4bb] Postdoctoral Research Position available at UT Southwestern Medical Center

This is posted as a favor for a collaborator, please do not respond to me but directly to Neal Alto. --- A postdoctoral research position is available in the laboratory of

Re: [ccp4bb] Granada Crystallization Boxes?

?If it weren't for the fact that trying to 3-D print translucent plastic is still problematic, you would think that this would be a perfect application of that technology. Diana ** Diana R. Tomchick Professor Departments of Biophysics and

Re: [ccp4bb] Granada Crystallization Boxes?

, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Jul 11, 2017, at 1:39 PM, Diana Tomchick <diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>> wrote: You can co

Re: [ccp4bb] Granada Crystallization Boxes?

You can continue to buy new ones from Tirana Science & Technology, which is a Spanish company. http://www.trianatech.com/index.php?option=com_content=article=65=88=en Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry

Re: [ccp4bb] Fine Phi Slicing

And the instrument makers (e.g., Rigaku and Bruker) currently sell multi-axis goniostats for in-house data collection--and not just for small-molecule purposes. Diana P.S. Ron, we still call 'em goniometer heads and goniostats at UT Southwestern. > On Jul 14, 2017, at 1:00 PM,

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

Or use Coot to generate the symmetry mates, then write out the symmetry-related coordinates. Many ways to achieve the same outcome, Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern

Re: [ccp4bb] refmac output

Yes, I agree! This (“Please look at my structure, and here are my files from the last cycle of refinement") happens to me almost every week. :) Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas

Re: [ccp4bb] pseudo-centering or twinning problem in P3

Maybe, but it may also indicate that the problem isn’t twinning, but simply pseudo symmetry. Zanuda is one way to double-check, and it takes approximately a day to re-process the data, run the MR and run Zanuda. Diana ** Diana R. Tomchick

Re: [ccp4bb] Protein or DNA crystals

It’s been my experience that protein crystals with that high a percentage of tryptophan residues (>2%) should give a very clearly positive result from a UV microscope such as a Jansi UVEX. Diana ** Diana R. Tomchick Professor Departments of

[ccp4bb] Research Track Assistant Professor Positions

and qualifications. About the UT Southwestern Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting and tackle biological problems in a comprehensive way

[ccp4bb] Fwd: biotech opportunity

From: Steven McKnight > Subject: favor Date: June 2, 2017 at 3:21:39 PM CDT To: Michael Rosen > Cc: Joseph Ready

Re: [ccp4bb] [phenixbb] comfortable OS X level

I’ve not had any problems; the current version is 10.2.5, so it’s pretty stable now. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

Re: [ccp4bb] [phenixbb] comfortable OS X level

diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Jun 7, 2017, at 11:25 AM, Scott Classen <sclas...@lbl.gov> wrote: 10.2 ? That OS is 15 years old. > On Jun 7, 2017, at 8:27 AM, Diana Tomchick > <diana.tomch...@utsouthwestern.edu> wrote: > > I

Re: [ccp4bb] preparing DL-Malic acid stock solution

As the pKa1 of malic acid is 3.4, it may be that the partially neutralized malic acid salt is less soluble than the acid or the fully neutralized salt. The pKa2 of malic acid is 5.1. Contact the people at Hampton Research https://www.hamptonresearch.com/contact_us.aspx and ask them. They sell

Re: [ccp4bb] High R/Rfree after MR

I sent this on Friday to Gianluca but forgot to also send it to the bulletin board, so I’m posting it now, as it relates to Eleanor’s response. __ It would also be worthwhile to consider the possibility of out-of-register errors in the sequence

Re: [ccp4bb] Fix sidechain outliers

Fitmunk works pretty well in the initial stages of model fitting. You will still need to manually check the results of any automated model fitting program to see if it makes sense; your brain is still your best tool, in the final analysis. Diana > On Sep 4, 2017, at 1:29 PM, Dominika Borek

Re: [ccp4bb] Overlapping ligand electron density

Matt, Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site,

Re: [ccp4bb] high TFZ score but 50% of Rfree

Do the following. 1) Perform density modification (NCS averaging and solvent flattening) 2) Run the new phases through a model building program (Buccaneer works for all resolutions, Arp/wArp works well for better than ~2.7 Å or better resolution) If this doesn’t give you a better quality model

Re: [ccp4bb] new ContaMiner features

It is also possible that it co-purifies via a nickel IMAC column purification step. The affinity of many E. coli proteins for such columns is well known. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of

Re: [ccp4bb] teaching question: graphics for chromebook?

If the chromebook has a USB port, and if the laptop can be booted using an external drive, you could boot the laptop with a Linux operating system and the educational version of PyMOL installed on a USB stick. Or you could just pay the $269/year for the Laboratory & Classroom subscription,

Re: [ccp4bb] Difficult experimental phasing

Estimating isomorphism by eyeballing the difference in unit cell lengths may mask significant non-isomorphism that is present. Iodine is a large atom and it is notoriously difficult to get an iodine derivative that is isomorphous to a native protein. Depending upon the chemistry of your mother

Re: [ccp4bb] Na-Binding Protein?

The human branched-chain alpha-ketoacid dehydrogenase requires a K+ ion to stabilize the binding of the cofactor thiamine diphosphate and to achieve maximum catalytic efficiency. See https://www.ncbi.nlm.nih.gov/pubmed/10745006 Diana ** Diana R.

Re: [ccp4bb] "Atomic resolution"

In the “good old days” we used to refer to “atomic resolution” as higher than 1.0 Å (or more specifically, at least 0.8 Å resolution), e.g. the resolution obtained by most small molecule structures, where you get at least 10 times the number of observables per refined parameter, and thus could

Re: [ccp4bb] protein quasicrystals?

Some of the high intensity, high resolution spots are possibly from ice. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX

Re: [ccp4bb] Structure solution - hexapeptide

I’ll second the use of ACORN. I was able to solve an RNA duplex structure with 1.4 Å data using the program, and it only took about 20 minutes of CPU time on an old (~5 years) Mac Pro. Diana ** Diana R. Tomchick Professor Departments of

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

May I add the comment that despite the fact that it would be great if all of the samples that I worked with would be stable at room temperature for 3 weeks, if I had applied that as a criterion for crystallization screening and subsequent structure determination, then my publication record

[ccp4bb] Research Specialist/Cryo-Electron Microscopist, UT Southwestern Medical Center

cryo-electron microscopy technology for protein structure determination. About the UT Southwestern Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting

Re: [ccp4bb] According correct space group assignment...

Several years ago I solved a small RNA structure by direct methods using the CCP4 program ACORN, and built the model using Nautilus. This was with data to only 1.25 Å resolution, collected at the Se edge, so there was no significant anomalous signal. I think that this worked like a charm

Re: [ccp4bb] Rfree going up after refinement

?Hi, I have seen this type of behavior happen often, albeit in phasing runs with Buccanneer and/or Phenix. Check the model statistics immediately after phasing, and compare them to the model statistics after refinement in Refmac. When I have observed this phenomenon, it's likely due to the

Re: [ccp4bb] A question related to Fe-S proteins

Is it possible that you have a case of domain swapping that causes the trimeric assembly? Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

[ccp4bb] Research Specialist/Cryo-Electron Microscopist, UT Southwestern Medical Center

single particle cryo-electron microscopy technology for protein structure determination. About the UT Southwestern Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together

Re: [ccp4bb] suggestions for cryoprotectant

Condition #3 isn’t far from the saturated conditions for lithium sulfate. Perhaps slightly increasing the lithium sulfate concentration will work, or using a related lithium salt. See Cryosalts: suppression of ice formation in macromolecular crystallography Acta Cryst D Volume

Re: [ccp4bb] visualising anis B factors

e University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf o

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

I hope you are compressing your images, typically that makes them 1/4 the original size. SBGrid and Wladek Minor also have image archival services. As I am replying from my cell phone while on vacation, the links to those services are not handy to me. But they have been mentioned many times on

Re: [ccp4bb] Literature on crystallization screen ingredients not showing up in crystal structure

Not being in a model does not show that it's really not there. This is especially true when considering crystals that diffract to rather low resolution (~2.8 - 3.5+ Å). You shouldn’t expect in that case to uniquely identify very many buffer components. Diana

Re: [ccp4bb] beryllium chloride

No, that should read [cid:2D6B8E73-AD29-4B8C-972A-06201D871588] Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816

Re: [ccp4bb] Mandatory mmCIF format for crystallographic depositions to the PDB

The PDB extract tool can be used to create the proper format mmCIF file from coordinates uploaded in PDB format. https://pdb-extract.wwpdb.org https://pdb-extract.wwpdb.org/tutorial.html Diana ** Diana R. Tomchick Professor Departments of

Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

> I do not believe comparing the average B to the Wilson B has any > utility at all. > > Dale Tronrud There are not many times that reading a CCP4bb posting makes me laugh out loud, but this one made my day. Thanks! Diana ** Diana R. Tomchick

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

The scenario I presented earlier works like a charm in refinement with the Phenix program suite. For example, I have used it for both mixed populations of ligands (e.g., AAMP and BADP) as well as phosphorylation (ASER and BSEP). Diana ** Diana R.

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

If you have the odd case where one residue (of the same number in the polypeptide chain) is a Leu and the alternative residue is a Phe, then it would be ALEU and BPHE, both residues would have the same residue number, and reset the occupancies to fractions that sum to 1.0. Diana

Re: [ccp4bb] High Rfree in last Shell

. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Apr 16, 2019, at 1:21 PM, Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu>> wrote: Why are the the values for R(free) in

Re: [ccp4bb] High Rfree in last Shell

Why are the the values for R(free) in parentheses higher than R(factor) in parentheses? I would not expect that to happen, if the same resolution limits for the last shell are used for both values. And I echo the previous commentator, please provide the resolution limits for the values in

Re: [ccp4bb] High Rfree in last Shell

Ah, even though it seems a long time ago, approximately one out of every two referee comments that I receive complain about our modern methods for processing, scaling and reporting our data collection/processing/refinement statistics. I’m afraid it’s an ongoing effort at education. Diana

Re: [ccp4bb] tNCS incompatible with cell dimensions

Your native Patterson indicates pseudo C-centering. Are you sure you don’t have space group C222(1)? If your space group is correct, it’s still pseudo C-centered. You should see that in the intensity-weighted reciprocal lattice. You could try re-indexing on just the most intense spots to give

Re: [ccp4bb] how many crystallographers are there?

Try asking the IUCr for information on crystallographers. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816

Re: [ccp4bb] pointless warning - space group ambiguity

You didn’t tell us what method and computer programs you are using for phasing. If you are using Molecular Replacement and not getting a solution, it could be that your model isn’t close enough to the actual solution. Diana ** Diana R. Tomchick

Re: [ccp4bb] Intergrown crystals and excess of nucleation

In addition to all the excellent suggestions to perform seeding, you could also try sitting drop vapor diffusion, and also different temperatures. Sometimes moving from 20 to 4 degrees does the trick. Diana ** Diana R. Tomchick Professor

Re: [ccp4bb] A crystallisation screen pH query.

Although it sounds as though this condition was not pH adjusted by the company, here are a couple of suggestions that are applicable to ANY commercial screen condition. 1) Try looking at the company's web site for details on how the solution was made, or failing that, try calling the company

Re: [ccp4bb] Hydrogens in PDB File

al factors. Alex From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu>> Reply-To: Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu>> Date: Friday, February 28, 2020 at 11:52 AM To: "CCP4BB

Re: [ccp4bb] What resolution - X-ray diffraction round this time

But that wouldn’t incorporate other useful information, such as percentage completeness in the outer shell and whether inclusion of the reflections in the outer shell for refinement actually effects the resulting structural model and map to a significant degree. Diana

Re: [ccp4bb] Hydrogens in PDB File

If you deposit an mmCIF file that contains both the observed and calculated structure factors from your final round of refinement, then the PDB auto-validation reports the same (or so close to the same as to be negligible) R factors. Phenix outputs all of this automatically for you if you

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Then ask more “junior women.” This isn’t rocket science, after alll. Diana ** Diana R. Tomchick Department of Biophysics, Rm. ND10.214A University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75061 USA 214-645-6383 (office) On Feb 5, 2020,

Re: [ccp4bb] Mixed oligomeric states in crystallo

Here’s two examples of heterooligomers that crystallized in a lattice with an extra monomer of one of the proteins. In both cases this was an unexpected result, but easily explained due to the low micro molar affinities for the complex. 4PKY 2CJS Diana

Re: [ccp4bb] powdery residue on pucks?

I believe my technician decided that it was due to the breakdown of the adsorbent foam in our oldish shipping dewar, as it stopped happening once we replaced that particular dewar. But I would be open to other explanations. Diana ** Diana R.

Re: [ccp4bb] disinfecting keyboards

?You could try doing what my technician does with her keyboard; she wraps it in a clear, thin food wrap that can be taped to the back of the keyboard. This is usually done to keep food and other things (liquids) from damaging the keyboard, but you could simply replace the wrap every time

Re: [ccp4bb] disinfecting keyboards

Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) From: CCP4 bulletin board on behalf of Diana

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

​Frankly this is a great idea for datasets on any projects. I've been so busy the last 3-4 years that I have been unable to do it for my projects, but now I should be able to get it done. Not to mention trying to solve a couple of those pesky structures that have proven tough nuts to crack.

Re: [ccp4bb] dimeric tag to induce the homodimerization of protein

Any dimeric tag should work if you add a long enough linker to satisfy your distance criterion. GST, for example. Download the coordinates and get a rough idea how long the linker would have to be for your protein. Diana ** Diana R. Tomchick

Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

I too have seen some horrendous low-resolution models, with correspondingly bad validation statistics. A little time spent cleaning up the outliers (geometric and others) rarely results in large reductions in R(free) for these types of datasets & models, but ultimately we as a community need to

Re: [ccp4bb] number of frames to get a full dataset?

There are lots of places where you could find this information (many textbooks, articles, etc.) but one that I use for classes is quite good due to ease of understanding. It’s part of the Proceedings of the CCP4 Study Weekend on Data Collection and Processing. There are other quite excellent

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

Make sure the 13” display is large enough to display all the GUIs for program suites that you are interested in. For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 GUI. Requirements are found here: https://hkl-xray.com/hardware-operating-systems Diana

Re: [ccp4bb] polarizer

If only glass is placed between the polarizer and analyzer, the crystal will not show artificial colors (try it in a 9-well Pyrex depression plate). The artificial colors come from the diffraction of visible light from the plastic ware, which depending upon the type of plastic and the way the

Re: [ccp4bb] polarizer

It's my understanding that you have two polarizers on your polarizer-microscope--one in the base, and the one that attaches to the magnifying lens. When you rotate the one on the lens so that it is 90 degrees to the one in the base, no (or very little) light should pass through to your eyes,

Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

Interesting observation. In our home X-ray lab, we constructed a liquid nitrogen dumping station from a large garbage can filled with sand to about 12 inches. To keep the sand out of the dewars we topped the sand with a large wad of screen-door netting. All items can easily be purchased from a

Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts

We no longer use the reusable bases for the same reasons, but we do re-use our bases. If you use superglue to glue the pins into the bases, you can remove the pins from the bases by soaking them in acetone. This works about 75% of the time, especially if you are careful not to use too much

Re: [ccp4bb] TNCS and oligomeric state

One of the most lucid explanations of how translational NCS results in peaks in a self-Patterson map is provided in Phil Evans’ classic paper, “Rotations and rotation matrices”, which is an Open Access publication. In particular, check out Figure 4, which illustrates a non-crystallographic dyad

Re: [ccp4bb] Fluka-branded PEG 3000

If you even still have a few milliliters of the original PEG solution, you could simply use that for mixing with the protein in the drop and use a different PEG solution for the reservoir, thereby ensuring a mother liquor that could either provide (or remove) a missing impurity. Diana

Re: [ccp4bb] Challenging Molecular Replacement

There are a large number of PAK clashes, I would regard this "solution" with caution. Have you inspected the solution to see where these clashes are occurring? If they are from long flexible loops or the termini, perhaps if you would trim the model to remove those clashes and re-run the MR

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Depending upon the amount of radiation exposure, the iron might be reduced (or more likely, in a mixed oxidation state) by the X-ray beam. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical

Re: [ccp4bb] Looking or Coot 0.9 or newer for OSX

The default version of Coot included in the latest CCP4 download (version 7.1.016) is 0.9.6. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A

Re: [ccp4bb] mysterious density

Contour the 2Fo-Fc map at lower sigma than 1.3, and see if the resulting density looks like MES. As others have said, if there is no specific pocket or interactions for the non-sulfonic acid head group, then I would expect that density to be weaker or smeared out due to positional disorder.

Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

I would say that in a small survey (~5-6) of bacterial enzymes from our lab, AlphaFold2 predicted exactly the constructs that were discovered by limited proteolysis and/or sequence alignment for currently unpublished structures. It’s a useful tool but I’ve also had two cases where it

Re: [ccp4bb] the structures of Nucleic acid

I have also found that there is significant anomalous signal from strontium near the Se K-edge, which is useful if one uses strontium chloride instead of potassium chloride (or in addition to KCl) during crystal growth. Diana ** Diana R. Tomchick

Re: [ccp4bb] Easy/Silly question

It's GLC otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-glucose. See PDB ID 1ANF also https://en.wikipedia.org/wiki/Maltose [https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Maltose2.svg/1200px-Maltose2.svg.png] Maltose -

Re: [ccp4bb] How to deal with tNCS?

I would second what Eleanor has to say about the relationship of your C2221 cell to the P212121 cell. When I have had cases where there is a peak in the self Patterson function that is as high as yours (99.471% is essentially 100%), it means that the peak at 1/2, 0, 0 in the self Patterson is

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Be aware that beryllium is also quite toxic. https://en.wikipedia.org/wiki/Acute_beryllium_poisoning Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

Re: [ccp4bb] Mystery blob

It’s the Easter Bunny! But seriously, it looks like more than one compound, perhaps hydrogen bonded to each other. Diana Tomchick Sent from my iPhone On Mar 7, 2024, at 7:32 AM, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:  EXTERNAL MAIL Anyone ANY ide

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

When you try to use LIG in Phenix it gives you an error message as it doesn’t know that LIG is obsoleted. Diana Sent from my iPhone > On Apr 26, 2024, at 10:08 AM, Yong Wang > <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk> wrote: > > EXTERNAL MAIL > > Dear all, > > Perhaps the issue is that

Re: [ccp4bb] add ligand with AceDRG

 AM, Deborah Harrus wrote:  Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand

Re: [ccp4bb] add ligand with AceDRG

t; Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG the

Re: [ccp4bb] add ligand with AceDRG

The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent