[ccp4bb] Senior Developer at LS-CAT sector 21 at the APS

*Apply to Job 43479 * *Department: *NSRC - LS-CAT *Salary/Grade: *ITS/80 *Job Summary:* This position is available at Argonne National

[ccp4bb] ACA Abstract requests for Evolution & Impact of Targeted Protein Degradation in Industry

Hi, Matt Clifton (Novartis) and I (Joe Patel, C4 Therapeutics) are organising a session around the impact structural methods have had in the field of targeted protein degradation at this year's virtual ACA meeting. The session is scheduled from 12pm till 3pm EDT on 5th August 2021 and we

[ccp4bb] Research Scientist Position, Structural Biology at C4 Therapeutics in Watertown, MA USA

consider applying for the role using the link below. https://easyapply.co/a/6fa7d973-53ef-443b-9e38-1b63b2968dad Regards, Joe Patel Joe Patel, Ph.D. Director, Biochemistry, Biophysics & Crystallography [C42] 490 Arsenal Way, Suite 200 Watertown, MA, 02472 www.c4therapeutics.com&

[ccp4bb] PhD positions in structural biology at the Astbury Centre, University of Leeds

-structure-motility-and-cellular-function/?p103997 for more details. Information on how to apply can be found in the links above. Please feel free to get in touch (j.j.b.cockb...@leeds.ac.uk) if you wish to discuss further or require any additional details. Kind regards, Joe

[ccp4bb] tenure-track academic fellowships in structural molecular biology at the University of Leeds

Hello everyone, Please see the job advert below regarding tenure-track academic fellowships in structural molecular biology at the University of Leeds. Cheers, Joe Dear All, A number of tenure-track academic fellowships in Structural Molecular Biology are now available at the University

[ccp4bb] Job opening for a structural biologist

Job opportunity: Eternity Bioscience is hiring a structure biologist. Details please see ： http://www.eternitybioscience.com/contact-us -- Best regards, Joe

[ccp4bb] Post-doctoral position in Structural Biology of Cilia, Astbury Centre, Leeds, UK

Dear All, A post-doctoral position is available immediately in the laboratory of Dr Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform structure-function studies on ciliary proteins. The position is funded by The Wellcome Trust and is available immediately for a period

[ccp4bb] 3D printing format

Sorry for the rather random question but has anyone out there used a 3D printer to print a protein structure? If so, what format did you need to convert the PDB into to allow the printer to interpret the data? Many thanks, Joe P Joe Patel FBLG Specialist

Re: [ccp4bb] Unusual electron density - any guesses??

indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have

[ccp4bb] Supplier for X-ray sensitive paper

this type of paper rather than X-ray film so as not to have to go through any developing stage and quickly visualize the location of the beam at different points beyond the position of the goniometer towards the detector. A USA supplier would be great but any would do. Many thanks, Joe P

[ccp4bb] question about CCP4 scripts

unique hklout ${CCP4_SCR}/unique_out.mtz eof labout F=F SIGF=SIGF symmetry p43212 resolution 1.6 cell 78.1 78.1 55.2 90.0 90.0 90.0 eof -- Best regards, Joe

Re: [ccp4bb] advices

if there is anything that you could improve before crystallization: Is your construct good enough? How is your protein quality--purity/homogeneity? Fine-tuning every step from gene to protein to crystal could eventually lead to good results. Joe On Tue, Jan 15, 2013 at 8:30 PM, Mike John

Re: [ccp4bb] protein degradation in crystal

Could you identify the cleavage sites by protein sequencing and design new constructs (truncated versions) accordingly? It might improve your crystal quality to get better resolution. Joe On Wed, Jan 16, 2013 at 9:22 AM, Tom Murray-Rust tom.murray.r...@gmail.comwrote: Just to add

Re: [ccp4bb] Ligand geometry obs. vs. ideal

to understand how far you are from ideal. Not really sure if this is what you might be after Joe P -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered

Re: [ccp4bb] HKL2000 indexing problem

If you have tried all of the other things suggested by others (especially beam-center and direction of rotation), you can try the keyword 'weak level' in indexing box (see page 29 on HKL manual http://hkl-xray.com/sites/default/files/manual_online.pdf or

Re: [ccp4bb] No diffraction

1. Try room temperature mounts (as suggested by others) 2. Expose the hell out of the crystal (5 min) on home source or go synchrotron 3. Run your protein through another column (ion exchange) even if it looks pure 4. Try an additive screen 5. Try limited proteolysis or methylation 6. If none of

Re: [ccp4bb] Lithium versus Sodium

to prove I had a sodium ion bound over magnesium which is the catalytically active ion Do you have ultra-high resolution? Something I did not Are there many examples in the pdb of proteins with Li+ refined? Sorry no real help to you, but curious since it brings up old memories... Joe P

[ccp4bb] Permanent Position for NMR spectroscopist at AstraZeneca, Alderley Park, UK

below. http://gs.globalsuccessor.com/fe/tpl_astrazenecav2.asp?newms=jjid=58285 newlang=1 Thanks, Joe P Dr Joe Patel _ AstraZeneca Discovery Sciences, Structure Biophysics UK 50S38, Mereside, Alderley Park

Re: [ccp4bb] MR question

If it is of moderate resolution (3 ish), uncheck automatic weighting in RefMac and constrain to 0.007-0.01. You're probably over-fitting your data. -Joe Joseph M. Watts, Ph.D. Research Scientist Syngenta Biotechnology, Inc.

Re: [ccp4bb] strange density

Hi Alex, Was it purified via a Ni2+ resin? Is the protein oligomeric in solution? Could it have stripped an ion out during purification and brought it all the way through to crystallisation? Have you tried refining a Ni2+ in the location? JP

[ccp4bb] Your suggestions needed: Difficulties in reproducing HT crystallization conditions. Thanks!

hits. But none of them has worked so far. This is the first time I encountered such a scale-up issue. I am running out of ideas, so hope you could give me some suggestions. Thank you in advance. -- Best regards, Joe

[ccp4bb] Your suggestions needed: Difficulties in reproducing HT crystallization conditions. Thanks!

hits. But none of them has worked so far. This is the first time I encountered such a scale-up issue. I am running out of ideas, so hope you could give me some suggestions. Thank you in advance. -- Best regards, Joe

[ccp4bb] Pittsburgh Diffraction Conference Oct 27-29

This is a reminder that the 64th Annual Pittsburgh Diffraction Conference will be in Pittsburgh Oct 27-29 at the Holiday Inn University Center. Registration and program information can be found at: www.pdc2010.net Joseph D. Ng

[ccp4bb] Accuracy of the position of coordinates

is the appropriate program to use. Thank you so much. Best regards, Joe Yap

[ccp4bb] Estimation of coordinate errors

. Best regards, Joe Yap

Re: [ccp4bb] question about the zinc binding protein

BTWBy the way I think, not a buffer abbreviation -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN.

[ccp4bb] DMMULTI question

/commente would be appreciated! Thanks Joe

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

I agree with Randy Read though - it's a mistake to get too carried away with the foul-play aspect of this. There were clearly very serious problems with those structures anyway. What it shows is that you can desposit just about anything in the PDB, which is quite worrying when you consider how

[ccp4bb] How to compare the binding affinity between two domains structurally?

that the interacting residues on the interface are also different. BTW, we were not able to purify individual domains, so we cannot measure the binding affinity by wet lab approaches (so far). Thank you in advance for your inputs. -- Best regards, Joe

Re: [ccp4bb] negative density peaks where there is no model.

Hi Andrew, If there is no *protein* model built into this region of the map, then it will be modelled by the bulk solvent correction - therefore, the negative peaks are telling you that the mean electron density there is lower than in the bulk solvent. Probably. Joe Hello everyone I have

Re: [ccp4bb] problems of co-crystallization of protein-DNA complex

Hi ruheng, Since you synthesized the oligos, you probably already know if there is any residual salt or buffer in your oligos. I don't know if that caused the problem. Sometimes people purify and desalt the oligos before the annealing step. Joe ruheng wrote: Dear CCP4bbers, I am now

[ccp4bb] Pictures of DDM crystals?

are helpful. Thank you for your attention. -- Best regards, Joe

Re: [ccp4bb] Pictures of DDM crystals?

I forgot the mention this: does anyone happen to have some pictures of DDM crystals? It would be very very helpful for me to take a look and get a sense how they look like. I appreciate your inputs and help. Thanks, Joe On Mon, Aug 10, 2009 at 4:47 PM, Joe gch...@gmail.com wrote: Hi all

Re: [ccp4bb] Scalepack error model?

and E2 thus tend to dominate the error model at high and low resolutions, respectively. Hope that helps, Joe Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS

Re: [ccp4bb] Scalepack error model?

and E2 thus tend to dominate the error model at high and low resolutions, respectively. Hope that helps, Joe Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS

Re: [ccp4bb] can I try crystallization in high salt?

You can try including some salt to the reservoir after mixing protein and well solution. Joe rui wrote: Dear All, I have a peri domain protein that is stable in high salt concentration(500 mM), if I dialysis to a lower salt buffer and then concentrate, it'll preticipate out. If I need

[ccp4bb] Rapid Access slot available at LS-CAT at the APS

The following slots are available at LS-CAT (sector-21) at the APS Available Rapid Access Data Collection for the Next 21 days Station Start Time Duration (Hours) 21-ID-D Jun 12, 2009 at 10:00 AM CDT 24 21-ID-D Jun 21, 2009 at 10:00 AM CDT 22 21-ID-D Jun 25, 2009 at 10:00 AM CDT 24 21-ID-F Jun

Re: [ccp4bb] Find water in coot

It should be under "Calculate Other modeling tools Find waters" Joe Raja Dey wrote: Hi, Is there any "Find Water..." button in the "MOdel/Fit/Refine" window in coot? I did not find it in version 0.6-pre. Raja Explore your hob

Re: [ccp4bb] Lost my protein

with different types of membrane. Joe Kornelius Zeth wrote: Hi Yanming, you can try adding 1 M of urea, 1% detergent (OG,DM) that often helps to keep proteins in solution. Best wishes Kornelius On Tue, 5 May 2009 09:06:09 -0700 yanming Zhang shanma...@yahoo.com wrote: Hi all

Re: [ccp4bb] Hanging vs. Sitting

) for optimization thereafter. As long as I have no problem getting reproducible conditions, I will stick to the one I found most efficient and convenient for myself. Joe Frank von Delft wrote: Sorry, disagree again: with the right plate type (e.g. SwissCi plates), it's far far easier from sitting

Re: [ccp4bb] Cryo-protectant

other ingredients (your protein buffer + well solution). I also introduced 5% glycerol to bring down % PEG3350. You can play around % PEG3350 and % glycerol to find a fine combination that is cryo-clear and makes you crystals happy. Joe Liew Chong Wai wrote: Hi all Thanks

[ccp4bb] pI for protein-detergent complexes

Hi, Is there a way to estimate pI for protein-detergent complexes? Thanks. Joe

Re: [ccp4bb] Refmac refinement with two ligands

Alex, The CCP4i 6.1.1 refmac allows you to combine multiple .cif using Merge LIBINs. Have you tried that? Joe aber...@mrc-lmb.cam.ac.uk wrote: Dear CCP4 community, I would like to refine a structure with two bound ligands using Refmac. However, the Rafmac GUI allows only one library

[ccp4bb] how generate maps only to cover atoms in pdb

Hi, I want to generate maps only covering atoms in the pdb file. I tried fft-creat map in ccp4i (output map to cover all atoms in pdb), but it actually also generated map in places other than pdb atoms. Are there any other ways to do this? Thank you. -- Best regards, Joe

Re: [ccp4bb] How to generate maps only to cover atoms in pdb

it is a right word) the map for each monomer and then display them in pymol or coot. Any better solutions? Thanks, Joe On Sun, Apr 19, 2009 at 11:06 AM, JOE CRYSTAL gch...@gmail.com wrote: Hi, I want to generate maps only covering atoms in the pdb file. I tried fft-creat map in ccp4i (output map

[ccp4bb] Beam Time at LS-CAT Sector-21 at APS

I would like to take the time to welcome all general users to the newest beam lines at the Advance Photon Source, Life Sciences CAT Sector 21. http://ls-cat.org http://protein.nsls.bnl.gov/ There is time available for rapid access, the dates are listed on the website and users can subscribe for

Re: [ccp4bb] Interaction between the domains

Contact in CCP4i can calculate the distance between specified chains/residues. Pymol can display hydrogen bonds too. Joe peter hudson wrote: Hello all I have a very quick question. Is there any programme, which can calculate the H-bond pattern or residues involved in H-bonds formation

[ccp4bb] Refmac failed at the end of run

:23:28 #CCP4I MESSAGE Task failed -- Best regards, Joe

[ccp4bb] Please recommend screen kits for membrane proteins

Sorry for the off-topic subject. I am new to membrane proteins. We already have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I want to know if there other kits out there you would recommend. Thanks a lot, Joe

[ccp4bb] Broken chain in Pymol display

Hi all, I tried to display a refined structure (final steps in phenix.refine) in Pymol, but several places are not connected. BTW, the structure displays normally in Coot and bond angle and length deviation are below 1.0 and 0.006, respectively. Thank you, Joe

[ccp4bb] Questions regarding Peptidoglycan-binding protein

or unspecifically associate with PG fragments from cell wall. My question is: *how to detect PG fragments in my protein sample*? I have tried denaturation-wash-renaturation steps, but I want to know if I have completely got rid of the possible contaminants. Thank you for suggestions. Joe

[ccp4bb] Poor electron density - polyAla or PolyGly?

like leaving this region empty. Any suggestions in this regards is highly appreciated! regards Joe

Re: [ccp4bb] Protein Color

the his-tags around traces of copper in my sample, which could explain the brown-ish colour. What happens if you concentrate the protein in the presence of EDTA? Joe Hello. I am working with a protein that turns a yellowish-brown color when it is concentrated to around 2 mg/ml or higher

Re: [ccp4bb] Question re: ice rings in diffraction data

). HTH, Joe Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing

[ccp4bb] coordinates of TCEP

from its chemical formula? thanks alot. -Joe

[ccp4bb] Problem with crystallization of Se-Met labeled protein

aa long polypeptide. I want to know what generally one should do when Se-Met containing proteins fail to crystallize. Thanks in advance. Joe PS: Since, protein contains 3 Cys residues.. I am also planning to try my luck with heavy atom compounds containing Hg.

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

are talking about sub-microliter drops. Best, Joe On Fri, Jan 18, 2008 at 12:28 PM, Lisa A Nagy [EMAIL PROTECTED] wrote: Al's Oil on the plates: What a nightmare!!! The oil creeps up the plate and over the sides. It dissolves adhesives. It makes me say bad words in multiple languages. Bigger

[ccp4bb] Characterization of common salt crystal forms?

that are very common in crystallization trials. Maybe it would be useful to tabulate common salt crystals to help guide optimization experiments. Has anyone else tried to use salt crystal information beyond ensuring that it is not protein? Joe Krahn

Re: [ccp4bb] DTT sensitive?

The other possibility is 400 mM imidazole in the buffer. The precipitate looks like silk. On 11/13/07, Bryan W. Lepore [EMAIL PROTECTED] wrote: you didn't say how you know its protein - is it? interesting though.

Re: [ccp4bb] DTT sensitive?

It did not contain DTT when frozen. On 11/13/07, deena [EMAIL PROTECTED] wrote: Are you sure its 1mM DTT, because DTT itself precipitates in the freezer. Deena On Nov 13, 2007, at 3:30 PM, Joe wrote: Hi there, I see enormous precipitate of my receptor protein when I take it out

Re: [ccp4bb] DTT sensitive?

, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Sent: Tuesday, November 13, 2007 2:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] DTT sensitive? Hi there, I see

[ccp4bb] problems with map quality, refinement and R/Rfree

acid in the map but due to few breaks in the N-terminal domain as well as poor density I am unable to assign any amino acid into the poly ala main chain. Frankly speaking, I do not know how to proceed further. I welcome any kind of suggestions which could help us in this case. Regards Joe

[ccp4bb] Nearly perfect twinned data????

really need your valuable suggestions to solve this problem. Regards Joe

Re: [ccp4bb] Covalently bound drug molecule

I was using X-PLOR at the time. I later switched to a PRESidue patch. I was not sure how many atoms must be added to a residue before a modified amino acid becomes a linked amino acid. The PDB seems a bit adverse to non-standard links. For example, why is NADP not two residues with a LINK? There

Re: [ccp4bb] Covalently bound drug molecule

link paramaters become a hassle, you might try the single-residue approach. Joe Hall Gareth wrote: Dear ccp4bb users, I am currently refining a crystal structure of a protein with a drug molecule in the active site. The drug molecule is seen, as expected, to covalently bind to the active site

Re: [ccp4bb] MSE

One more comment on MSE: Does anyone know why MSE was defined without a 'delta' on the selenium? Isn't that obviously wrong? Selenium-delta should be SED , just like S-delta is SD , so it can't be left off just because selenium is not a carbon. Phil Evans wrote: flame As an aside, does anyone

Re: [ccp4bb] PDB format survey?

format. With any luck, some RCSB or wwPDB people would participate as well. Joe Krahn

[ccp4bb] PDB format survey?

OpenPDB format? Joe Krahn

Re: [ccp4bb] PDB format survey?

willing to work toward switching to mmCIF if RCSB showed more interest in collaborating with the user community. If we can't even get involvement in something as simple as the PDB format, why should we think working with mmCIF will be any better? Joe Krahn

[ccp4bb] ---solved---Fwd: [ccp4bb] problem in running DM (NCS averaging)

Dear all, Thank you so much for your valuable thoughts. The problem is gone after I used rotation matrix instead of O matrix. Now DM is running fine. Thanks. Best regards, Joe -- Forwarded message -- From: Stein, ND (Norman) [EMAIL PROTECTED] Date: Jul 31, 2007 8:13

[ccp4bb] problem in running DM (NCS averaging)

Dear all, I tried to run DM for NCS averaging (DM module in CCP4i 6.0.2 installed under Windows XP), but the running failed at different stages with various error message as listed below. I was told it could be an installation problem, but I don't know how to fix it. I am wondering if you

[ccp4bb] Stop the new PDB format!

be part of the decision making process. I just sent the following letter to the wwPDB, which is where comments about the new format are supposed to go. If you will be at the ACA meeting, I encourage you to complain loudly. Joe Krahn

[ccp4bb] Combining MR and MAD phases

Hi, I have a 1.7 A native dataset, a good MR solution for 2/3 of the protein, and MAD phases to 3 A. How should I combine the MR phases with the MAD phases? Thanks, Joe

Re: [ccp4bb] Protein-DNA complex for crystallization

Hi Kumar, I also have the same issue. If you get any helpful response, could you forward me a copy? Thank you. P.S. Could anyone who has any comments or suggestions on this issue also forward the response to ccp4bb? Thank you in advance. Best, Joe On 7/16/07, bputcha [EMAIL PROTECTED

[ccp4bb] extend resolution in refmac

Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe

[ccp4bb] Solving structure of protein-protein complexes using MR

doesn't provide good packing of the complex inside the unit cell. Due to low scattering contribution of the smaller protein, we are unable to refine any possible solutions using REFMAC. We welcome any kind of suggestions in this regard. Thanking you in advance. Joe

[ccp4bb] How to determine ligand binding from diffraction pattern?

if the ligand is actually bound. Thank you very much! Best, Joe