Re: [ccp4bb] Off topic question

[Georg Hochberg]

Dear Reza,

CD hit will do exactly that.

Cheers,
Georg

Sent from my iPhone

On Jan 3, 2019, at 2:41 PM, Reza Khayat 
mailto:rkha...@ccny.cuny.edu>> wrote:


​Hi,


Happy new year to all!  A bit of an off topic question.  Does anyone know of a 
method/program to extract the most distinct "n" (n>2) sequences from a sequence 
alignment?  Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031



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Re: [ccp4bb] Off topic question

[Javier Gonzalez]

Hi Reza, happy new year!
The choice would depend on your alignment (aminoacid or nucleotides? are
the sequences closely or distantly related? is it a large alignment? are
there many gaps?)... Anyway, I think the safest, unbiased way to determine
a group of outliers might be to compute a phylogenetic tree and look for an
outgroup. But if the set of sequences is too large you might want (first)
to use a clustering algorithm, such as CD-HIT (
http://weizhongli-lab.org/cd-hit/).
HTH,
Javier

On Thu, Jan 3, 2019 at 6:08 PM Ethan A Merritt 
wrote:

> On Thursday, January 3, 2019 12:40:05 PM PST Reza Khayat wrote:
> > ?Hi,
> >
> >
> > Happy new year to all!  A bit of an off topic question.  Does anyone
> know of a method/program to extract the most distinct "n" (n>2) sequences
> from a sequence alignment?  Thanks.
>
> If these putative "most distinct" sequences are hypothesized to belong
> together,  then i suggest K-means clustering.  If they are hypothesized
> to be unrelated individual outliers then I think you would just take the
> worst scores using whatever metric you used to create original alignment.
>
> Ethan
>
> >
> >
> > Best wishes,
> > Reza
> >
> >
> > Reza Khayat, PhD
> > Assistant Professor
> > City College of New York
> > Department of Chemistry
> > New York, NY 10031
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
Email  LinkedIn




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Re: [ccp4bb] Off topic question

[Ethan A Merritt]

On Thursday, January 3, 2019 12:40:05 PM PST Reza Khayat wrote:
> ?Hi,
> 
> 
> Happy new year to all!  A bit of an off topic question.  Does anyone know of 
> a method/program to extract the most distinct "n" (n>2) sequences from a 
> sequence alignment?  Thanks.

If these putative "most distinct" sequences are hypothesized to belong
together,  then i suggest K-means clustering.  If they are hypothesized
to be unrelated individual outliers then I think you would just take the
worst scores using whatever metric you used to create original alignment.

Ethan

> 
> 
> Best wishes,
> Reza
> 
> 
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] Off topic question

[Zhijie Li]

PCA?

On Jan 3, 2019, at 3:41 PM, Reza Khayat 
mailto:rkha...@ccny.cuny.edu>> wrote:


​Hi,


Happy new year to all!  A bit of an off topic question.  Does anyone know of a 
method/program to extract the most distinct "n" (n>2) sequences from a sequence 
alignment?  Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031



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[ccp4bb] Off topic question

[Reza Khayat]

?Hi,


Happy new year to all!  A bit of an off topic question.  Does anyone know of a 
method/program to extract the most distinct "n" (n>2) sequences from a sequence 
alignment?  Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031



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[ccp4bb] CCP-EM Spring Symposium: 29 April - 1 May, Nottingham University

[Colin Palmer - UKRI STFC]

Dear all,

We are pleased to announce that registration is now open for the fifth annual 
CCP-EM Spring Symposium. Sign up on the event website before 25 January for an 
Early Bird discount:

http://www.cvent.com/d/xbqsqk

The Spring Symposium aims to provide a forum to highlight state of the art 
developments in computational cryo-EM and related themes as well as showcasing 
outstanding recent applications. We aim to promote an inclusive, friendly 
atmosphere welcoming both old and new to the community and there is the 
opportunity to present your work via a poster or a selected talk.

Topics include instrument technology, sample preparation, image processing, 
single particle reconstruction, tomography and model building.

The conference will be held 29th April - 1st May at the University of 
Nottingham, UK. A provisional programme is available on the event website.

Confirmed speakers include:

John Rubinstein (University of Toronto)
Sjors Scheres (MRC-LMB)

David Bhella (University of Glasgow)
Thomas Braun (University of Basel)
Doryen Bubeck (Imperial College London)
Wim Hagen (EMBL)
Wanda Kukulski (MRC-LMB)
Stephen Muench (University of Leeds)
Stefan Pfeffer (University of Heidelberg)
Shaun Rawson (Harvard Medical School)
Sonja Welsch (Thermo Fisher Scientific)
Pamela Williams (Astex Pharmaceuticals)

Michele Darrow (TTP Labtech)
Giulia Weissenberger (CryoSol)

Plus: what's new at CCP-EM, EBI and eBIC

Scientific organisers:

John Briggs (MRC-LMB)
Rebecca Thompson (University of Leeds)

Registration site:
http://www.cvent.com/d/xbqsqk

Registration fees:
PI/Industrial: £225.00 (Early Bird price £175.00 before 25 Jan)
Student/PostDoc: £175.00 (Early Bird price £125.00 before 25 Jan)

We have also ensured reasonably priced accommodation is available from 
Nottingham University (£60/room/night; available on registration).


We hope to see you there!

Best wishes,

Colin, Tom and the rest of the CCP-EM team


-- 
Dr. Colin Palmer
CCP-EM | www.ccpem.ac.uk | @ccp_em

Research Complex at Harwell
STFC Rutherford Appleton Laboratory
Didcot OX11 0FA, UK
+44 1235 567864



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Re: [ccp4bb] opentrons pipetting robot

[Paul Paukstelis]

I have long thought about developing an open-source crystallization robot
based on the now ubiquitous 3D printing linear motion systems. They are
certainly plenty precise for doing crystallization plating. Probably having
two heads, a 12-channel syringe system for screen dispensing and a second
head for sample dispensing. I'd thought that a non-contact sample dispenser
would be the way to go, but that significantly complicates it. Maybe even
an added bonus would be adding a USB microscope camera mount to the sample
carriage to do visualization.

On Thu, Jan 3, 2019 at 10:21 AM Tim Craig  wrote:

> The opentron liquid handler is currently in what I would consider an alpha
> stage of development in both hardware and software, when compared to more
> expensive liquid handlers produced by companies like tecan, hamilton,
> agilent, etc.  It is considerably less useful due to the lack of software
> control as well as hardware like plate readers, centrifuges, multichannel
> pipette heads of appropriate volumes.  You should think of the opentrons as
> the raspberry pi (circa 2012) of liquid handlers.
>
> The control software is not currently stable, and they release upgrades
> frequently that will break working programs.  With enough discussion on
> their github you can generally get them to fix these kinds of errors in a
> couple of weeks.  I recently went through a process getting the dispensing
> and aspirating speeds to be recognized properly be the software
> (they were being
> ignored).This will be a critical feature for you to use if you're
> handling liquids of different viscosities.
>
> The OT2 currently does not have a pipettor smaller than the P10, so you
> will likely be out of luck on setting up trays, even at a 1+1 uL drop
> ratio.  If you just want to make screens this robot could be a good option
> for you, though it does not have crystallography-centric software to make
> pipetting the correct solutions easy.
>
> We are currently using it to do phytip purifications of proteins in small
> scale, and it seems to be doing the job reasonably well after all the bugs
> have been worked around, which took a significant amount of time.
> Enjoy,
> -Tim
>
> On Tue, Jan 1, 2019 at 10:01 AM Artem Evdokimov 
> wrote:
>
>> Good morning and Happy New Year to you
>>
>> In brief, it can be used to create screens although programming multiple
>> ingredients with varying viscosities will initially be a fairly steep
>> challenge since the software is not specific to crystallization. It can be
>> done though and provided that you can re-use protocols (I.e. today you set
>> up PEG 3350 versus salt and pH and tomorrow you set up PEG 6000 versus salt
>> and pH without changing concentrations) it can even be effective.
>>
>> You would likely need to write your own code for gradients and suchlike
>> but maybe you can borrow from existing protocols a bit. It is all in Python
>> anyway.
>>
>> I would not use this robot for setting drops unless there is so much
>> protein available that 1ul + 1ul drops are not wasteful. The pipettors are
>> essentially the same (in terms of tolerances and volume limits) as your
>> average wet lab hardware. Now, if you have a willing colleague with
>> mechanical and coding mojo at your disposal you can probably modify the
>> robot to use a crystallization friendly operating device, assuming you can
>> get a hold of an accurate sub microliter dispenser with an open API. The
>> robot API is open towards change.
>>
>> In a nutshell this robot is sort of like a large 3D printer chassis with
>> a deck and pipettors bolted on. If you love to tinker this is a machine for
>> you. Cannot beat the price.
>>
>> Artem
>>
>> On Mon, Dec 31, 2018, 12:46 Doug Juers >
>>> Hello All,
>>>
>>> I've just learned about the opentrons pipetting robot, which appears to
>>> be quite affordable relative to other robots. I'm wondering if anyone here
>>> on ccp4 bb has any experience with it - for creating crystallization
>>> screens and/or setting drops?
>>>
>>> Best,
>>> Doug
>>>
>>>
>>> -
>>> Douglas Juers
>>> Physics Department
>>> Program in BBMB
>>> Whitman College
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
> Tim Craig PhD
> Chief Scientific Officer - HarkerBIO
> Mobile: (661) 993-5576
> tim.cr...@harkerbio.com
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Refinement with native and anomalous data

[Eleanor Dodson]

I think any decision depends on the resolution of your two data sets. If
they are very different I would choose the higher resolution one.

If that is the Anom data then I would use the anom signal at least in the
first cycles to improve the phases..

Eleanor

On Thu, 3 Jan 2019 at 14:59, Piotr Wilk  wrote:

> Dear CCP4 experts,
>
> I'd like to ask your opinion about using anomalous signal in refinement of
> crystal structures in addition to using high resolution native data.
> I am working on a series of structures for which I have collected two data
> sets (from the same crystal):
> 1 - native with higher resolution
> 2 - anomalous at MN absorption edge peak.
> The structures were solved with MR and preliminary refinement using the
> native data only yields decent statistics, but I also use anomalous data to
> verify presence and position of manganese ions. For this I used ANODE which
> lists four strong peaks (~30 sigma) as expected for manganese ions and
> around 45 weaker peaks (~9-5 sigma) for sulfur atoms in Cys and Met. I am
> happy to use this information in model building but I was also wondering if
> (and how) beneficial would it be to use both high resolution structure
> factors and somehow lower resolution yet highly specific anomalous signal
> in the same round of refinement?
> In Refmac5 I can use either refinement with "no prior phase information"
> taking FP and SIGFP or "SAD data directly" with SIGFP F(+) SIGF(+) F(-)
> SIGF(-), but I didn't find any "MAD" option to use both.
> I have the following columns in my mtz files:
> for native data: H K L FP SIGFP FreeRflag
> for anomalous data : H K L FP SIGFP F(+) SIGF(+) F(-) SIGF(-) FreeRflag
> or :   H K L FP SIGFP DANO SIGDANO ISYM FreeRflag
>
> I could use CAD to merge the interesting columns into a single mtz file
> containing:
>  H K L FP SIGFP FreeRflag F(+) SIGF(+) F(-) SIGF(-) DANO SIGDANO
>
> I'd appreciate any comments or advise how to use both sources of
> information in the refinement.
>
> I wish you all a Happy New Year.
> Kind regards,
> Piotrek
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Job opening

[Ronnie]

A career opportunity if you want to pivot your structure Biology experience for 
something new.Check out this job: Protein Antibody Engineer
https://www.linkedin.com/jobs/view/1031138315



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Re: [ccp4bb] opentrons pipetting robot

[Tim Craig]

The opentron liquid handler is currently in what I would consider an alpha
stage of development in both hardware and software, when compared to more
expensive liquid handlers produced by companies like tecan, hamilton,
agilent, etc.  It is considerably less useful due to the lack of software
control as well as hardware like plate readers, centrifuges, multichannel
pipette heads of appropriate volumes.  You should think of the opentrons as
the raspberry pi (circa 2012) of liquid handlers.

The control software is not currently stable, and they release upgrades
frequently that will break working programs.  With enough discussion on
their github you can generally get them to fix these kinds of errors in a
couple of weeks.  I recently went through a process getting the dispensing
and aspirating speeds to be recognized properly be the software
(they were being
ignored).This will be a critical feature for you to use if you're
handling liquids of different viscosities.

The OT2 currently does not have a pipettor smaller than the P10, so you
will likely be out of luck on setting up trays, even at a 1+1 uL drop
ratio.  If you just want to make screens this robot could be a good option
for you, though it does not have crystallography-centric software to make
pipetting the correct solutions easy.

We are currently using it to do phytip purifications of proteins in small
scale, and it seems to be doing the job reasonably well after all the bugs
have been worked around, which took a significant amount of time.
Enjoy,
-Tim

On Tue, Jan 1, 2019 at 10:01 AM Artem Evdokimov 
wrote:

> Good morning and Happy New Year to you
>
> In brief, it can be used to create screens although programming multiple
> ingredients with varying viscosities will initially be a fairly steep
> challenge since the software is not specific to crystallization. It can be
> done though and provided that you can re-use protocols (I.e. today you set
> up PEG 3350 versus salt and pH and tomorrow you set up PEG 6000 versus salt
> and pH without changing concentrations) it can even be effective.
>
> You would likely need to write your own code for gradients and suchlike
> but maybe you can borrow from existing protocols a bit. It is all in Python
> anyway.
>
> I would not use this robot for setting drops unless there is so much
> protein available that 1ul + 1ul drops are not wasteful. The pipettors are
> essentially the same (in terms of tolerances and volume limits) as your
> average wet lab hardware. Now, if you have a willing colleague with
> mechanical and coding mojo at your disposal you can probably modify the
> robot to use a crystallization friendly operating device, assuming you can
> get a hold of an accurate sub microliter dispenser with an open API. The
> robot API is open towards change.
>
> In a nutshell this robot is sort of like a large 3D printer chassis with a
> deck and pipettors bolted on. If you love to tinker this is a machine for
> you. Cannot beat the price.
>
> Artem
>
> On Mon, Dec 31, 2018, 12:46 Doug Juers 
>> Hello All,
>>
>> I've just learned about the opentrons pipetting robot, which appears to
>> be quite affordable relative to other robots. I'm wondering if anyone here
>> on ccp4 bb has any experience with it - for creating crystallization
>> screens and/or setting drops?
>>
>> Best,
>> Doug
>>
>>
>> -
>> Douglas Juers
>> Physics Department
>> Program in BBMB
>> Whitman College
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
Tim Craig PhD
Chief Scientific Officer - HarkerBIO
Mobile: (661) 993-5576
tim.cr...@harkerbio.com



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[ccp4bb] Refinement with native and anomalous data

[Piotr Wilk]

Dear CCP4 experts,

I'd like to ask your opinion about using anomalous signal in refinement of
crystal structures in addition to using high resolution native data.
I am working on a series of structures for which I have collected two data
sets (from the same crystal):
1 - native with higher resolution
2 - anomalous at MN absorption edge peak.
The structures were solved with MR and preliminary refinement using the
native data only yields decent statistics, but I also use anomalous data to
verify presence and position of manganese ions. For this I used ANODE which
lists four strong peaks (~30 sigma) as expected for manganese ions and
around 45 weaker peaks (~9-5 sigma) for sulfur atoms in Cys and Met. I am
happy to use this information in model building but I was also wondering if
(and how) beneficial would it be to use both high resolution structure
factors and somehow lower resolution yet highly specific anomalous signal
in the same round of refinement?
In Refmac5 I can use either refinement with "no prior phase information"
taking FP and SIGFP or "SAD data directly" with SIGFP F(+) SIGF(+) F(-)
SIGF(-), but I didn't find any "MAD" option to use both.
I have the following columns in my mtz files:
for native data: H K L FP SIGFP FreeRflag
for anomalous data : H K L FP SIGFP F(+) SIGF(+) F(-) SIGF(-) FreeRflag
or :   H K L FP SIGFP DANO SIGDANO ISYM FreeRflag

I could use CAD to merge the interesting columns into a single mtz file
containing:
 H K L FP SIGFP FreeRflag F(+) SIGF(+) F(-) SIGF(-) DANO SIGDANO

I'd appreciate any comments or advise how to use both sources of
information in the refinement.

I wish you all a Happy New Year.
Kind regards,
Piotrek



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[ccp4bb] 12th CCP4/APS Crystallographic School in the US

[Xu, Qingping]

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From 
data collection to structure refinement and beyond” will be held on June 17-24, 
2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near 
Chicago, Illinois, USA. All details can be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near 
Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic 
computing workshop. Data collection workshop includes beamline training, data 
collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M 
and Eiger 16M detectors respectively, and data processing. For data collection, 
only the participants' crystals will be used. Crystallographic computation 
workshop will feature many modern crystallographic software packages taught by 
authors and other experts. The daily schedule will be organized in three 
sections – lectures, tutorials, and hands-on (interactive trouble-shooting of 
the technical difficulties the participants face in their projects). We have 
had considerable success resolving these problems in past years, attested by 
resulting publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, 
contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career 
faculty, along with commercial/industrial researchers are encouraged to apply. 
Only 20 applicants will be selected for participation. Participants of the 
workshop are strongly encouraged to bring their own problem data sets or 
crystals so the problems can be addressed during data collection and/or 
computation workshops.

Application: Application deadline is April 15th, 2019. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2019/application.php.

Fees: The registration for application is free but there is $500 participation 
fee for the selected academic students and $950 for the industrial researchers. 
The link for the on-line payments and instructions will be provided once the 
selection process is completed. The students will be responsible for their 
transportation and lodging. The workshop organizers can assist in making the 
lodging reservations at the Argonne Guest House. The workshop will cover all 
other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping



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Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie

[Carter, Charlie]

I, for one, was very happy to see Marin’s remark, which pointed something 
everyone is shoving under the rug.

By far the most significant source for information to US citizens is FOX news, 
which is pay rolled to brainwash as many as they reach. Even public television 
and NPR have been hammered into accepting a false equivalence. WE ARE a fake 
news people.

Charlie

On Jan 2, 2019, at 5:57 PM, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:

I know this is a joke, but we in the USA are not a fake news people, and please 
don’t punish us for the sins of our leadership--it’s painful for many of us.





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