Re: [ccp4bb] unexplained density

What does anomalous difference Fourier look like? -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Annemarie Weber Sent: Monday, February 03, 2014 11:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unexplained density Dear all, I am refining a

Re: [ccp4bb] experimental phasing at low resolution

Dear Vijay, I managed success on a large, 4.5 Ang SeMet phasing years ago. I strongly recommend trying to get a heavy atom derivative - even a crappy one - that allows you to use difference Fouriers to find your Seleniums. For me this was the only approach that worked, and it required

Re: [ccp4bb] Death of Rmerge

Rpim (from the East) just told me You don't need to be helped any longer. You've always had the power to go back to Kansas. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Oganesyan, Vaheh Sent: Thursday, May 31, 2012 2:27 PM To:

Re: [ccp4bb] Off-topic: Best Scripting Language

Now is the time when I start waxing nostalgic about the old days when there used to be entire threads on this bulletin board about Fortran format statement syntax for parsing various files.and I read them with great interest How did I get to be such a geezer? -Original Message-

Re: [ccp4bb] Off-topic: Best Scripting Language

After this religious debate concludes, I propose we return to the old standby - vi versus emacs. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Thursday, September 13, 2012 5:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb]

Re: [ccp4bb] 3D alignment of points (atoms)

I did this exact thing ages ago to place a domain using just predicted SeMet positions using O's lsq commands. Cumbersome syntax as I recall, but worked great. Thanks, Steve On Dec 28, 2012, at 10:18 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Dave, If you're still

Re: [ccp4bb] Who invented PDB format?

I love this footnote from the JMB paper: Requests should be accompanied with a new 2400 ft reel of magnetic tape, and a check or purchase order for U.S. $34.30 made to the order of Brookhaven National Laboratory, to cover postage and handling. This charge is subject to change in the future.

Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

BLASPHEMY! haha From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, March 18, 2013 1:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List? I don't want to crystallize the protein--I have another

Re: [ccp4bb] Program or server to predict Kd from complex structure

For the low cost of $10 USD, this should be about as reliable :) http://www.amazon.com/Mattel-30188-Magic-8-Ball/dp/B1ZWV7 Not trying to be a curmudgeon, but this is a really hard problem! Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf

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All- We currently have two positions open for x-ray crystallographers at Merck Research Labs in Pennsylvania. The official job posting is pasted below, and if you are interested in applying, please apply formally through the Merck Website (www.merck.com/careers) with Job ID BIO001876 Best

[ccp4bb] Crystallographer Position Available at Merck Research Laboratories

Hello all, We currently have positions open for x-ray crystallographers at Merck Research Laboratories in Pennsylvania. The official job posting is pasted below, and if you are interested in applying, please apply formally through the Merck Website with Job ID BIO001876.

Re: [ccp4bb] Replacement for arp_waters?

Might I add yet another call for the reinstatement of arp_waters - a very useful program indeed. Steve From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: Tuesday, January 20, 2009 2:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject:

[ccp4bb] Crystallographer Position Available at Merck Research Laboratories

All- We currently have one open position for an x-ray crystallographer at Merck Research Labs in Pennsylvania. The official job posting is pasted below, and if you are interested in applying, please apply formally through the Merck Website (www.merck.com/careers) with Job ID BIO001940. Best

Re: [ccp4bb] Ligand present in only one monomer in NCS

VERY, very common in the Pharma setting where we do hundreds of ligand-bound structures on a given target. Other permutations of this scenario, such as only one monomer's ligand displacing a ligand used for co-crystallization when trying to exchange by soaking, etc. Zsolt and I could share renin

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

There is a time-honored tradition of PhD students struggling through format conversion issues. Where is the fun and learning opportunity if everything ran smoothly? ;) Cheers, Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Felix Frolow

Re: [ccp4bb] Lactose refinement

If your resolution is high enough to support a deviation, then I don't see why not. I would probably stick with a chair conformation unless you are at high resolution or have convincing other evidence for the deviation. What often works well (and is easiest) is to define the 4 atoms that are the

Re: [ccp4bb] Strange spots

Gerard, I happen to have inherited a copy of Sir John's book from Joe Becker some years ago. Don't get your hopes up as the effect is apparently unexplained: No satisfactory explanation for these features has yet been found, but they are probably related to defects in the crystal lattice.

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Hi Everyone, Merck Research Laboratories has an opening for a summer intern in the Structural Chemistry (X-ray crystallography) groups located in either Kenilworth, NJ or West Point, PA. The idea is to have someone comfortable with programming and mathematics to explore some computational ideas

[ccp4bb] AMP-PNP Hydrolysis

Hi there, Was recently looking at a structure of an enzyme with AMP-PNP added to the crystallization mix, and all I see is density for ADP. I was wondering if hydrolysis of AMP-PNP to ADP is relatively common - either as a result of extended time in crystallization or exposure of the resultant

Re: [ccp4bb] off-topic: 2 peaks on Cation

Possibly deamidation of the protein, in particluar one or more lysines. What does the Mass spec look like? Cheers, Steve From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ulli Hain Sent: Friday, February 18, 2011 12:14 PM To:

Re: [ccp4bb] off-topic: 2 peaks on Cation

I'll swap you for the deamination, as that pertains to lysines...it's been a long week :) Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, February 18, 2011 2:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] how to combine the experimental phase and molecular replacement phase

Seconding David's suggestion, I have had this issue on several occasions and I would highly recommend using SHARP. In my experience, SHARP does a superior job handling this type of data. Best of luck- Steve From: CCP4 bulletin board

Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector

We have a version of HKL200 that supports the Pilatus6M. That said, most here prefer XDS for processing. Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: Wednesday, July 20, 2011 7:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject:

[ccp4bb] Molrep and Coot bugs

Hello all- (Paging Paul and Alexei) I recently came across a difficulty in Coot and Molrep in parsing PDB files containing insertion residues of the type where the residue number is the same but with an A, B, etc appendage. For example, PDB file 2CMR has several instances of the following

Re: [ccp4bb] Silver staining Coomassie stained gels

Now that's a nifty trick I hadn't heard of before! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Artem Evdokimov Sent: Friday, September 16, 2011 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Silver staining Coomassie stained

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

I will second Ian's recommendation for GRADE from the Global Phasing group. GRADE overcomes nearly all of the shortcomings we have encountered with other approaches for ligand dictionary generation. Best- Steve -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] Merging data collected at two different wavelength

But if we were to follow that convention we would have been stuck with Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, MuRDER. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, January

Re: [ccp4bb] advice on laptop for crystallography

We have been using IBM (now Lenovo) T43P laptops for several years with great success and minimal issues (knock on wood). We are able to run everything (including HKL2000) with no problems on these machines. I am sure that the newer T60 series would behave similarly. Good luck - Steve

[ccp4bb] Protein Biochemistry Positions at Merck

Hello All- I figured I would post this here since there are some protein biochemists who frequent the site, and many of the crystallographers may know of protein biochemists who might be looking for a job. Please pass this along to any potentially interested parties. Thanks! Steve P.S. Please

Re: [ccp4bb] Enzyme inhibitor

You don't give details on the assay, but if it is a fluorescence or colorimetric screen, you might have interference. Is the compound precipitating and/or aggregating? Good luck- Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ezra

[ccp4bb] Byron Bender?

Hi everyone, Does anyone by chance have a Byron bender that they would be interested in selling or know where I could purchase one? Charles Supper doesn't seem to sell them anymore. Thanks! Steve Notice: This e-mail message, together with any attachments, contains information of Merck

[ccp4bb] Coot pudding? (a.k.a N-linked carbohydrate addition)

Hi everyone- I was searching for some information on what might be the best way to add N-linked sugars in coot, and Google has let me down. Searching adding sugars in coot returns a very nice recipe for Coot Pudding. Recipe for Coot Pudding - American Coots http://www.beakycoot.com/pudding.html

Re: [ccp4bb] H32 or R 3 2 :H

I believe that Coot also outputs R 3 2 :H (Paul can clarify). /start minor rant We need some standardization on the hexagonal setting for R32. Having just suffered through a fairly brutal structure determination in this space group, I can say that there are some 'issues' with this. For instance

Re: [ccp4bb] H32 or R 3 2 :H

Thanks Peter. The unfortunate thing is that not all of the programs are able to understand these different notations, and that they preferentially use different ones. It would be nice if we all agreed to standardize. I, personally, have no problem with R 3 2 :H since that is what it really is.

Re: [ccp4bb] Lots of noise in structure

Rajan, I'll second what Eleanor and George have said - high symmetry space groups with noisy Intensity measurements (perhaps it was a weak data set with high Rmerge?) really exaggerates the amount of garbage that you see in the maps. Cheers- Steve From:

Re: [ccp4bb] Refining against images instead of only reflections

Jacob- Based on your question, you would likely be interested in doing some literature searches for the pioneering work of George Phillips and the utilization of diffuse scattering information. What you are thinking about has already been broached - nearly 20 yrs ago. It is likely that a

Re: [ccp4bb] R-sym and R-merge

Wow, can I quote this in the response to the next review that I get back where someone complains about the usage of Rsym? Believe me, I have seen it twice! Cheers, Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dale Tronrud Sent:

Re: [ccp4bb] PEG interaction with Trp in active site

Any chance that it is myristate or some other fatty acid? Good luck- Steve On Fri, Feb 19, 2010 at 3:42 AM, Marek Frischerkase frischerkasema...@yahoo.de wrote: Hello, sorry for my off topic question. I found a PEG molecule bound to the active site of my enzyme structure. And I did not

Re: [ccp4bb] 3D fitting

Would a simple hack, like renaming all of the atoms in each file to be 'CA' and then using a conventional alignment program work? Maybe I am caffeine deficient at the moment, but that seems worth trying. Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]

Re: [ccp4bb] activation of thiol group

Not knowing more details about the enzyme, etc, makes this a little difficult. I would think you might need a more polarizing group nearby to shift the pKa. The first thing that jumps to mind for me is that the water molecule itself is what is activated in this case, making it nucleophilic.

Re: [ccp4bb] Phasing statistics

Frank- Are you referring to our colleagues personal qualities, or the projects on which they work? :) From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Frank von Delft (I don't know the answer, btw, but our membranous colleagues surely

Re: [ccp4bb] Phasing statistics

This is an interesting thread, and perhaps I should not dive in on such a heady topic, BUT, I do want to point out my own particular bias regarding FOM that is not entirely consistent with James' point of view. In my experience, the FOM obtained after density modification runs are almost always

Re: [ccp4bb] Why Does Detwinning Not Work?

I seem to recall that Gerard was also looking at incorporating proper ML refinement for twinned data into the Global Phasing software, but I’m not sure on the status. Best, Steve From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Tuesday, October 11,

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

And again, has anyone seen the code to even know what's going on "under the hood"? Thanks, Steve > On Nov 29, 2016, at 8:35 PM, dusan turk wrote: > > Guys, > > I have a two issues to add here: > > 1. RSZS validation does not tolerate chain IDs longer than 1 character, >

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

Is the code publically available for the RSRZ calculation? Thanks, Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Tuesday, November 29, 2016 12:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculation of RSRZ

Re: [ccp4bb] "reset" a structure before re-refinement

Frank, Given that experimental electron density maps resulting from structure factors with a figure of merit of 0.5 are still interpretable, I don't think that "wiggling" the phases will be so bad. Fom of 0.5 corresponds to a phase error of 60 degrees, which is a pretty big shift. Interesting

Re: [ccp4bb] mystery feature near a PLP substrate

This looks suspiciously like Cartoon moose-head. Is it possible that you have contamination in your buffers? We once had this problem when using Canadian water. [Related

Re: [ccp4bb] Molrep

Methinks this is sage reasoning on the part of Dr Dodson Good luck Steve On May 27, 2017, at 6:46 AM, Eleanor Dodson > wrote: no idea really - looks like a bug.. There is a limit on the Radius of gyration whch i thinks is < 0 .5 *

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I would like to alert the community to an opportunity at Merck Research Laboratories. Please do not respond directly to me, all applications must be done through the online system at the link below:

Re: [ccp4bb] LINK vs LINKR

Hey now, I resemble that remark ;) Sent from my iPhone On Dec 10, 2017, at 3:53 PM, Bernhard Rupp > wrote: or at least for the fossils still vi-ing PDB files… Thx, BR Notice: This e-mail message, together with any attachments,

Re: [ccp4bb] Se-SAD phasing

Great point Jeff. Unfortunately I have “been there and got the T-shirt”, so I can sympathize with this situation! From: CCP4 bulletin board On Behalf Of Jeffrey B Bonanno Sent: Thursday, July 18, 2019 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Se-SAD phasing EXTERNAL EMAIL – Use

Re: [ccp4bb] MX data processing with GPUs??

We are doing more and more large sets of fragment and other ligand screening by x-ray these days, sometimes with the good folks at Diamond, sometimes elsewhere. I only see this trend increasing (at least for us) in the future as beamlines get even brighter and these types of screens can be

Re: [ccp4bb] Vote for cryoEM

“But we have the BEST ratings!.” Sent from my iPhone On Mar 31, 2020, at 12:26 PM, Bernhard Rupp wrote:  EXTERNAL EMAIL – Use caution with any links or file attachments. So…Science has come down to a popularity contest on social media. Best, BR From: CCP4 bulletin board On Behalf Of

Re: [ccp4bb] Using SFall for map conversion

Sadly I am “well-seasoned” enough to remember the vax-Linux byte swaps. Little endian vs big endian, and the whole thing. I was not expecting the Convex reference here which brings back great memories of the Johns Hopkins Convex and the frigid room it resided in that sounded like you put your

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

A wonderful idea Gerard and Clemens. Sent from my iPhone > On Mar 18, 2020, at 6:31 PM, Gerard Bricogne wrote: > > EXTERNAL EMAIL – Use caution with any links or file attachments. > > Dear colleagues, > > Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease >

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Re: [ccp4bb] visual mask editor?

You used to be able to do this in O (dating myself) From: CCP4 bulletin board On Behalf Of Bernhard Rupp Sent: Thursday, May 28, 2020 12:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] visual mask editor? EXTERNAL EMAIL – Use caution with any links or file attachments. Brief question: Does

Re: [ccp4bb] blocking activated thiol

I would try iodoacetamide. Sent from my iPhone > On Feb 25, 2021, at 7:58 PM, David wrote: > > EXTERNAL EMAIL – Use caution with any links or file attachments. > > I would like to know how to block activated groups on Thiol-activated > Sepharose 4B (after coupling a peptide). The

Re: [ccp4bb] cation-aromatic database

Might anyone be aware of a similar database tracking small molecule ligands making cation-pi or pi-cation interactions with proteins? Cheers, Steve On Apr 20, 2021, at 3:41 PM, Christine Gee wrote:  EXTERNAL EMAIL – Use caution with any links or file attachments. Hi Stephan, It seems to