Re: [ccp4bb] Off topic -- Job post

[Eric Montemayor]

Hi Xiaoshan,

I am interested in applying, but do you think that an experienced
protein-RNA crystallographer with a physical chemistry background would be
given consideration?  It so, I'll send a CV and cover letter through
official channels.

-- 
Eric J. Montemayor, Ph.D.
Assistant Scientist
University of Wisconsin-Madison
145 Biochemistry Laboratories
433 Babcock Drive
Madison, WI 53706
512.784.5981
https://www.linkedin.com/in/ericmontemayor

http://about.me/montemayor


On Wed, Mar 25, 2015 at 7:05 PM, Min, Xiaoshan  wrote:

>  Dear friends,
>
>
>
> I would like to draw your attention to an opening in our structural
> biology group at Amgen San Francisco.  Please apply through the web portal
>
>
>
>
> http://careers.amgen.com/en/jobs/descriptions/scientist-protein-biochemist-crystallographer-south-san-francisco-job-5231739
>
>
>
> The job description is at the end of this email.
>
>
>
> Cheers,
>
>
>
> Xiaoshan Min
>
> Molecular Structure
>
> Amgen San Francisco
>
> 650-2442412
>
>
>
>
>
> *Scientist - Protein Biochemist / Crystallographer*
>
> *Auto Req #:* 25895BR
> *Career Categories: *Research
> *Location: *US - CA - South San Francisco
>
> *Amgen Job Description *
>
> Amgen is a leading global biotechnology company, with a mission to serve
> patients around the world. As a science-based, patient-focused
> organization, we discover and develop innovative therapies to treat serious
> illnesses. Our medicines have made a dramatic difference in the lives of
> millions. To underpin our commitment to serve patients, Amgen is expanding
> our Research and Development facilities in South San Francisco, CA (ASF).
>
> We are looking for a highly motivated and talented protein biochemist or
> crystallographer to join the ASF Structural Biology group. This laboratory
> provides comprehensive molecular insight and structure-based design for
> drug target assessment, mechanism of action, protein-protein and
> protein-ligand interactions, as well as protein engineering to facilitate
> drug discovery across various important therapeutic areas. The candidate
> will have the opportunity to contribute directly to the exciting drug
> discovery process through structural studies on a wide variety of important
> biological systems, including human integral membrane proteins.
>
> The candidate will be responsible for leading projects through the entire
> protein crystallographic process, including construct design, protein
> purification, characterization, crystallization, X-ray data collection,
> structure determination and analysis. The candidate will be working closely
> with molecular biologists and protein biochemists in the protein technology
> team. The candidate will also interact directly with computational and
> medicinal chemists and protein engineering teams for structure-based drug
> design projects. The candidate must have strong interpersonal skills to
> work in interdisciplinary project teams
>
> *Basic Qualifications *
>
> - Doctorate degree
> OR
> - Master’s degree & 5 years of scientific experience
> OR
> - Bachelor’s degree & 7 years of scientific experience
>
> *Preferred Qualifications *
>
> - PhD in protein biochemistry, crystallography, or related discipline with
> significant postdoctoral research experience
> - Proven ability to design and perform experiments from protein expression
> to structure determination
> - Knowledge of state-of-the-art membrane protein structural biology
> techniques including all aspects of construct design, expression,
> purification, crystallization screening/optimization (including LCP and
> LCP-FRAP)
> - Expertise in protein biochemical and biophysical characterization
> - Experience with X-ray free electron laser and/or cryo-EM will be highly
> desirable
> - Excellent presentation skills (written and oral) that enhance team-based
> progress are required
> - Ability to work independently and effectively within timelines and to
> collaborate in a multidisciplinary environment
>
> Amgen is an Equal Opportunity/Affirmative Action employer and will
> consider all qualified applicants for employment without regard to race,
> color, religion, sex, national origin, protected veteran status, or
> disability status.
>
>
>

[ccp4bb] Off topic -- Job post

[Min, Xiaoshan]

Dear friends,

I would like to draw your attention to an opening in our structural biology 
group at Amgen San Francisco.  Please apply through the web portal

http://careers.amgen.com/en/jobs/descriptions/scientist-protein-biochemist-crystallographer-south-san-francisco-job-5231739

The job description is at the end of this email.

Cheers,

Xiaoshan Min
Molecular Structure
Amgen San Francisco
650-2442412


Scientist - Protein Biochemist / Crystallographer
Auto Req #: 25895BR
Career Categories: Research
Location: US - CA - South San Francisco
Amgen Job Description
Amgen is a leading global biotechnology company, with a mission to serve 
patients around the world. As a science-based, patient-focused organization, we 
discover and develop innovative therapies to treat serious illnesses. Our 
medicines have made a dramatic difference in the lives of millions. To underpin 
our commitment to serve patients, Amgen is expanding our Research and 
Development facilities in South San Francisco, CA (ASF).

We are looking for a highly motivated and talented protein biochemist or 
crystallographer to join the ASF Structural Biology group. This laboratory 
provides comprehensive molecular insight and structure-based design for drug 
target assessment, mechanism of action, protein-protein and protein-ligand 
interactions, as well as protein engineering to facilitate drug discovery 
across various important therapeutic areas. The candidate will have the 
opportunity to contribute directly to the exciting drug discovery process 
through structural studies on a wide variety of important biological systems, 
including human integral membrane proteins.

The candidate will be responsible for leading projects through the entire 
protein crystallographic process, including construct design, protein 
purification, characterization, crystallization, X-ray data collection, 
structure determination and analysis. The candidate will be working closely 
with molecular biologists and protein biochemists in the protein technology 
team. The candidate will also interact directly with computational and 
medicinal chemists and protein engineering teams for structure-based drug 
design projects. The candidate must have strong interpersonal skills to work in 
interdisciplinary project teams

Basic Qualifications
- Doctorate degree
OR
- Master's degree & 5 years of scientific experience
OR
- Bachelor's degree & 7 years of scientific experience

Preferred Qualifications
- PhD in protein biochemistry, crystallography, or related discipline with 
significant postdoctoral research experience
- Proven ability to design and perform experiments from protein expression to 
structure determination
- Knowledge of state-of-the-art membrane protein structural biology techniques 
including all aspects of construct design, expression, purification, 
crystallization screening/optimization (including LCP and LCP-FRAP)
- Expertise in protein biochemical and biophysical characterization
- Experience with X-ray free electron laser and/or cryo-EM will be highly 
desirable
- Excellent presentation skills (written and oral) that enhance team-based 
progress are required
- Ability to work independently and effectively within timelines and to 
collaborate in a multidisciplinary environment

Amgen is an Equal Opportunity/Affirmative Action employer and will consider all 
qualified applicants for employment without regard to race, color, religion, 
sex, national origin, protected veteran status, or disability status.

Re: [ccp4bb] nVidia quadro

[Kay Diederichs]

On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  wrote:

>You could check the nVidia page of officially supported displays. It 
>includes a search tab so you can check for "Built-in Emitter."
>http://www.nvidia.com/object/3d-vision-displays.html
>
>Performing that search brings up 5 contenders. Good luck finding any of 
>these products still for sale.

Unfortunately, this NVidia page has not been updated for years.

The qualifier "3D-fähig (aktiv)" at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top
 should indicate a built-in emitter, but I looked at some of the descriptions 
of these 11 monitors and was unable to confirm that they indeed have a built-in 
emitter. So one has to research every specific case.

I changed the wording on the wiki page.

Kay
 

>
>
>
>On 03/25/15 12:00, Andreas Schenk wrote:
>> Thank you for assembling all that information about NVidia 3D vision 2 
>> on Linux.
>>
>> Is there a good list somewhere with monitors that have a built-in 
>> emitter and are confirmed to work under Linux?
>> I looked at the list at 
>> http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+%28aktiv%29#xf_top
>>  
>> and it seems that a lot of manufacturers are marketing their monitors 
>> as 3D Vision2 ready or 3D capable just because they support running at 
>> 120 Hz, even if they don't have a built-in emitter.
>>
>> Best,
>> Andreas
>>
>>
>> On 25.03.2015 05:16, Kay Diederichs wrote:
>>> Sorry to come late into the discussion, and just to mention: it would 
>>> be wrong if readers of CCP4BB get the impression that  "Quadro cards 
>>> that support quad buffered stereo" have to be high-end. To the 
>>> contrary, an entry-class Quadro K620 together with a €250 Nvidia 3D 
>>> Vision 2 compatible monitor (with built-in emitter) gives you very 
>>> nice stereo on Linux. There is more info at 
>>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo#Nvidia_3D_Vision_2
>>>  
>>> .
>>>
>>> To have higher resolution than 1920x1080 you may need some 
>>> combination of higher-end monitor and (separate) emitter, and that 
>>> would indeed require a 3-pin DIN connector and an expensive Quadro 
>>> card. Also, an expensive Quadro is of course faster - but entry cards 
>>> are, in contrast to popular belief, fast enough for crystallographic 
>>> electron density + model inspection and modelling.
>>>
>>> In summary, the computer gamers have been supporting us 
>>> crystallographers to the point that Stereo is quite affordable.
>>>
>>> best,
>>>
>>> Kay
>>>
>>> On Tue, 24 Mar 2015 18:05:20 +, Oganesyan, Vaheh 
>>>  wrote:
>>>
 Colleagues,

 I’d like to thank everyone who took time to answer my question 
 regarding Quadro cards that support quad buffered stereo. I now hope 
 to build a workstation with >Quadro 5000.

 Regards,

 Vaheh Oganesyan
 www.medimmune.com

>
>
>-- 
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu

[ccp4bb] Cryo-EM Subgroup of the Biophysical Society

[Wang, Da-Neng]

Sorry for the off-topic post:

Dear Colleagues,

It is a remarkable time for Cryo-EM! Given a very successful Cryo-EM Symposium 
at the Annual Meeting of the Biophysical Society in Baltimore last month, the 
idea arose to create an official Cryo-EM Subgroup of the Biophysical Society. 
There would be many advantages to having such an official subgroup, the 
principal one being that we would be able to organize a Subgroup Scientific 
Meeting every year on Saturday at the Annual Meeting of the Society. Since > 
6,000 people attend these annual meetings (including quite a few cryo-EM 
people) the scientific session on Saturday would be a wonderful forum for 
presenting new results in methods, techniques and applications to biological 
problems. We envision a session that could be held perhaps 7:30 - 10:00 pm, 
which would not conflict with other subgroup meetings, and would allow for 
five-seven talks that might be selected from submitted abstracts or from 
nominations. There would be many people outside of the cryo-EM community who 
would be interested in such talks, and these might be in addition to the 
cryo-EM talks that are given within the regular Platform Sessions and Symposia. 
The Subgroup would also be able to help nominate Cryo-EM people for Society 
awards, as well as help to increase the visibility of cryo-EM within the 
Society, since many cryo-EM people have been associated with the Society for 
many years. There are also wonderful opportunities for cryo-EM people to 
interact with people using techniques ranging from molecular dynamics to 
fluorescence. So we see many benefits to having such a subgroup, and no 
downside.

To form this subgroup, we need 100 signatures from current (2015) Regular, 
Emeritus or Early Career members of the Society (unfortunately student members 
are not counted). To sign this petition, simply send an email to 
subgro...@biophysics.org indicating your 
support.

We have created a link that will allow you to see the proposed bylaws of the 
subgroup:

http://www.biophysics.org/CryoEM

If you are a member of the Society, please sign the petition! If you are not a 
member, please join so that you may then sign the petition!

Regards,
Bridget Carragher
Yifan Cheng
Edward Egelman (President of the Biophysical Society)
Irina Serysheva
David Stokes
Da-Neng Wang

Re: [ccp4bb] nVidia quadro

[David Schuller]

You could check the nVidia page of officially supported displays. It 
includes a search tab so you can check for "Built-in Emitter."

http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any of 
these products still for sale.




On 03/25/15 12:00, Andreas Schenk wrote:
Thank you for assembling all that information about NVidia 3D vision 2 
on Linux.


Is there a good list somewhere with monitors that have a built-in 
emitter and are confirmed to work under Linux?
I looked at the list at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+%28aktiv%29#xf_top 
and it seems that a lot of manufacturers are marketing their monitors 
as 3D Vision2 ready or 3D capable just because they support running at 
120 Hz, even if they don't have a built-in emitter.


Best,
Andreas


On 25.03.2015 05:16, Kay Diederichs wrote:
Sorry to come late into the discussion, and just to mention: it would 
be wrong if readers of CCP4BB get the impression that  "Quadro cards 
that support quad buffered stereo" have to be high-end. To the 
contrary, an entry-class Quadro K620 together with a €250 Nvidia 3D 
Vision 2 compatible monitor (with built-in emitter) gives you very 
nice stereo on Linux. There is more info at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo#Nvidia_3D_Vision_2 
.


To have higher resolution than 1920x1080 you may need some 
combination of higher-end monitor and (separate) emitter, and that 
would indeed require a 3-pin DIN connector and an expensive Quadro 
card. Also, an expensive Quadro is of course faster - but entry cards 
are, in contrast to popular belief, fast enough for crystallographic 
electron density + model inspection and modelling.


In summary, the computer gamers have been supporting us 
crystallographers to the point that Stereo is quite affordable.


best,

Kay

On Tue, 24 Mar 2015 18:05:20 +, Oganesyan, Vaheh 
 wrote:



Colleagues,

I’d like to thank everyone who took time to answer my question 
regarding Quadro cards that support quad buffered stereo. I now hope 
to build a workstation with >Quadro 5000.


Regards,

Vaheh Oganesyan
www.medimmune.com




--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] [OT]: Can anyone recommend a good reference for creating CVs or resumes for US biotech?

[William G. Scott]

Apologies for the (somewhat) off-topic question.

I’m trying to help someone (a virologist/immunologist) create a viable resume 
or cv for obtaining a biotech industrial job in the US.  (Since she is from the 
UK, her idea is to construct a chronological life history dump, punctuated with 
bitter sarcasm and strange verb tenses.)

If anyone has a good source for successful examples or templates, I would be 
incredibly grateful.

Many thanks in advance.

Bill





William G. Scott

http://scottlab.ucsc.edu/~wgscott

Re: [ccp4bb] nVidia quadro

[Andreas Schenk]

Thank you for assembling all that information about NVidia 3D vision 2 
on Linux.


Is there a good list somewhere with monitors that have a built-in 
emitter and are confirmed to work under Linux?
I looked at the list at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+%28aktiv%29#xf_top 
and it seems that a lot of manufacturers are marketing their monitors as 
3D Vision2 ready or 3D capable just because they support running at 120 
Hz, even if they don't have a built-in emitter.


Best,
Andreas


On 25.03.2015 05:16, Kay Diederichs wrote:

Sorry to come late into the discussion, and just to mention: it would be wrong if readers 
of CCP4BB get the impression that  "Quadro cards that support quad buffered 
stereo" have to be high-end. To the contrary, an entry-class Quadro K620 together 
with a €250 Nvidia 3D Vision 2 compatible monitor (with built-in emitter) gives you very 
nice stereo on Linux. There is more info at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo#Nvidia_3D_Vision_2 .

To have higher resolution than 1920x1080 you may need some combination of 
higher-end monitor and (separate) emitter, and that would indeed require a 
3-pin DIN connector and an expensive Quadro card. Also, an expensive Quadro is 
of course faster - but entry cards are, in contrast to popular belief, fast 
enough for crystallographic electron density + model inspection and modelling.

In summary, the computer gamers have been supporting us crystallographers to 
the point that Stereo is quite affordable.

best,

Kay

On Tue, 24 Mar 2015 18:05:20 +, Oganesyan, Vaheh  
wrote:


Colleagues,

I’d like to thank everyone who took time to answer my question regarding Quadro 
cards that support quad buffered stereo. I now hope to build a workstation with 
>Quadro 5000.

Regards,

Vaheh Oganesyan
www.medimmune.com

[ccp4bb] off-topic: different R-factor values shown in PDB page vs PDB file

[sreetama das]

Hi,Sorry for a slightly off-topic question.
I just noticed that for some pdb files, the value of R-factor shown on the PDB 
web page is different from the value in the file obtained by clicking the link 
"display file". Why is this so?
examples where I noticed:4jzc , where the PDB page 
(http://www.rcsb.org/pdb/explore/explore.do?structureId=4JZC) shows 

| R-Value:  |  0.990 (obs.)  |
|  R-Free:  |  0.248  |


while the file shows :REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R 
VALUE : 0.248 

3gkq, etc.
Any idea why this is happening ?
Thanks and regards,Sreetama
 

[ccp4bb] Ultrafast X-ray Summer School 2015 in Hamburg (application deadline: March 31)

[Sang-Kil Son]

Dear Colleagues,

We would like to remind you that the deadline for application to Ultrafast 
X-ray Summer School 2015 is approaching. UXSS 2015 will take place at DESY in 
Hamburg, Germany in the period from June 22, 2015 to June 25, 2015. UXSS 2015 
is jointly organized by the Center for Free-Electron Laser Science (CFEL) at 
DESY and the PULSE institute at SLAC National Accelerator Laboratory. The 
summer school program will be highly interdisciplinary, with topics ranging 
from accelerator physics to molecular biology. A list of speakers can be found 
at the end of this message.

http://conferences.cfel.de/uxss_2015/

Applications for participation in UXSS 2015 have been accepted. Please visit 
the above link and click on 'Application’. The application deadline is March 
31, 2015. 

Please note that the number of summer school participants will be limited. In 
order to facilitate the selection of participants, we are asking applicants to 
provide a short text describing their educational and scientific background and 
their motivation for applying for participation in UXSS 2015. The applicants 
will be asked to pay a registration fee in the amount of 100 EUR. Accepted 
applicants will receive financial support for travel and local expenses, 
provided by the VolkswagenStiftung.

Please forward this announcement to doctoral students and postdoctoral research 
associates who you think might be interested in participating in UXSS 2015.

Sincerely yours,
Sang-Kil Son, CFEL, DESY
Mariano Trigo, PULSE, SLAC


List of speakers at UXSS 2015


- Giorgio Margaritondo, EPFL, Switzerland: X-ray light sources

- Robin Santra, DESY & Univ. of Hamburg, Germany: Fundamentals of x-ray--matter 
interaction

- David Reis, SLAC & Stanford Univ., USA: Ultrafast x-ray application in 
condensed matter physics

- Linda Young, Argonne Natl. Lab., USA: Atomic and molecular physics using 
ultrafast x-rays

- Markus Gühr, SLAC, USA: Ultrafast chemical dynamics

- Simone Techert, DESY & Univ. of Göttingen, Germany: Time-resolved structural 
biology and chemistry

- Thomas White, DESY, Germany: Serial femtosecond crystallography

- Wilfried Wurth, DESY & Univ. of Hamburg, Germany: Ultrafast electronic 
dynamics in solids

- Ulf Zastrau, Univ. of Jena, Germany: Matter under extreme conditions

Re: [ccp4bb] nVidia quadro

[Kay Diederichs]

Sorry to come late into the discussion, and just to mention: it would be wrong 
if readers of CCP4BB get the impression that  "Quadro cards that support quad 
buffered stereo" have to be high-end. To the contrary, an entry-class Quadro 
K620 together with a €250 Nvidia 3D Vision 2 compatible monitor (with built-in 
emitter) gives you very nice stereo on Linux. There is more info at 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo#Nvidia_3D_Vision_2
 .

To have higher resolution than 1920x1080 you may need some combination of 
higher-end monitor and (separate) emitter, and that would indeed require a 
3-pin DIN connector and an expensive Quadro card. Also, an expensive Quadro is 
of course faster - but entry cards are, in contrast to popular belief, fast 
enough for crystallographic electron density + model inspection and modelling. 

In summary, the computer gamers have been supporting us crystallographers to 
the point that Stereo is quite affordable.

best,

Kay

On Tue, 24 Mar 2015 18:05:20 +, Oganesyan, Vaheh  
wrote:

>Colleagues,
>
>I’d like to thank everyone who took time to answer my question regarding 
>Quadro cards that support quad buffered stereo. I now hope to build a 
>workstation with >Quadro 5000.
>
>Regards,
>
>Vaheh Oganesyan
>www.medimmune.com
>