Re: [ccp4bb] Tools for identifying possible contaminants

[Mike S]

I think this may do the contaminant search you are looking for.
ContaMiner (kaust.edu.sa)


Best,
Mike

On Wed, Jul 3, 2024 at 12:04 PM Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> We have a unit cell that is too small for our expected protein and suspect
> we have crystalised a contaminant.
>
> Does anyone have any recommendations on which tools we could use to
> identify the possible contaminant? I've tried SIMAD on ccp4cloud and it
> doesn't suggest anything reasonable.
>
> Kind regards,
> Kyle
>
> --
>
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Re: [ccp4bb] nearestcell

[Mike S]

Hi Kay,

http://flops.arcib.org:8084/sauc-1.1.1/

similar to the nearest-cell server, which seems to change its link and is
harder to find (or stale link)
https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi

HTH,
Mike

On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Dear all,
>
> I seem to remember a tool called "nearestcell", a command-line equivalent
> of the Oxford Nearest-Cell web server which appears to be offline.
> However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point
> me to it or give alternatives, please? (I did try the PDB's advanced search
> but it is not made for this purpose)
>
> Thanks, and a happy and successful 2024 to everybody!
>
> Kay
>
> 
>
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Re: [ccp4bb] binding pockets...

[Mike S]

Have you tried P2Rank?  It is quite fast, and there is a standalone version
that has command line options to run against all coordinate files in a
directory using batch mode.

https://prankweb.cz/
https://prankweb.cz/about
https://github.com/rdk/p2rank

You can try the web version to see how it performs with one of your
favorites.  I like the automatically created pymol scripts as well.  It
does occasionally split a larger pocket into smaller ones, similar to the
fpocket behavior, but perhaps not quite as frequent.

-Mike

On Wed, Jan 4, 2023 at 6:31 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> THX for the replies -
>
> > On 3 Jan 2023, at 22:56, Bernhard Rupp  wrote:
> >
> > There is also a service from our Polish friends:
> > called Spaceball (jokes aside) that calculates the volume of protein
> cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/).
> > and the services in Hamburg are useful for visualization of binding
> pockets and channels
> > https://proteins.plus/
>
> I really want something that I can put iin a script, not a web-page. These
> both appear to be web interfaces
>
> > James Holton -
> >
> > PanDDA?
>
> PanDDA is really for density analysis across putative changed-state
> datasets - I have many thousands of models to inspect that have no
> associated experimental datasets
>
> > Andre Godoy -
> >
> > if you mean predicting binding sites, FT map is quite good
> >
>
> Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php
>
> I’m really after alternatives to programs like:
>
> pyKVFinder (but that won’t install easily from PYPI on my Mac
> because my OS is too old - if anyone wants to buy me a new big, fast Mac to
> replace my old, fast Mac I should be able to install that easily!!) or
>
> fpocket (which works okay but is splitting up “obvious"
> single-site pockets into multiple pockets).
>
> Plus they need to be able to run from a script (or from the command-line
> so it can be scripted) - web interfaces are okay if you have a few
> examples, but when you’re analysing 1000 - 1500 models a day, clicking
> buttons gets a little boring!
>
> Sorry my initial post wasn’t clearer
>
> Harry
> 
>
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Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

[Mike S]

Since we've already gone down this rabbit hole (pun intended), there's been
quite a bit written in the last year about the 'value of a statistical
life' and pandemic insurance.

https://www.forbes.com/sites/theapothecary/2020/03/27/how-economists-calculate-the-costs-and-benefits-of-covid-19-lockdowns/?sh=2f2e73046f63

A few companies tried to sell pandemic insurance prior to 2019, but no one
thought it was worth the cost.
https://www.insurancejournal.com/news/national/2020/04/03/563224.htm

Sorry to reduce the S/N ratio on CCP4BB - I blame pandemic fatigue.

Best,
Mike

On Fri, Feb 19, 2021 at 6:47 AM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> I have been following this discussion with interest, without having any
> informed opinions to throw in..
> (Except as the daughter of an Australian farmer I still see myxomatosis as
> a blessing - my father said in his youth to make a living he spent 10months
> of every year trying to control the rabbit population, and 2 months on
> proper farming - if he didnt there would be no pasture at all, and the
> infection reduced the rabbit population to something manageable.)
>
> But it is a challenging morality - is protecting my aged life worth
> creating n million unemployed, etc,etc?
> However it is human instinct to try to protect oneself and one's community
> and that is what we geared up to do, and woe betide any politician who
> suggests otherwise,
>
> Roll on herd immunity, mass vaccination and some return to proper concerns
> like Brexit!
>
> Eleanor
>
> On Fri, 19 Feb 2021 at 10:54, Robbie Joosten 
> wrote:
>
>> Hi Tim,
>>
>> Very good points. The big picture is hard to grasp and we end up taking
>> political choices rather than anything else. I'm very glad that we can
>> outsource these choices to others every four year here.
>>
>> Lockdowns may save lives in the here and now, but the global economic
>> damage makes life for others much harder to a point that it may actually
>> kill them. Economic decline in the First World may be something with which
>> that we can deal but, like viruses, it blows over to other parts of the
>> world where economic growth is the real life saver. Does the prolonging of
>> a reasonably measurable number well-lived lives in the West outweigh the
>> extinguishing of a hard-to-assess number of much younger lives in the rest
>> of the world? I'm glad I don't have to make that call.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Tim
>> > Gruene
>> > Sent: Friday, February 19, 2021 09:33
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"
>> >
>> > Hi Jessica,
>> >
>> > one comment: death cannot be prevented. It is a certainty as soon as you
>> > are born (well, 9 months before).
>> >
>> > While this seems an obvious subtlety, many of the current measures seems
>> > to be influenced by the (probably unconscious) belief one can defeat
>> death.
>> > We can only reduce the risk to die at a certain moment and of a certain
>> > cause.
>> >
>> > The example of rabbits in Australia also illustrates how simple minded
>> > humans generally are: we focus on one thing, but usually fail to take a
>> larger
>> > picture into account.
>> >
>> > Cheers,
>> > Tim
>> >
>> >
>> >
>> > On Thu, 18 Feb 2021 08:16:59 -0800 Jessica Bruhn
>> >  wrote:
>> >
>> > > Hello,
>> > >
>> > > There have been some really excellent points raised by others
>> > > (informed consent, feasibility, etc), but I would like to share a
>> > > story about another time humans tried to release a virus on a wild
>> > > population in order to further an arguably noble goal:
>> > >
>> > > In the 1850s European rabbits were introduced in Australia for sport
>> > > hunting. They quickly did what bunnies do and started to become a real
>> > > problem. In the 1950s, scientists decided to introduce myxoma virus to
>> > > Australia, which is 90-99% fatal for European rabbits, but less lethal
>> > > for the native rabbits. They intentionally released this virus and in
>> > > the first year the mortality rate was 99.8% for the European rabbits.
>> > > Yay, right??? Unfortunately, in the subsequent year the mortality rate
>> > > fell to 25% and steadily continued to fall until it was lower than the
>> > > reproductive rate of the European rabbits. The host-virus interaction
>> > > played itself out: less-virulent viruses arose and resistant rabbits
>> > > were selected for.
>> > >
>> > > To me it seems unwise to assume a replication competent virus
>> > > (engineered or not) would refrain from mutating and adapting upon
>> > > release, especially over the time course that would be required to
>> > > infect all 7 billion+ humans on this planet. To me, I feel our options
>> > > are (1) reach herd immunity through natural infection and accept the
>> > > preventable deaths of many millions of people or (2) continue with
>> > > non-pharmaceutical interventions (ma

[ccp4bb] Position available: Protein biochemist at Civetta Therapeutics

[Mike S]

https://careers-civetta.icims.com/jobs/1395/job

Overview

Civetta Therapeutics (Cambridge, MA) is recruiting a Scientist to Senior
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Civetta Therapeutics provides equal employment opportunities (EEO) to all
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*Notice to Third-Party Recruiters/Staffing Agencies:* Recruitment is
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will only be accepted from staffing agency/recruiters if there is a signed
contract in place. Recruiters are requested to not contact our hiring
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present candidates. In the event a staffing agency/third-party recruiter
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interested in working with Civetta Therapeutics can submit their
information to cont...@civettatherapeutics.com, and we will contact you if
needed.



PM18

#LI-DNI



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[ccp4bb] Job Posting: Director, Structural Biology and Biophysics - Takeda Pharmaceuticals

[Mike S]

*Job Description: *



Director - Structural Biology and Biophysics

Job ID 1602180

Location San Diego, California, United States;



*OBJECTIVES:*



The Director of Structural Biology and Biophysics leads all activities in
the Structural Biology and Biophysics group at TCAL, including Molecular
Biology, Protein Chemistry, Crystallography and Biophysics.  The Director
works closely with Takeda Drug Discovery Unit (DDU) leadership teams
globally to maintain prioritization and alignment of the group’s efforts
with global Takeda drug discovery efforts in order to insure timeliness and
impactfulness of the group’s research outputs.  The Director cultivates the
group’s proactive, collaborative, innovative and outward looking culture
and insures that the group is employing the most current, effective and
applicable technologies to achieve its research results.


For more information, and to apply, please follow this link:
http://bit.ly/2ldPsgj

Re: [ccp4bb] Sister CCPs

[Mike S]

I'm sorry, but did you just use the words "crystallographers" and "modest"
in the same sentence?  :-)

On Thu, Feb 13, 2014 at 6:41 AM, Eleanor Dodson
wrote:

> I agree with Frank - it keeps crystallographers modest to know how
> challenging wet lab stuff still is..
> Eleanor
>
> On 12 February 2014 19:23, Robbie Joosten 
> wrote:
> > It's not an e-mail bulletin board, but Researchgate seems to be quite
> > popular for wet lab questions. IMO the Q&A section of the social network
> is
> > a bit messy. That said, the quality seems to improve gradually.
> >
> > Cheers,
> > Robbie
> >
> > Sent from my Windows Phone
> > 
> > Van: Paul Emsley
> > Verzonden: 12-2-2014 19:23
> > Aan: CCP4BB@JISCMAIL.AC.UK
> > Onderwerp: Re: [ccp4bb] Sister CCPs
> >
> >
> > On 12/02/14 15:59, George Sheldrick wrote:
> >> It would be so nice to have a 'sister CCP' for questions aboud wet-lab
> >> problems that have nothing to do with CCP4 or crystallographic
> >> computing, The is clearly a big need for it, and those of us who try
> >> to keep out of wet-labs would not have to wade though it all.
> >
> >
> > FWIW, the remit of CCP4BB, held at jiscmail-central, is describes as:
> >
> > /The CCP4BB mailing list is for discussions on the use of the CCP4
> > suite, and macromolecular crystallography in general./
> >
> >
> >
> > Thus wet-lab questions are not off-topic (not that anyone recently
> > described them as such).
> >
> > Having said that, Jiscmail mailing lists are easy to set-up (providing
> > that you can reasonably expect that the mailing list will improve
> > knowledge sharing within the UK centered academic community) and
> > relatively low maintenance. I, for one, would not be entirely unhappy to
> > miss out on questions about lysis.
> >
> > Paul.
>

[ccp4bb] Postdoc Position at Millennium Pharmaceuticals

[Mike S]

Post-Doctoral Program: Structural Biology (protein crystallography)

for more details and to submit an application, see

http://www.millennium.com/careers/
requisition 6606

Happy Holidays.

Re: [ccp4bb] real-space vs. reciprocal space refinement

[Mike S]

Thanks to everyone who has responded so far.  I'd like to provide a few more
details since I'm also interested in the practical ramifications of the
theoretical arguments presented thus far.

1. density map at 3.2 A resolution was used to refine a model that had
already been built and refined at 2.0 A.
2. bound small molecule ligand was fit into the difference density using RSR
within Coot (with tight geometric restraints as generated by ProDRG).
3. ligand was not refined any further using standard reciprocal space
methods.
4. to my eyes, the ligand fit didn't look very good (even factoring in the
resolution of the maps).
5. I would have started with RSR in Coot and then followed with something
like Refmac, but was told the results wouldn't be any different.
6. debate ensues, starting with this quote I pulled from one of Michael
Chapman's papers in *Acta Cryst.* (1999). D*55*, 464-468:

"...real-space methods have been largely superseded by reciprocal-space
methods owing to the implicit dependence of real-space methods upon the
phases used to calculate the electron-density map, which are often much less
accurate than the diffraction amplitudes."

Thanks again for the responses -- this "gray-haired" crystallographer has
enjoyed the commentary on a subject that sometimes gets taken for granted.

Regards,
Mike

[ccp4bb] real-space vs. reciprocal space refinement

[Mike S]

Dear CCP4 experts,

Recently, I was debating a colleague on the pros/cons of refinement done in
reciprocal space compared to refinement in real space.

I always thought reciprocal space refinement was preferable since measured
amplitudes will be more accurate than calculated phases (unless good
experimental phases are available).  My colleague argued that with sigmaA
and maximum-likelihood methods, calculated phases are much "better" than
they were in the past and the two refinement techniques are equivalent in
terms of robustness.  He said the reason most software hasn't switched
entirely to real-space refinement is due to computational issues.

Please help enlighten me.  All comments/diatribes welcome.

Thanks,
Mike

[ccp4bb] disorder, solvent content, and diffraction limit

[Mike S]

Greetings,

I've taken a protein (structure known) with some disordered termini and
created a new truncated construct that lacks these disordered bits (approx.
5% by mass of the total protein).

To my delight, the new construct crystallizes much more readily than the
full-length one (more hits in screening, nicer looking crystals, etc.)
However, while the crystallization is more robust and the crystals look much
"nicer", they don't diffract as well as the full-length crystals (go from
around 2.7 angs for full-length to 3.2 or worse for truncated construct).

While the truncated form gives many more crystallization hits than
full-length, optimization always gives the same crystal form (same space
group and unit cell dimensions), no matter which conditions are used.

Given that I've removed floppy bits from my protein, I would have expected
improved diffraction.  But since I keep getting the same unit cell, I wonder
if I've just increased the solvent content in my truncated construct
crystals (less mass per same unit volume).

Does this rationale make sense?  Is it possible that the disordered parts I
removed were in some way restraining the ordered parts of the structure?
Should I keep searching for a new crystal form with improved lattice
packing?  btw, I have tried several different approaches to dehydrate the
crystals and none has successfully improved diffraction.

Thanks for your help.

-Mike