Re: [ccp4bb] Room temperature change from 25ºC to 20ºC

Hi Mark, Well, you don't have to look far. Spain (kind of where you are), France, Germany they will start cooling as well to reach that temperature for most of the year. I don’t think it will be feasible considering going green is what Europe wants to achieve. Jürgen > On Apr 1, 2024, at

Re: [ccp4bb] Glide fails to generate accurate docking pose

You could a) change the force field used b) increase the docking resolution c) switch to a different program e.g. FRED from OpenEye d) examine if you limited the amount of generated confirmers for your ligand. If you have two or three rotatable bonds you can easily generate >1000. And it seems

Re: [ccp4bb] What could these crystals be?

You could also run them on a gel if you don’t want to shot with canons on small birds. Jürgen > On Nov 8, 2023, at 11:33 AM, M T wrote: > > Dear Careina, > > If you have easy access to mass spectrometry, you can try to fish/rince your > « pumpkin seeds » and send them to mass to try to

Re: [ccp4bb] What could these crystals be?

Have you tried crushing these up and seeding? Jürgen ___ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University Cleveland, OH 44106 https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC > On

Re: [ccp4bb] Dry shipper in limbo

The AirTag is a good idea, I shall implement that. I’ve had samples stuck from Canada to US, also in Memphis. It was just protein on dry ice but needless to say when it arrived it was very dry but no ice. Hopefully you will be lucky and retrieve your samples within the next 14 days. Jürgen

Re: [ccp4bb] Structure prediction - waiting to happen

I was afraid of this happening at some point and decided to start a new career ~ten years ago and use structures only as a tool and never put them into the centerpiece of a grant. My fall back option is either a cocktail bar or starting a restaurant. The Triple M’s always work Mojito, Martini,

Re: [ccp4bb] Alexey Vagin

Sorry to hear, he helped me a very long time ago during my PhD time when I was running into troubles with some of his programs. The York CCzp4 weekends were fun indeed, finishing off some wines tgat Paul Adam’s had stored away. Jürgen __ Jürgen Bosch, PhD,

Re: [ccp4bb] To Trim or Not to To Trim

ncy would reflect that. But not the coordinates in any proper > way. > Debanu > > On Fri, Mar 10, 2023 at 8:58 AM Jurgen Bosch <mailto:jxb...@case.edu>> wrote: >> Going back to RIP phasing methods :-) >> So Harry in your particular case occupancy of zero would

Re: [ccp4bb] To Trim or Not to To Trim

Going back to RIP phasing methods :-) So Harry in your particular case occupancy of zero would actually reflect reality for those “combusted” atoms. Jürgen > On Mar 10, 2023, at 11:56 AM, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > One other thing

Re: [ccp4bb] To Trim or Not to To Trim

I’d say no trimming to side chains for the following reason: There are non-structural biologists using PDB files and if atoms are missing they don’t know what to do. A better approach is where no side chain density allows support of placement, pick the most common rotamer and set the occupancy

Re: [ccp4bb] Coot 1

Yay!! I can now blend it with blender. Jürgen __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC Johns Hopkins University Bloomberg

Re: [ccp4bb] am I doing this right?

The EM and Cryo-EM world might have something to say about that perhaps. Isn’t RIP phasing coming from what you are describing as well? Just curious, Jürgen __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University

Re: [ccp4bb] Analysis of NMR ensembles

On May 26, 2021, at 11:28 AM, Harry Powell - CCP4BB > wrote: > > Hi Jurgen > > NMR structures don’t appear to have B_factors, or at least not meaningful > ones (e.g. in 2kv5 they’re all 0.00…). > > thanks for the response, though > > Harry > >&g

Re: [ccp4bb] Analysis of NMR ensembles

How about color by B-factor and look for the cold areas and hot areas? Jürgen > On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Given that there are plenty of people on this BB who are structural > biologists rather than

Re: [ccp4bb] 3D Printer Model of the Coronavirus

Very, it spreads virtually. P.S. three printers are running soon __ Jürgen Bosch, Ph.D. Division of Pediatric Pulmonology and Allergy/Immunology Case Western Reserve University 2109 Adelbert Rd , BRB 835 Cleveland, OH 44106 Phone: 216.368.7565 Fax:

Re: [ccp4bb] Apple Mac M1 chip machines and compatibility with structural biology software?

Only issue is that the MacBook Air has a 13” display but I didn’t want to wait for a 16” MacBook Pro with Apple Silicon. I’m waiting for the adapter to hook up my Cinema Display from 2010 (?) and I hope that it will also work for the Zalman for 3D visualization. Another issue is I run out of

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

oscope for $50, and that works >> MUCH better. In fact, I'd say its competitive with the $5k microscope we >> use to look at crystals. However, $50 is a lot in the third world. I've >> heard that drugs that cost more than $1/pill are essentially unobtainable in >> many

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

That looks like gravel from the driveway where the dewar was tossed around Jürgen > On Dec 4, 2020, at 11:04 AM, Tanner, John J. wrote: > > When we opened our CX100 shipping dewar returned from APS via FedEx this > week, we observed what appears to be tiny rocks on the rim below the foam >

[ccp4bb] Announcing our COVID19 Dashboard

Hi all, We developed a different type of dashboard to make complex data more easily available also for non-researchers. We have launched the website currently focusing on the United States only, but plan on expanding our visualization and predictions worldwide in a future update to the site.

Re: [ccp4bb] COOT download site

Looks as if Clemens will be jumping straight into the future now with the new link. Were you on Coot 0.069? Jürgen > On Jun 4, 2020, at 10:54 AM, Paul Emsley wrote: > > On 04/06/2020 15:41, Clemens Grimm wrote: >> Dear All, >> >> accessing the COOT download pages at >> >>

Re: [ccp4bb] visual mask editor - why

Give this a shot: https://www.eyesopen.com/afitt At least in Vida from the same suite of programs, you can select such a blob as you describe and export it in a useful way. Jürgen ___ Jürgen Bosch, Ph.D. Division of

Re: [ccp4bb] visual mask editor?

Sehr geehrter Herr Hofkristallamt, Depending on your learning style, you might want to look into blender. https://www.blender.org/download/ Together with eMPV you can do some magic from scratch. You could also use any other CAD program end export the file one

Re: [ccp4bb] disinfecting keyboards

Must have been wearing a traditional Scottish outfit :-) Jürgen > On May 6, 2020, at 11:19 AM, Tristan Croll wrote: > > You got off lucky. An old friend of mine learned this lesson when on a > particularly sunny day he spent an hour out on a New Zealand glacier in > shorts with no

Re: [ccp4bb] disinfecting keyboards

You really just need two keyboards per computer, every user change, just add the used keyboards into the hutch, the rest should take care of itself then. You are at the source to successfully blast these little viruses Jürgen > On Apr 29, 2020, at 3:30 PM, James Holton wrote: > > Keyboards

Re: [ccp4bb] disinfecting keyboards

Somehow this reminds me of the scene of Scotty talking into the mouse when he is instructed to use the keyboard to interact with the computer. How is voice recognition these days on Linux? This email was not typed but spoken by Siri on my laptop. Jürgen > On Apr 29, 2020, at 2:59 PM, Sravya

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

You could also crawl through patents of sausage making. If they published now it is likely they have patented it since it sounds as if it an incredible important method for adding flavors to sausages. Jürgen > On Apr 7, 2020, at 12:23 PM, Artem Evdokimov > wrote: > > Sadly, I agree: it is

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

Honestly, as a Zugreister to Bavaria and now living in a Sausage Diaspora (by Bavarian standards), I would take any sausage available. Educational Sausages might be the way to go. You could ask a Sausage Modeler who previously participated in a Sausage-CASP competition to reach out to the

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

cting-the-seasonality-of-covid/ > <https://oldwivesandvirologists.blog/predicting-the-seasonality-of-covid/> > > Thx and stay warm (see my blog) > > Patrick > > > > On Thu, Apr 2, 2020 at 4:57 PM Jurgen Bosch <mailto:jxb...@case.edu>> wrote: > I

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

ion approach for SARS Cov2 -- using the >> indiscriminate collateral activity of Cas12 nuclease -- has been reported >> here: https://www.biorxiv.org/content/10.1101/2020.02.29.971127v1.full.pdf >> <https://www.biorxiv.org/content/10.1101/2020.02.29.971127v1.full.pdf>

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

. >> >> A similar fluorescent detection approach for SARS Cov2 -- using the >> indiscriminate collateral activity of Cas12 nuclease -- has been reported >> here: https://www.biorxiv.org/content/10.1101/2020.02.29.971127v1.full.pdf >> <https://www.biorxiv.org/content/10

Re: [ccp4bb] COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight

#theBB is too slow :-), Honestly, we probably should have an official CCP4BB Twitter account monitored by a few administrators to post relevant things more publicly - just a thought. Thanks for the update and good to know it’s moving forward fast. I had to renew my license for a software I use

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

One problem I see is the sputum, there’s a reason why swabs are made to get sufficient viral material. Since stool samples test PCR positive that might be an easier approach to get sufficient viral material. As a side note, these are not infectious anymore, or at least one has not been able to

Re: [ccp4bb] Vote for cryoEM

I personally tweet, and I know a lot of well established scientists that tweet too. Don't pretend Twitter is only junk, there are a lot of serious scientist tweeting good and valuable information. True there are enough stupid people tweeting BS. Jürgen P.S. Follow me on Twitter @Bosch_Lab >

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Think of completeness with an analogy to turkey. Say you happen to find a one-legged turkey (incomplete by conventional standard) you could still stuff it and put it in the oven and enjoy 93% of the turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-) Happy

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

Just because we have modern technology doesn't mean we have socially made progress or for that matter made mental progress regarding women in science, which in my opinion is a huge mistake . Despite many efforts, many fields are still very male dominated. Eddie, I like you stirring up the

Re: [ccp4bb] Thanks to informal query respondents

Your Figure 1 suggest a secret message - or at least I view it that way. The early steps “basic research” seems to be funded by Euros, while the in silico part is funded in Dollars. Or was that unintentional ? Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School

Re: [ccp4bb] Off-topic: Request for DNA

Synthesize your gene: [advertisement on] https://www.idtdna.com [/advertisment off] Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] Gadolinium complexes- phosphate buffer

Also you can treat your SeMET as heavy atom derivative with your native dataset. J?rgen .. J?rgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] on space group

Shameless self-promotion aka advertisement: http://lupo.jhsph.edu/boschlab/Xray_Workshop.html Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North

Re: [ccp4bb] [RANT] Reject Papers describing non-open source software

Can you get a license ? I know of several software that have components from other developers from which one needs to obtain a separate license. Was the discountinued software superseded by something more superior ? Can you send me an off list reply including the software name ? J?rgen

Re: [ccp4bb] CYS mod

BME around ? Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742tel:%2B1-410-614-4742

Re: [ccp4bb] XDS INP

Edit your XDS.INP file to look like this: !JOB= XYCORR INIT COLSPOT IDXREF JOB=DEFPIX INTEGRATE CORRECT Then rerun ads and be happy thereafter. and RTFM ! Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular

Re: [ccp4bb] XDS INP

The process failed. You mean it didn’t process the data past the indexing routine? That just means you need to actually change some values and type in a couple of commands into XDS.INP - not everything can be designed to be point click. Look at IDXREF.LP and check out what the suggested space

Re: [ccp4bb] APBS

Why not ? Look at the partner protein is there a similar charge reversal present? The function is preserved (interaction of both proteins) in different species but the charges have swapped over time in evolution while the backbone scaffold (fold) of the protein was maintained. Just as an

Re: [ccp4bb] Thin plate crystals

Along those lines suggested by David I would say these crystals are way too big. Try freezing some when they are smaller. It would also be worth trying to freeze in meshes to support the fragile plate instead of conventional loops. J?rgen .. J?rgen Bosch Johns Hopkins

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

Just to clarify, I think what Kay meant with strategy is that you don't just shoot at the crystal and collect. You should figure out what is the optimum start and end point of your data collection. Best to be cautious and not immediately go for highest resolution and not fry your crystal. A 4 A

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

like that in the good old times? HTH, Kay On Fri, 17 Apr 2015 11:55:42 +, Jurgen Bosch jbos...@jhu.edumailto:jbos...@jhu.edu wrote: Just to clarify, I think what Kay meant with strategy is that you don't just shoot at the crystal and collect. You should figure out what is the optimum start

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

15:49:21 MESZ, schrieb Jurgen Bosch jbos...@jhu.edumailto:jbos...@jhu.edu: I would disagree. My philosophy is: assume this is your only diffracting crystal, maximize the outcome by investing some thoughts into it before being sorry. Therefore, run strategy and optimize for anomalous pairs being

Re: [ccp4bb] XDS Processing with Translated Detector and Radiation Sensitive Crystals

Hi Christopher, you should also limit the resolution to say 6 A on the first pass to get your correct cell parameters. Your low I/sigI suggests that the indexing did not pick up the correct orientation of the crystal. You should also see this in your INTEGRATE.LP file if you look at the spot

Re: [ccp4bb] on NCS restraint

yes. Have two sets of NCS operators one that describe the four subunits and one describing the two subunits. If during the refinement of your structure you should find out that the subunits are not identical to each other you can relax the NCS weights. Jürgen .. Jürgen

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

You two should absolutely invest in the 1TB SSD option as well, I have essentially the machine you describe, but it is now already 14 months old. So the newer models will be maybe 30% more powerful in overall performance. The geek bench score of my Macpro 2010 (48GB RAM, dual hexa core)

Re: [ccp4bb] Manuscript PRL

This one surely will be cited quite a bit, well done Herr Hofkristallrat J?rgen .. J?rgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] how to recover my data

Dear Smith, Wouldn’t it be easier to reprocess your data and do a MR with your rescued PDB file and start from there ? Instead of trying to mess around with the non-readable mtz file ? You should have those raw images somewhere, perhaps even at the beam line if you have not made your own

Re: [ccp4bb] Protein-Ligand Crystallization

Hi Monica, A different option is they both bind but destabilize your protein (as you suggested). This will likely not help much if you are trying to co-crystallize them. But there are couple of examples out there in the literature that show the contrary, despite destabilizing Tm they got

Re: [ccp4bb] How to apply NCS restraint to a ligand in refmac?

Hi Ethan, DM with a mask of the ligand in chain A then applying the NCS matrices and looking at the resulting density perhaps ? Theoretically it should improve, this is of course assuming that your ligand does not adopt different conformations in the three chains. In Refmac you can also add a

Re: [ccp4bb] coot 0.8.1 freezes my graphics

Wrong board, try sending it to the cootbb Jūrgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Streetx-apple-data-detectors://4, W8708 Baltimore,

Re: [ccp4bb] Post-translational modification of cystine

lower left corner, I buy a water molecule there .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office:

Re: [ccp4bb] Queries regarding bead beater and french press.

[Advertisement on] Avestin Emulsiflex C5 [/Advrtisement off] Google is your friend. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street,

Re: [ccp4bb] question related to MTZ file

I assume you mean with initial mtz file the one derived from Mosflm after processing your images. If so, then how about running that file through scala http://www.ccp4.ac.uk/html/scala.html ? I bet there are some tutorials on the CCP4 webpage on that topic. Jürgen ..

Re: [ccp4bb] PDB deposition - sequence file

I would disagree. You list as sequence what you cloned and expressed. If you are missing parts then you have to describe why e.g. Proteolysis or disordered etc. Best to actually do a mass spec analysis on those crystals since a significant portion is missing. Jūrgen ..

Re: [ccp4bb] crystallography software on mac

Hi Lisa, you made quite a jump from 10.6 (released august 2009) to 10.10 ! You definitely will need to update your Fink - I assume you are familiar with Bill Scott’s page http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.10 Regarding Pymol - have you accepted the conditions for

Re: [ccp4bb] asymmetric homotrimer in the asu

Not sure if you are looking for something similar like this perhaps: http://www.rcsb.org/pdb/explore.do?structureId=2AUC Trimer in asu but all different. Jūrgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular

Re: [ccp4bb] Correct usage of AIMLESS in combination with XDS/XSCALE

Hi Renato, have a look at the first example: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale A minimal input file to combine two datasets into one file is: OUTPUT_FILE=fae-native.ahkl INPUT_FILE= ../fae-native/xds_1/XDS_ASCII.HKL INPUT_FILE= ../fae-native/xds_2/XDS_ASCII.HKL

Re: [ccp4bb] Correct usage of AIMLESS in combination with XDS/XSCALE

You can also do this in XDSCONV.INP simply change the output to what you prefer Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street,

Re: [ccp4bb] Correct usage of AIMLESS in combination with XDS/XSCALE

Best is what at the end provides the solution :-) Kay Diedrich recently had a thread about two weeks ago about the pro and cons of various options of scaling and why not to do certain things. I’m sure google in combination with CCP$ will help find that thread …. I believe it was called “To

Re: [ccp4bb] Regarding prediction of Binding pocket

Dear Sanjit, use the BD with lots of grains of salt and verify with a real experiment that the found binding pocket is real, else this is waste of money. If you know of a known ligand to interact with your particular protein, you can use this as a test BUT depending what your input model is

[ccp4bb] offtopic - Ebola Forum Webcast @JHSPH

I know this has not much to do with crystallography, but I think it’s worth the time reading and deciding if you want to watch the webcast that took place yesterday at Johns Hopkins School of Public Health. http://www.jhsph.edu/events/2014/ebola-forum/

Re: [ccp4bb] crystallization with hydrophobic ligands

An alternative is to dissolve your compound in MeOH and dispense it either manually or via robot, let the plate sit sometime in the hood for faster evaporation and then add your protein + reservoir. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public

Re: [ccp4bb] I222 - P22121 space-group ambiguity

I think Eleanor was looking at the cell axis in particular a and b they are off by almost 10%, hence unlikely to be identical, unless I missed something there. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] Biolayer Interferometry

Whatever you decide to do, it is good practice to confirm your “hit” with an orthogonal method. Interactions in both directions with the same piece of equipment is a start but that in my eyes does not count as another method. If you are trying to decide between the Blitz and an Octet I would

Re: [ccp4bb] XDS.INP for X25

This helps: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI But you also have my script off list :-) Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria

Re: [ccp4bb] Space group numbers

Yes, we ran into exactly that issue as well. Jūrgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Streetx-apple-data-detectors://4, W8708

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

, Jurgen Bosch jbos...@jhu.edumailto:jbos...@jhu.edu wrote: Dear BB, or in particular Phaser developers :-) This must be part of British humor right (or was that the Canadian influence Randy) ? eLLG indicates that placement of ensemble ensemble_1 will be straightforward The data are sufficient

[ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

Dear BB, or in particular Phaser developers :-) This must be part of British humor right (or was that the Canadian influence Randy) ? eLLG indicates that placement of ensemble ensemble_1 will be straightforward The data are sufficient to exceed the eLLG target The search space is finite 143

Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?

Coot? Measure angle I assume you just want that value and not a script to run for multiple occasions? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] XDSGUI @ OSX 10.9.5 (13F34)

, since the emails did not go to the list. Engin On 9/23/14 3:35 PM, Jurgen Bosch wrote: Thanks Engin, the collective wisdom of the CCP4BB helped again within 10 minutes of sending off my email (even though the timestamp says something different). Thanks - now I’m happy and can process some data

[ccp4bb] XDSGUI @ OSX 10.9.5 (13F34)

Dear BB, can anybody reproduce the problem with XDSGUI on the very latest Mac OSX update (from this weekend). I am unable to run generate_XDS.INP with useful input parameters from the diffraction images. It might just be a permission think perhaps that Apple has introduced in the last

Re: [ccp4bb] composite omit map

http://www.ccp4.ac.uk/html/comit.html .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office:

Re: [ccp4bb] Generate small molecule library

you can do this via SMILES and your own script in any flavor and then use your preferred program afterwards. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research

[ccp4bb] test

Dear BB, sorry for the email I’m just validating that after 6 months abstinence I’m back on the CCP4BB and can actually post. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins

Re: [ccp4bb] linux question

Google for knopix Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894

Re: [ccp4bb] Reg. Protein purification

How about using an anion exchanger after your NTA step ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone:

Re: [ccp4bb] IMAC and Low Ionic Strength

Hi Jacob, an alternative explenation might be your protein does not bind via the tag to the resin but unspecifically. What happens if you add the recommended NaCl concentration? Does it fall off too? Just a thought, Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School

Re: [ccp4bb] small molecule soaking screening

Additional to all other suggestions you can also mix your ligand at low concentration to lots of low concentrated protein and then concentrate your protein over time. The advantage, ligands with low solubility can bind to your protein while you are concentrating it. And then I would

Re: [ccp4bb] small molecule library

Try Emerald, reasonable price, nö comment. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742

Re: [ccp4bb] heavy atom derivative choice

There is a Xenon chamber at 14-1 if I remember it correctly. I never had luck though. How about Iodine or Gadolinium? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute