Re: [ccp4bb] Open position - data management in biophysics

[Navdeep Sidhu]

Dear Gerlind, Markus, All:

Well, sometimes the (written) promise of a 2-year contract also ends up
boiling down systematically (for some PIs) to only a 6-month contract
after all.--And that after you've spent half a year or more and multiple
trips to the country concerned trying to get a work visa and housing,
all at your own expense--particularly tough for migrants and their families:

"Many come here with a promise of a two-year contract, which later turns
out to be a six month scholarship, which is renewed six months at a
time. Many feel that they have been fooled."
 - From Palle Liljebaeck. "Postdoctoral fellows at KI must be given
better terms." Naturvetarna (Sweden), Nov. 7, 2013
.

(By the way, work contracts often entail health, pension and other
benefits which may be limited or unavailable on a scholarship.)

Fortunately, many PIs don't agree with such practices. But they do
occur, including unfortunately for jobs advertized on the CCP4 bulletin
board--and so perhaps the IUCr or other institutions can help set better
standards.

Cheers,
Navdeep


---
On 20.01.21 22:34, Gerlind Sulzenbacher wrote:
> Dear Markus,
> 
> thank you for opening this discussion.
> 
> I'd like to add that in some countries, like France, where I work, this
> goes often along with with 12 months contracts.
> Imagine moving continent, eventually with family (yes, PostDocs happen
> to have a family) just for a 12 months contract, under the conditions
> you mentioned.
> Sad, as you said, ... and I am quite sure that it has not always been
> like that.
> I wish all members of the BB a good mood,
> Best,
> gerlind
> 
> 
> On 20/01/2021 21:48, Markus Heckmann wrote:
>> Dear PI s, and senior scientists' involved in recruitment,
>>
>> Why do so many (especially postdoc) positions these days indicate:
>>
>>> Readiness for high workload
>>> able to work independently but also effectively and collaboratively
>>> with other lab member
>>> Candidates should have a documented publication record in
>>> peer-reviewed journals, able to work both independently and as an
>>> effective team member.
>> Do the candidates need to subtly understand that they need to work on
>> weekends or holidays? And what does it mean by independently and
>> collaboratively at the same time. Or is this a template from HR
>> departments.
>>
>> Was it always like this in science world or we too need to work like
>> amazon warehouse workers (you can google it and see the pain)?
>>
>> Saddened...
>>
>> Mark
>> (not trying to point out any single PI/person but overall it is the
>> same words repeated...)
>>
>>
>>
>>> We are opening a new position for an upcoming European project.
>>>
>>> *We are looking for an expert in scientific programming with
>>> experience in
>>> scientific data processing for a European project focused on
>>> Standards for
>>> Data Archival and Exploitation. *
>>>
>>> Job description:
>>>
>>> We offer attractive work connected to development of data management
>>> infrastructure for biophysical data in the frame of an international
>>> project at the Institute of Biotechnology in the centre of excellence
>>> Biocev. The main responsibility lies in definition of data standards and
>>> models for biophysical data, development of algorithms, design of user
>>> interface, and realization of a pilot database of biophysical data. The
>>> person is expected to actively participate in multilateral international
>>> negotiations, to drive the tasks fulfillment in collaboration with the
>>> local international partners, and to present the results.
>>>
>>
>>> Dear all,
>>>
>>> Two postdoctoral positions are available in the laboratory of Dr.
>>> Pengxiang
>>> Huang, Assistant Professor and CPRIT scholar in cancer research in the
>>> Department of Molecular and Cellular Biology at Baylor College of
>>> Medicine.
>>> With the long-standing interest in sterol lipids, the Huang lab
>>> investigates
>>> the poorly understood mechanisms involved in Hedgehog (Hh) and Wnt
>>> signal
>>> transduction, two related pathways that play critical roles in
>>> development,
>>> regeneration and cancer. We utilize a combination of biochemistry, cell,
>>> chemical and structural biology approaches, including both X-ray
>>> crystallography and Cryo-EM. Our recent work identified cholesterol
>>> as the
>>> endogenous ligand for Smoothened, the key signal transduer and
>>> oncoprotein
>>> in the Hh pathway (Cell. 166:1176-87). We also characterized the
>>> structural
>>> and oncogenic basis of Smoothened activation, demonstrating for the
>>> first
>>> time the active conformation of a class F GPCR (Cell. 174:312-24). The
>>> highly interdisciplinary and collaborative environment of our group will
>>> thus provide unique career development opportunities for future
>>> postdoctoral
>>> trainees.
>>>
>>> We are seeking highly-motivated candidates 

[ccp4bb] Biochemist Postdoc Fellow to join the SIBYLS group at LBNL

[Michal Hammel]

We looking for a new team player in the SIBYLS group at the
Lawrence Berkeley Lab.

https://lbl.referrals.selectminds.com/jobs/biochemist-postdoc-fellow-3498

Lawrence Berkeley National Lab’s (LBNL) Biosciences Division has an opening
for a Biochemist Postdoc Fellow to join the team.
In this exciting role, you will develop and apply biophysical and
biochemical techniques to address questions relevant to understanding
structural cell biology for multi-component biological macromolecules. You
will aid in the characterization of biological processes.

You will be part of a team that designs, develops, and applies synchrotron
methods to characterize macromolecules and the assemblies they form.
Primary tools will include small angle X-ray scattering (SAXS). However
accessible and ancillary techniques include X-ray crystallography,
cryo-electron microscopy, and X-ray tomography. We seek to develop and
improve overlaps with all techniques either in the joint application or
through software development. You will develop and maintain software for
SAXS analysis or the collection of SAXS data. You will work at the Advanced
Light Source synchrotron and be required to develop interdisciplinary
skills to communicate with other beamline staff, engineers, and physicists
responsible for beamline application and development.


Best Michal

https://bl1231.als.lbl.gov/
_
Michal Hammel PhD
Scientist at SIBYLS Beamline
Advanced Light Source
Lawrence Berkeley National Laboratory

1 Cyclotron Road
MS 6R2100
Berkeley, CA 94720
(phone) 510-495-8179
(cell) 510-457-6317
_



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Re: [ccp4bb] Open position - data management in biophysics

[Gerlind Sulzenbacher]

Dear Markus,

thank you for opening this discussion.

I'd like to add that in some countries, like France, where I work, this 
goes often along with with 12 months contracts.
Imagine moving continent, eventually with family (yes, PostDocs happen 
to have a family) just for a 12 months contract, under the conditions 
you mentioned.
Sad, as you said, ... and I am quite sure that it has not always been 
like that.

I wish all members of the BB a good mood,
Best,
gerlind


On 20/01/2021 21:48, Markus Heckmann wrote:

Dear PI s, and senior scientists' involved in recruitment,

Why do so many (especially postdoc) positions these days indicate:


Readiness for high workload
able to work independently but also effectively and collaboratively with other 
lab member
Candidates should have a documented publication record in peer-reviewed 
journals, able to work both independently and as an effective team member.

Do the candidates need to subtly understand that they need to work on
weekends or holidays? And what does it mean by independently and
collaboratively at the same time. Or is this a template from HR
departments.

Was it always like this in science world or we too need to work like
amazon warehouse workers (you can google it and see the pain)?

Saddened...

Mark
(not trying to point out any single PI/person but overall it is the
same words repeated...)




We are opening a new position for an upcoming European project.

*We are looking for an expert in scientific programming with experience in
scientific data processing for a European project focused on Standards for
Data Archival and Exploitation. *

Job description:

We offer attractive work connected to development of data management
infrastructure for biophysical data in the frame of an international
project at the Institute of Biotechnology in the centre of excellence
Biocev. The main responsibility lies in definition of data standards and
models for biophysical data, development of algorithms, design of user
interface, and realization of a pilot database of biophysical data. The
person is expected to actively participate in multilateral international
negotiations, to drive the tasks fulfillment in collaboration with the
local international partners, and to present the results.




Dear all,

Two postdoctoral positions are available in the laboratory of Dr. Pengxiang
Huang, Assistant Professor and CPRIT scholar in cancer research in the
Department of Molecular and Cellular Biology at Baylor College of Medicine.
With the long-standing interest in sterol lipids, the Huang lab investigates
the poorly understood mechanisms involved in Hedgehog (Hh) and Wnt signal
transduction, two related pathways that play critical roles in development,
regeneration and cancer. We utilize a combination of biochemistry, cell,
chemical and structural biology approaches, including both X-ray
crystallography and Cryo-EM. Our recent work identified cholesterol as the
endogenous ligand for Smoothened, the key signal transduer and oncoprotein
in the Hh pathway (Cell. 166:1176-87). We also characterized the structural
and oncogenic basis of Smoothened activation, demonstrating for the first
time the active conformation of a class F GPCR (Cell. 174:312-24). The
highly interdisciplinary and collaborative environment of our group will
thus provide unique career development opportunities for future postdoctoral
trainees.

We are seeking highly-motivated candidates with a Ph.D. in biomedical
sciences and significant experience in molecular biology, protein
biochemistry and/or cell biology. Prior knowledge in structural biology
(X-ray crystallography or Cryo-EM) is highly desirable, but not required.
Candidates should have a documented publication record in peer-reviewed
journals, able to work both independently and as an effective team member.

To apply, please send your CV, a short summary of research experience, and
three reference letters to cnssolve[at]gmail.com.


collaborative research environment focused on structural/molecular mechanism
of broadly neutralizing antibodies specific to MPER segment of the gp41
subunit in membrane environments, its implication to immunogen design and
immunogenicity. The laboratory provides a rich training environment and
access to cutting-edge techniques.

Highly-motivated candidates with a recent PhD or MD/PhD in biomedical
sciences and significant experience in molecular biology and biochemistry
are encouraged to apply. Skills in molecular biology, biochemistry and
extensive biomolecular NMR experience are essential.  Candidates should have
a documented publication record in peer-reviewed journals. We are seeking a
candidate with excellent writing and communication skills, able to work
independently but also effectively and collaboratively with other lab
members. Applicants should include a short statement of research goals, CV
and three references with their application.

Re: [ccp4bb] Open position - data management in biophysics

[Markus Heckmann]

Dear PI s, and senior scientists' involved in recruitment,

Why do so many (especially postdoc) positions these days indicate:

> Readiness for high workload

> able to work independently but also effectively and collaboratively with 
> other lab member

> Candidates should have a documented publication record in peer-reviewed 
> journals, able to work both independently and as an effective team member.

Do the candidates need to subtly understand that they need to work on
weekends or holidays? And what does it mean by independently and
collaboratively at the same time. Or is this a template from HR
departments.

Was it always like this in science world or we too need to work like
amazon warehouse workers (you can google it and see the pain)?

Saddened...

Mark
(not trying to point out any single PI/person but overall it is the
same words repeated...)



> We are opening a new position for an upcoming European project.
>
> *We are looking for an expert in scientific programming with experience in
> scientific data processing for a European project focused on Standards for
> Data Archival and Exploitation. *
>
> Job description:
>
> We offer attractive work connected to development of data management
> infrastructure for biophysical data in the frame of an international
> project at the Institute of Biotechnology in the centre of excellence
> Biocev. The main responsibility lies in definition of data standards and
> models for biophysical data, development of algorithms, design of user
> interface, and realization of a pilot database of biophysical data. The
> person is expected to actively participate in multilateral international
> negotiations, to drive the tasks fulfillment in collaboration with the
> local international partners, and to present the results.
>


> Dear all,
>
> Two postdoctoral positions are available in the laboratory of Dr. Pengxiang
> Huang, Assistant Professor and CPRIT scholar in cancer research in the
> Department of Molecular and Cellular Biology at Baylor College of Medicine.
> With the long-standing interest in sterol lipids, the Huang lab investigates
> the poorly understood mechanisms involved in Hedgehog (Hh) and Wnt signal
> transduction, two related pathways that play critical roles in development,
> regeneration and cancer. We utilize a combination of biochemistry, cell,
> chemical and structural biology approaches, including both X-ray
> crystallography and Cryo-EM. Our recent work identified cholesterol as the
> endogenous ligand for Smoothened, the key signal transduer and oncoprotein
> in the Hh pathway (Cell. 166:1176-87). We also characterized the structural
> and oncogenic basis of Smoothened activation, demonstrating for the first
> time the active conformation of a class F GPCR (Cell. 174:312-24). The
> highly interdisciplinary and collaborative environment of our group will
> thus provide unique career development opportunities for future postdoctoral
> trainees.
>
> We are seeking highly-motivated candidates with a Ph.D. in biomedical
> sciences and significant experience in molecular biology, protein
> biochemistry and/or cell biology. Prior knowledge in structural biology
> (X-ray crystallography or Cryo-EM) is highly desirable, but not required.
> Candidates should have a documented publication record in peer-reviewed
> journals, able to work both independently and as an effective team member.
>
> To apply, please send your CV, a short summary of research experience, and
> three reference letters to cnssolve[at]gmail.com.
>
>

> collaborative research environment focused on structural/molecular mechanism
> of broadly neutralizing antibodies specific to MPER segment of the gp41
> subunit in membrane environments, its implication to immunogen design and
> immunogenicity. The laboratory provides a rich training environment and
> access to cutting-edge techniques.
>
> Highly-motivated candidates with a recent PhD or MD/PhD in biomedical
> sciences and significant experience in molecular biology and biochemistry
> are encouraged to apply. Skills in molecular biology, biochemistry and
> extensive biomolecular NMR experience are essential.  Candidates should have
> a documented publication record in peer-reviewed journals. We are seeking a
> candidate with excellent writing and communication skills, able to work
> independently but also effectively and collaboratively with other lab
> members. Applicants should include a short statement of research goals, CV
> and three references with their application.
>



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Re: [ccp4bb] increased Rfree after ligand fitting refinement

[Eleanor Dodson]

Well - there are several possible reasons for that .
The least pleasing is that you have built the ligand in the wrong place,
but leaving that aside.

When you add something to your model the coordinates are rather approximate
and the B factors are usually set to some quite arbitrary value, so it
takes several cycles of refinement for these to be corrected. Then you have
probably only added a small percentage of the model, so the R factors will
not change very much.. The best check is to re-inspect the map after
refinement and see if the ligand fits snugly into the density.
Good luck Eleanor

On Wed, 20 Jan 2021 at 18:10, Pavel Afonine  wrote:

> Hi Wajahat,
>
> first off, there is a dedicated mailing list for Phenix specific questions
> (http://phenix-online.org/).
>
> You need to run more than one refinement cycle before you try making sense
> of R factors.
>
> Pavel
>
> On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan 
> wrote:
>
>> Dear all,
>>
>>
>> I have just started with X-ray diffraction.
>> I would appreciate any ideas as to why after one cycle of phenix.refine ,
>> the Rfree value increased for my ligand fitted model molecular replacement
>> solution model.
>>
>> Thanks
>>
>> Wajahat
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] increased Rfree after ligand fitting refinement

[Pavel Afonine]

Hi Wajahat,

first off, there is a dedicated mailing list for Phenix specific questions (
http://phenix-online.org/).

You need to run more than one refinement cycle before you try making sense
of R factors.

Pavel

On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan 
wrote:

> Dear all,
>
>
> I have just started with X-ray diffraction.
> I would appreciate any ideas as to why after one cycle of phenix.refine ,
> the Rfree value increased for my ligand fitted model molecular replacement
> solution model.
>
> Thanks
>
> Wajahat
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] increased Rfree after ligand fitting refinement

[Wajahat ali khan]

Dear all,


I have just started with X-ray diffraction. 
I would appreciate any ideas as to why after one cycle of phenix.refine , the 
Rfree value increased for my ligand fitted model molecular replacement solution 
model.

Thanks

Wajahat



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[ccp4bb] increased Rfree after ligand fitting refinement

[WAJAHAT ALI KHAN]

Dear all,


I have just started with X-ray diffraction. I would appreciate any ideas as
to why after one cycle of phenix.refine , the Rfree value increased for the
ligand fitted model.

Thanks

Wajahat



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Re: [ccp4bb] PISA

[Jon Cooper]

Dear Sam

I can only suggest trying the old trick of editing the pdb file and giving all 
the DNA bases the same residue number. As you are using the old gui you might 
be able to do the same with pdbset or pdbcur, or maybe a graphics program.

Cheers, Jon Cooper

Sent from ProtonMail mobile

 Original Message 
On 20 Jan 2021, 13:27, Sam Tang wrote:

> Dear community
>
> I ran PISA from CCP4i to analyze a protein-ssDNA complex with non-standard 
> modified nucleotides. It turns out that PISA identifies each nucleotide in 
> the DNA chain as a ligand (i.e. I have 7 DNA bases and PISA calls out 7 
> ligands). May I solicit your experience if there is a way to force PISA to 
> recognize the DNA as one single ligand? Thanks a lot.
>
> Best regards
> Sam
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] PISA

[Sam Tang]

Dear community

I ran PISA from CCP4i to analyze a protein-ssDNA complex with non-standard
modified nucleotides. It turns out that PISA identifies each nucleotide in
the DNA chain as a ligand (i.e. I have 7 DNA bases and PISA calls out 7
ligands). May I solicit your experience if there is a way to force PISA to
recognize the DNA as one single ligand? Thanks a lot.

Best regards
Sam



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