Re: [ccp4bb] How to compare between electron density maps?

[Pavel Afonine]

phenix.match_maps can overlay model B and map B onto model A and map A. A
and B can be any symmetry and box (unit cell) dimensions. Model A and map A
stay in its original frame of reference. Let me know should you have
questions.

Pavel

On Mon, May 11, 2020 at 3:19 PM Murpholino Peligro 
wrote:

> I want to compare electron density features of map A from protein A and
> map B from protein B...
>
> Because each map has a different rmsd level...
>
> ...what is the best way to compare electron density between maps?
>
> Is there a way to normalize maps or something like that?
>
> Thanks
>
> --
>
> 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] CryoEM Research Scientist Position at Vertex Pharmaceuticals

[Alexander Kintzer]

Hello All,

Vertex Pharmaceuticals is seeking a highly motivated and experienced Cryo
Electron Microscopy (CryoEM) Data Scientist to join our San Diego Protein
Sciences team.

The individual will develop and implement state-of-the-art algorithms and
methods to optimize and improve current CryoEM structural biology workflows
to deliver high resolution structures of proteins within and outside its
cellular context. This includes the development, automation and
implementation of efficient approaches for CryoEM data collection, image
processing, 3D-structure determination, and analysis.

If you are interested, please apply via the following link and/or respond
to this post.

https://www.linkedin.com/jobs/view/1843496166/

Thank you,
Alex Kintzer, Ph.D.

Research Scientist II

*Vertex Pharmaceuticals*
3215 Merryfield Row, San Diego, CA 92121



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Re: [ccp4bb] How to compare between electron density maps?

[00000c2488af9525-dmarc-request]

Hello, you certainly could normalise maps (i.e. have a map of (density minus average)/rms) with mapman in the Uppsala suite and you can ask Phenix to make the electron electron density normalised when it generates a map (set "map scaling" to "sigma"). The web suggests you can do it with XDLmapman, if you can get hold of it since its deprecated. I wrote a 'jiffy' to do it for ccp4 and x-plor maps but the output is x-plor format. Drop me a line if any interest (or just google for "maidaid map ucl" and the page comes up as top hit). Mapman also used to allow maps to be compared by correlation coefficient. Probably I missed the point of your question but hope some of this helps.Jon CooperOn 11 May 2020 23:18, Murpholino Peligro  wrote: I want to compare electron density features of map A from protein A and map B from protein B...Because each map has a different rmsd level... ...what is the best way to compare electron density between maps?Is there a way to normalize maps or something like that?Thanks


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On 11 May 2020 23:18, Murpholino Peligro  wrote: I want to compare electron density features of map A from protein A and map B from protein B...Because each map has a different rmsd level... ...what is the best way to compare electron density between maps?Is there a way to normalize maps or something like that?Thanks


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On 11 May 2020 23:18, Murpholino Peligro  wrote: I want to compare electron density features of map A from protein A and map B from protein B...Because each map has a different rmsd level... ...what is the best way to compare electron density between maps?Is there a way to normalize maps or something like that?Thanks


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On 11 May 2020 23:18, Murpholino Peligro  wrote: I want to compare electron density features of map A from protein A and map B from protein B...Because each map has a different rmsd level... ...what is the best way to compare electron density between maps?Is there a way to normalize maps or something like that?Thanks


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On 11 May 2020 23:18, Murpholino Peligro  wrote: I want to compare electron density features of map A from protein A and map B from protein B...Because each map has a different rmsd level... ...what is the best way to compare electron density between maps?Is there a way to normalize maps or something like that?Thanks


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[ccp4bb] How to compare between electron density maps?

[Murpholino Peligro]

 I want to compare electron density features of map A from protein A and
map B from protein B...

Because each map has a different rmsd level...

...what is the best way to compare electron density between maps?

Is there a way to normalize maps or something like that?

Thanks



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[ccp4bb] NSLS II is accepting Rapid Access Proposals for COVID-19 related research

[Stojanoff, Vivian]

Dear All


Hope that you and your family are doing well,



NSLS-II is offering a streamlined and expedited rapid access proposal process 
for groups that require beam time for structural biology projects directly 
related to COVID-19.


The Center for Biomolecular Structure 
team is supporting remote macromolecular crystallography experiments at the AMX 
and FMX beamlines as well as solution scattering experiments at the LiX 
beamline.



Use the COVID-19 Rapid Access 
form to submit a 
proposal for COVID-19 related research.


Do not hesitate to contact us if we can help with any questions


Kind regards,



Your CBMS Team,

Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e nsls.lifescien...@gmail.com; 
lifescie...@bnl.gov
w https://www.bnl.gov/ps/lifesciences/
BNL | Center for Biomolecular Structure
The Center is embedded in the National Synchrotron Light Source II (NSLS-II), a 
state-of-the-art synchrotron light source located at the U.S. Department of 
Energy’s (DOE) Brookhaven National Laboratory and adjacent to the Laboratory of 
BioMolecular Structure (LBMS), an advanced cryo-electron microscopy center.
www.bnl.gov





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[ccp4bb] Online Course on Neutron Scattering Applications in Structural Biology

[Meilleur, Flora]

ORNL Online Course on Neutron Scattering Applications in Structural Biology 
(https://conference.sns.gov/event/217/)

June 1 - June 5, 2020

2:00 pm - 5:30 pm EST

Registration (free) is now open and will close May 17, 2020.

This online course is designed for graduate students, post-doctoral researchers 
and faculty with knowledge of structure and function of biological 
macromolecules but with limited to no experience with neutron sciences. The 
course will cover the basics of deuterium labeling, small angle neutron 
scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and 
neutron crystallography. Instrumentation, sample preparation, data collection 
and processing will be introduced for each neutron technique.




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[ccp4bb] Call for Microscope Time Proposals at the Stanford-SLAC Cryo-EM Center (S2C2)

[Dunn, Lisa B.]

June 1, 2020 is the next deadline for submitting proposals for microscope time 
at the Stanford-SLAC Cryo-EM Center (S2C2).

Additional electron cryo-microscope capacity is in place at our facility.  We 
hope to resume regular user operations in June in a phased approach beginning 
with remote data collection.   Information about the project application 
process is available at:  
https://cryoem.slac.stanford.edu/s2c2/project-requests .  Register in the user 
portal at https://userportal.slac.stanford.edu/ to submit your proposal.

If you have any questions about your application, including our preliminary 
data and biosafety requirements, please feel free to send a message to 
s...@slac.stanford.edu.

The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators


The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Fw: DIALS error

[Demou, Maria]

From: Demou, Maria 
Sent: Monday, May 11, 2020 3:33 PM
To: matthew.rodrig...@diamond.ac.uk 
Subject: Re: DIALS error

I believe the expected unit cell is 222 212121, space group P1. I tried 
increasing the max cell but still no results..


From: matthew.rodrig...@diamond.ac.uk 
Sent: Monday, May 11, 2020 2:04 PM
To: Demou, Maria 
Subject: DIALS error

Hi Maria,


I'm not an expert but have had the same problem before. Do you know the 
expected unit cell?


Sometimes the max_cell is automatically set too low. I would try re-running the 
job and manually set the max_cell to 200 or something and see if it runs to 
completion.


Good luck!


Matt.

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Re: [ccp4bb] DIALS error

[Fuentes-Montero, Luis (DLSLtd,RAL,LSCI)]

Dear Maria,

The files  3_experiments,expt and 3_reflections.refl nust be inside the 
directory dui_files created by dui

warmest regards,

Luiso.

From: CCP4 bulletin board  on behalf of Winter, Graeme 
(DLSLtd,RAL,LSCI) 
Sent: 11 May 2020 14:58
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] DIALS error

Dear Maria

Please could you send (off list) the 3_experiments,expt and 3_reflections.refl 
files? Happy to take a look. I expect it’s related to your experiment geometry 
(beam centre or similar)

Thanks Graeme

On 11 May 2020, at 14:22, Demou, Maria 
mailto:maria.demou...@ucl.ac.uk>> wrote:

Hello,
I am very new to DIALS, and I have been trying to index these images, however 
whatever parameters I put there is no suitable lattice. I used half the images 
as the rest I was told had radiation damage, but still there is no result.



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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and not 
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are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] DIALS error

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear Maria

Please could you send (off list) the 3_experiments,expt and 3_reflections.refl 
files? Happy to take a look. I expect it’s related to your experiment geometry 
(beam centre or similar)

Thanks Graeme

On 11 May 2020, at 14:22, Demou, Maria 
mailto:maria.demou...@ucl.ac.uk>> wrote:

Hello,
I am very new to DIALS, and I have been trying to index these images, however 
whatever parameters I put there is no suitable lattice. I used half the images 
as the rest I was told had radiation damage, but still there is no result.



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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

[lyguo]

The Multiscale Research Institute for Complex Systems (MRICS) at Fudan 
University is located at the Zhangjiang Campus of Fudan University and is 
supported by the Shanghai High-level Talents Program.  MRICS is strongly 
committed to the development of novel and effective multi-scale imaging 
technology that spans microscopic molecular structures all the way to 
macroscopic medical imaging, with the aim to provide unprecedented spatial and 
temporal insights into the structures and functions of living beings at all 
levels (molecules, cells, tissues, organs and even whole organisms).  
Specifically for structural biology, MRICS is equipped with a state-of-the-art 
cryo-EM facility that includes FEI Titan Krios with Volta phase plate, Glacios, 
Talos and Aquilos.  MRICS is also located next to Shanghai Synchrotron 
Radiation Facility for X-ray crystallography.
 
Our team includes Nobel laureate and international leading interdisciplinary 
experts.
 
We have new openings for multiple postdoctoral fellows in structural biology 
who will mainly study important biological systems by means of cryo-electron 
microscopy including single-particle and tomography. 
   
Requirements: 
 
The applicants should have a recent Ph.D. degree (within two years of 
graduation) or will have a Ph.D. degree within the next six months in biology 
or chemistry-related fields, be devoted to excellence in scientific research, 
have strong sense of responsibility, and be highly motivated and hardworking.  
For these positions, extensive experience in protein expression and 
purification is a must, while prior experience in X-ray crystallography or 
cryo-EM is a plus, but is not required.  
 
Compensation: 
 
1)We offer internationally competitive salary, fringe benefits and yearly 
bonus.  The level of salary will be determined according to the applicant's 
experience and qualification; 
2)Low-rent housing on campus is provided; 
3)There are ample opportunities to collaborate with world-renown 
laboratories;
4)We provide support for applying for funding opportunities whenever 
applicable.  
 
Shanghai is one of the most cosmopolitan cities in China with strong economy 
and vibrant scientific community. 
 
For interested applicants, please submit postdoctoral application packages (a 
combined pdf) including resumes, representative publications, phone numbers and 
email addresses of three academic referees to mrics...@fudan.edu.cn.
 
We look forward to your joining of our first-class team!



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