Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

What’s your spacegroup ? RWork / RFree? Twinning by any chance? Jürgen __ 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] need someone officially settle a pdb dispute for a publication

raph. Jürgen ______ 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: 216.368.4223 https://www.linkedin.com/in/jubosch/ CEO

Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

Can’t help you with this, however, I have a couple of PDB deposits that I did not publish on and if somebody took them and used my coordinates that’s fine as long as they cite the DOI affiliated with the deposition. Now the question for you, were A and B collaborating on this? If so then

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

Hi Chandra, If I remember correctly, the SSRL beam lines 12-2 and 14-1 allow kappa offset plus you can swing out the detector. You might have to come up with a special collection strategy, that you collect in resolution bins to avoid overlaps. Jürgen P.S. my previous messages got blocked,

Re: [ccp4bb] raw data deposition

Which trps protein check the MSGPP or SGPP website they might have what you are looking for. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street

Re: [ccp4bb] Off-topic: DSF thermo cycler low temp limit

CD spec with Pelletier is an option too 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

Re: [ccp4bb] UV imaging of crystals

. Excuse was to few tryptophans So in theory it is nice but a cheaper variant might be to add Gfp to your protein and screen for something green. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins

Re: [ccp4bb] Mac OSX 10.7 Lion

disturbing feature about this integrated auto backup is sometimes your Mac goes idle before you can typebecause it is saving another version. This is particularly annoying when you edit large Keynote files. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public

Re: [ccp4bb] PyMol plugin

Symexp is not sufficient for hour purpose ? 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] Apochromatic and Achromatic

on apo- or achromatic lenses. 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

Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?

Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health

Re: [ccp4bb] hello

? 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 Fax: +1-410

Re: [ccp4bb] citric acid + 40%MPD (pHI -H1 condition)

It will freeze out of the drop. So that's good. 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

Re: [ccp4bb] Help! low resolution protein-DNA complex

Another thing you should bookmark and check out is the Molprobity page (google for it), upload your pdb file and let it evaluate what you have done. The chart it generates will guide you through your structure and you will be able to do a good job. Jürgen .. Jürgen Bosch

Re: [ccp4bb] Problems in refinement

60% occupied Zn site perhaps ? Q2 do you have leftover atoms from a previous dual conformation refinement ? Try deleting the corresponding residues in a texteditor and not coot to ensure they are really gone, then rebuild the section into the new diff- map. Jürgen .. Jürgen

Re: [ccp4bb] Tev Cleavage issue !!

. Good luck ! 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 Fax

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

I assume TLS is supported or do we have to wait for version 1.1 ? When will you have a 10.7 (lion) standalone version compiled ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Try the program Hollow. Or visit USF and find the cavity script. There's also Carver out there but I never got it really to work for my purposes, but it's been written for channels. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] while on the subject of stereo

I never thought I would agree with Tassos :-) But same experience 3D and wiggling with a snaked ligand makes live so much easier. It helps to have a fast graphics card though. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] while on the subject of stereo

I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutter glasses feel like bricks. I would estimate them to at least 270g. After one hour wearing them you feel them on your nose. Jürgen .. Jürgen Bosch Johns Hopkins

Re: [ccp4bb] how to use mac to solve structures

Just google for crystallography on os x and you will find Bill Scott's excellent guide through the galaxy. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North

Re: [ccp4bb] Merging data to increase multiplicity

Bad data = processing with XDS 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

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

script later 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 Fax

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

lambda distance 2theta 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

Re: [ccp4bb] Tough 'shell' on disturbed drop

Often you can also avoid this skin formation by adding a bit of your reservoir solution first to make it a larger droplet. Then the microtools as mentioned earlier or just two loops Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] Question on calculation of RMSD

methods ? From a structural/functional perspective one method will highlight the real differences in terms of movements. For an initial understanding I recommend SSM and a morphing movie, that helps dissecting what might be going on. Jürgen .. Jürgen Bosch Johns Hopkins

Re: [ccp4bb] Crystal gel band

acid to 10%. 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 Fax: +1-410-955-3655 http

Re: [ccp4bb] Lysis of Pichia pastoris

to be replaced every three to four months. The only other alternative would be a glass beater and regularly autoclave and clean the glass beads. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute

Re: [ccp4bb] Lysis of Pichia pastoris

(for you). Then you keep grinding until you have a nice pesto. Thinking about this, we should do that for smaller amounts instead of diluting the cells so that they can be run through the Emulsiflex ... Need to go to my freezer and pull out a pellet and grind them up. Jürgen - Jürgen Bosch

Re: [ccp4bb] How to get PDB of small molecule which is not available in data base..??

Pubchem ? Hicup ? Prodrg ? 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

Re: [ccp4bb] DLS

could get a sense of your sample homogeneity via SEC instead Just a thought, 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

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

in the morning 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 Fax: +1

Re: [ccp4bb] Help with Optimizing Crystals

for alternative buffer conditions using DSF and then pick a condition under which it seems to be very stable according to its melting temperature in the buffer. You've spared us the details of your purification procedure, maybe a polishing step at the end with a SEC might do wonders. Jürgen - Jürgen Bosch

Re: [ccp4bb] Help with Optimizing Crystals

Hi. Here is some additional information. 1. The purification method that I used included Ni, tag cleavage, and SEC as a final step. I have tried samples from three different purification batches that range in purity, and even the batch with the worst purity seems to produce

Re: [ccp4bb] Hardware question

Hi Ed, I have four of those http://www.newegg.com/Product/Product.aspx?Item=N82E16822136514 and would now buy these http://www.newegg.com/Product/Product.aspx?Item=N82E16822136764 DELLete it, I mean the quote you have and shop somewhere else. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg

Re: [ccp4bb] **Possible spam**cryoprotetant for 35% Dioxane

And if you are not so into reading papers, you can use this database http://idb.exst.jaxa.jp/db_data/protein/search-e.php? Jürgen P.S. Who wants to write an App for that, wouldn't this be very handy at the beamline ? I take 5% of the income for the idea :-) - Jürgen Bosch Johns Hopkins

Re: [ccp4bb] JAC (2010), 43,1242-1249

Thank you all for not sharing the pdf. 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] Refinement

are indicating Did you run Phaser in P222 + all other possible space groups or did you feed it with P212121 and only ran it in this space group ? - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North

[ccp4bb] JAC (2010), 43,1242-1249

Lesenswert ! Worth reading ! http://journals.iucr.org/j/issues/2010/05/02/issconts.html Could somebody send me the pdf from Bayes 1763 ? Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute

Re: [ccp4bb] quantum diffraction

Can't find your reference unless you are referring to this one: JOURNAL OF MODERN OPTICS, 1994, VOL .41, NO .12, 2413-2423 In case I'm wrong, could you post the direct link for download of Dale's paper ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] Too many microcrystals.......

with your reservoir and spin it down, then setup the tray but not adding additional reservoir to it. How about temperature ? Is your protein more soluble at 4˚C or 37˚C ? Just some thought before the sun rises, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] The color of GFP crystals?

What GFP did you use, your pH is 4.6 or something around there according to your picture. If the pH is true GFP will be colorless. You certainly have some more GFP lying around (without your protein fused to it), just titrate it and see what pH dependency you have. Jürgen - Jürgen Bosch Johns

Re: [ccp4bb] Micromatrix seeding using the mosquito

3) seed. In that case the combination of 2+3 is always 100nl and we start out with 5 nl Seed stock. In the IntelliPlates (3well) we play the protein/reservoir ratio game + seed Reproducibility is pretty good. We keep our seed stock where we grew the crystals e.g. 20˚C or 4˚C. Jürgen - Jürgen

Re: [ccp4bb] Regarding quality of protein for crystallization

How about incomplete TEV cleavage ? Your protein is a dimer/multimer in solution and some of it is cleaved and some not and they stick together and are separated on the SDS gel ? Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology

Re: [ccp4bb] Regarding quality of protein for crystallization

What are the minor differences in peptides ? Any PTM's perhaps ? 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] protein turns brown

[FeS] clluster ? Or some metal bound to your protein ? Is it dark brown or yellowish brown ? What's your protein concentration ? 25 mg/ml ? Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research

Re: [ccp4bb] How to define NCS in REFMAC

-values WEIG MATR 0.1 DAMP 0.5 0.5 SCALe TYPE BULK SCALe LSSCale SCALe LSSCale ANISotropic SCAL MLSC NCYC 10 TEMP 1.0 4.0 6.0 6.0 10.0 MONI MANY DIST 4 TORS 4 ANGL 4 CHIR 4 VDWR 3 NCSR 4 PLAN 4 NCSR 4 BFAC 4 BINS 10 EOF - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] Fab purification and crystallization

I assume you separate your complex over a size exclusion before setting up trays ? If not try that and see if you get better crystals. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615

Re: [ccp4bb] why I can't reproduce R based on the same program?

I see in your script you used Weight Auto - play a bit with that value and you will find a better fit. Have you used the same TLS groups ? I don't see that you are using TLS refinement in your script. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] Reverse Translatase

A large amount of hypotheticals can be found in Plasmodium :-) 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

Re: [ccp4bb] Anybody using PVM by any chance ?

Fixed it, details are available if somebody is interested in them. 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

[ccp4bb] Anybody using PVM by any chance ?

. If there is somebody on the BB with PVM experience, please contact me off the board. Thanks in advance, 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

Re: [ccp4bb] Problem with getting protein-inhibitor complex structure

. 5939-46 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 Fax: +1-410-955-3655 http

Re: [ccp4bb] Your Ccp4 question

- 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 Fax: +1-410-955-3655 http://web.mac.com

Re: [ccp4bb] Problem with getting protein-inhibitor complex structure

- 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 Fax: +1-410-955-3655 http://web.mac.com

Re: [ccp4bb] DM NCS averaging question

- 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 Fax: +1-410-955-3655 http://web.mac.com

Re: [ccp4bb] database-assisted data archive

Do you want the frames to be accessible too ? If not, then a.wiki would be an easy solution. Alternatively a Filemaker database would do the trick too. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns

Re: [ccp4bb] I-TASSER predicts NADPH binding, need to confirm with experiment

Check the thermal stability with and without your ligand. You could do this via CD or with the help of Sypro Orange in a RT-PCR machine. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria

Re: [ccp4bb] Data processing problem with mosflm

for additional keywords. 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 Fax: +1-410-955-3655

Re: [ccp4bb] A strange case of MR

Your beta and gamma angle in P1 are awfully close to 90 degrees. Are you sure about P1 ? Could it be C2 with beta of 104 ˚ ? I'm assuming the CRYST card below belongs to your structure right ? Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] Structure Based Sequence Alignment

Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522 - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street

Re: [ccp4bb] Finding best model for molecular replacement

.pdbs into Mr Bump. - 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 Fax: +1-410-955

Re: [ccp4bb] Finding best model for molecular replacement

PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468 - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North

Re: [ccp4bb] Finding best model for molecular replacement

know the JCSG has had some luck with this approach, but they have full-time programmers and something like 400 CPUs. -Nat - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] Help needed in solving a MAD dataset

, and once you get it running, it is totally worth it. - 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

[ccp4bb] Hope for breakthroughs

http://www.ebi.ac.uk/chemblntd And the related publication Thousands of chemical starting points for antimalarial lead identification http://www.nature.com/nature/journal/v465/n7296/pdf/nature09107.pdf Good luck with the goldmine ! Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public

Re: [ccp4bb] Native Gel Theory and Practice

Not quite correct, look into Blue Native PAGE. There you can seperate natively by mass. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street

Re: [ccp4bb] Native Gel Theory and Practice

of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr On 19/05/2010 13:01, Jürgen Bosch wrote: Not quite correct, look into Blue Native PAGE. There you

Re: [ccp4bb] Help needed in solving a MAD dataset

-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe

Re: [ccp4bb] Translational pseudosymmetry?

, this is not necessarily a reliable estimate. The questions are, how far off are we, and in what direction (i.e., are these shifts underestimates or overestimates)? Is there a way to obtain a reliable estimate? Thanks in advance, Owen - Jürgen Bosch Johns Hopkins Bloomberg School

Re: [ccp4bb] co-crystallization VS crystal soaking

a complex in solution and then co-crystallize. Another tip, use your apo-form crystals to streak seed crystallization attempts with new ligands. When you co-crystallize play with the molarity ratio of your ligand. Jürgen Bosch et al. Using fragment cocktail crystallography to assist inhibitor

Re: [ccp4bb] Ion exchange protein lost

light on this on where shall I be going wrong. thanks and regards, meg - 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

Re: [ccp4bb] testers needed

://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch - - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health

Re: [ccp4bb] MacBookPro problems

, the monitor is not recognized and so it is completely dark. The Mac does not show the monitor in the dialogues but an error message. -- Joachim - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615

[ccp4bb] merging Pymol sessions ? Non-CCP4 question

them out. Thanks, 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 Fax: +1-410-955

Re: [ccp4bb] Mysterious Crystals?

, what could be the reason for this mysterious crystals? Are they protein or PEG or what? Thanks very much. Tc - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street

Re: [ccp4bb] Cryo Vs crystal size

PS: Taken care of less solvent to be present in the loop - 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

Re: [ccp4bb] To model or not to model...

that I may be kicking a hornet nest here but I would genuinely like to know what people think. Thanks, Katherine Sippel SIPPEL,KATHERINE H Ph. D. candidate Department of Biochemistry and Molecular Biology College of Medicine University of Florida - Jürgen Bosch Johns Hopkins Bloomberg

Re: [ccp4bb] crystals as carry-on items

Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA - 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

Re: [ccp4bb] TLS, NCS and refinement

and continue from there 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 Fax

Re: [ccp4bb] solve structure by molecular replacement

, there are other options available even CCP4 ones e.g. Mosflm or non-CCP4 e.g. XDS. or d*TREK 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

Re: [ccp4bb] 3D fitting

; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse / - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708

Re: [ccp4bb] Expression of a protein of 43KDa

Fax: (630) 252-0687 - 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 Fax: +1-410-955-3655 http

Re: [ccp4bb] Crystal rescue

without exception although they belong to different space groups. So, I wonder whether these kind of pattern is caused by Tacsimate (I don't know what it is) and how to rescue these crystals. Any suggestions or comments? Thanks a lot! Best, Zhiyi bad.png - Jürgen Bosch Johns Hopkins

Re: [ccp4bb] Zalman LCD availability / suitability

.. 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 Fax: +1-410-955-3655 http

Re: [ccp4bb] Zalman LCD availability

Yes, contact mark.gar...@asipartner.com and ask for it. ASI – Fremont, California 48289 Fremont Blvd. Fremont, California 94538 Jürgen On Jan 14, 2010, at 10:07 PM, William G. Scott wrote: Does anyone know how to get extra glasses? - Jürgen Bosch Johns Hopkins Bloomberg School of Public

Re: [ccp4bb] Judging a homology model

to know which model for C will be better and why? Thanks for your answer… Happy New Year to you all, Raja The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns

Re: [ccp4bb] happy holidays

for the three step purification today and have the protein ready to go into trays tomorrow. On Dec 24, 2009, at 6:43 AM, Vellieux Frederic wrote: Well, very few people still at work... So I take this opportunity to wish you all a Happy Holiday season. And see you next year! Fred. - Jürgen Bosch

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

(lab) +302551030615, http://utopia.duth.gr/~glykos/ - 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] Regarding Open Source

inexperienced. I guess it was 5 to 5 when someone read your proposal and had to leave. 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

Re: [ccp4bb] looking for a computer program called Biomatx

will need). Has anyone heard of this computer program? If so, could you kindly point me in the right direction? Thanks a ton in advance, Fred. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615

Re: [ccp4bb] sulfur sad phasing

) CNRS, Universités d'Aix-Marseille I II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 - Jürgen Bosch Johns Hopkins Bloomberg

Re: [ccp4bb] Zalman monitor on Linux and Coot

? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics card. I would like to move to LCDs. Thanks for all inputs Ajit B. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular

Re: [ccp4bb] SeMet Peak wavelength and f_prime and f_doubleprime

. Thanks. James. - 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 Fax: +1-410-955-3655 http

Re: [ccp4bb] small molecule library

be soaking the protein with the compounds, followed by SEC and MS analysis. Anybody tried directly soaking crystals followed by X-ray analysis? Thanks alot already in advance for your help. Sincerely, Christopher - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department

Re: [ccp4bb] Phase separation to crystals

. Will the Additives like Ethanol or 2- propanol help in this condition? Should I not use NaCl in the mix? Changing temperature from 4degree to 25 degree will help? Please advice. Thanks a lot. James - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] To get the crystal faster...

not work. All suggestions from the experts are welcome. Thanks. James - 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] Questions about cryoprotectant

on the web) and before flash annealing diffracted to maybe 5A. I brought this data set home with 2.2Å longest cell 220 Å (shot at SSRl 9-2) Good luck, Jürgen On Oct 7, 2009, at 4:54 PM, ycheng wrote: - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream

, FAX: (44)-1865-613201 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk http://www.biop.ox.ac.uk/www/garman/gindex.html - - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

P6122 or P6522 make sure you get it right, otherwise the SpaceGroupPolicePatrol will get you :-) 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

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