[ccp4bb] Fixing input anisotropic scale parameters in Refmac5

[Mark Wilson]

Dear Colleagues,
I would like to run test refinements in Refmac5 where I can provide anisotropic 
scale parameters, fix them, and then proceed with restrained refinement of 
other model parameters.  I could not find how to do this in the 
documentation-is this possible?

Best regards,
Mark

Mark A. Wilson
Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine St.
Lincoln, NE 68588




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[ccp4bb] Webinar: Solving structural biology challenges with home-lab capabilities at Center for Molecular Structure

[Anasuya Adibhatla]

Dear fellow crystallographers,

Please join us in the webinar titled “Solving structural biology challenges 
with the home-lab capabilities at the Centre of Molecular Structure”
Link: 
https://www.excillum.com/communications/webinars/solving-structural-biology-challenges-with-the-home-lab-capabilities-at-cms/

View this email in your 
browser


[https://mcusercontent.com/fe7f3bc92445f225a8ec91149/images/fbbe4b27-aa68-47f6-93a4-25dca6b002fe.png]
[https://mcusercontent.com/fe7f3bc92445f225a8ec91149/images/a30505ee-a989-4a5b-88cb-64838ee7e3d8.jpg]


Solving structural biology challenges with the home-lab capabilities at CMS

Date: April 28
Time: 3 pm CEST


[https://mcusercontent.com/fe7f3bc92445f225a8ec91149/images/c3660e1e-2c3e-4fee-b875-7d8106492fb9.jpg]
[https://mcusercontent.com/fe7f3bc92445f225a8ec91149/images/7b9575c2-3498-407e-a4bf-c3d126ead829.jpg]

Speakers: Dr Jan Dohnálek, guarantor and head of CMS, Dr Jan Stránský, head of 
CF Diffraction techniques at CMS, and Dr Cyril Barinka, Institute of 
Biotechnology, Laboratory of Structural Biology.

The Centre of Molecular Structure (CMS) provides services and access to 
state-of-art instruments, which cover a wide range of techniques required by 
not only structural biologists. CMS operates as part of the Czech 
Infrastructure for Integrative Structural Biology (CIISB), and European 
infrastructures Instruct-ERIC and MOSBRI. CMS is organized in 5 core 
facilities: CF Protein Production , CF Biophysics, CF Crystallization of 
proteins and nucleic acids, CF Diffraction techniques, and CF Structural Mass 
Spectrometry.

[https://mcusercontent.com/fe7f3bc92445f225a8ec91149/images/17d88c34-899c-4f0b-ad6d-fe0163902f17.png]
CF Diffraction techniques employs two laboratory X-ray instruments equipped 
with high flux MetalJet X-ray 

[ccp4bb] PostDoc Postion for Time-Resolved Serial Synchrotron Crystallography at ESRF ID29

[Daniele de Sanctis]

Hi  all,

we are currently looking for a motivated PostDoc researcher to join the
ID29 upgrade team at the ESRF and contribute to develop
novel sample delivery systems and tools for time resolved serial
crystallography experiments.

The new ID29 is currently being upgraded in a new serial time-resolved
crystallography beamline that can fully profit from the ESRF Extremely
Brilliant Source. The beamline will deliver >10^15 ph/s in a submicron beam
size with a wide band pass monochromator and allow for exposure time of a
few microseconds. It is equipped with the latest generation MD3upSSX and a
Jungfrau detector (more information are presented here
https://www.youtube.com/watch?app=desktop=B1fB9xvouLE).

Applications should be submitted to the ESRF portal
https://esrf.gestmax.eu/1500/1/postdoc-id29/en_US?backlink=search

Best regards


Daniele



ἀρετή
---
Daniele de Sanctis
Structural Biology Group
ESRF - The European Synchrotron
Grenoble, France
Tel 33 (0)4 76 88 2869

http://www.esrf.eu/id29



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Re: [ccp4bb] Job opportunity for structural biologists and biophysicists at Vertex Pharmaceuticals in Oxford - new link

[Liz Carpenter]

Dear All,
Following on from my previous posting we have one more position to fill at 
Vertex for a structural biologist with experience in biophysics, structural 
biology and protein biochemistry to join our expanding team in Oxford.
Experience in working with challenging membrane proteins and protein complexes, 
using both cryo-EM and crystallography, would be advantageous for these roles.

If you have a passion for tackling difficult targets and being involved in 
developing therapies for patients with serious genetic diseases, please follow 
the link below to learn more about this position.

https://vrtx.wd5.myworkdayjobs.com/Vertex_Careers/job/Oxford-United-Kingdom/Structural-Biology-and-Biophysics-Research-Scientist_REQ-11435-2

With best wishes,
Liz Carpenter



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immediately by replying to this message, and destroy all copies of this message 
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[ccp4bb] Open position for a Biochemist/Assay Development Scientist at FoRx Therapeutics

[Sotirios Sotiriou]

Dear All,



FoRx Therapeutics is a privately held drug discovery company based in Basel, 
Switzerland. The company focuses on drugging key molecular targets involved in 
DNA Replication Stress, which constitutes an exciting and innovative approach 
in the development of novel anticancer drugs. FoRx is backed by a syndicate of 
investors that include the Novartis Venture Fund, Pfizer Ventures, M Ventures, 
Omega Funds and LSP Venture Capital.



We are looking for a highly motivated and skilled Biochemist / Assay 
Development Scientist to join our growing team. This is an exciting opportunity 
to become an integral part of an innovative and dynamic start-up company.



Key responsibilities of this role include, but are not limited to:



* Expression and purification of recombinant proteins

* Develop and perform a diverse set of biochemical assays, in 
particular enzymatic (e.g. enzyme activity and kinetics) and substrate binding 
assays

* Design biophysics-grade protein constructs and pilot / contribute to 
the optimization of purification protocols

* Screen small molecule ligands on purified protein in microplate-based 
assay formats to drive the understanding of SAR relationships using manual and 
automated systems

* Crystallize or work in close collaboration with crystallographers to 
crystallize protein-ligand complexes in support of structure-aided drug 
development

* Organize experimental results to be shared with project teams; 
maintain clear experimental records using ELN (electronic lab notebook)



Qualifications:



* Recent PhD degree in Biochemistry or similar (e.g. Structural Biology)

* 1-2 years of relevant experience in industry would be a strong plus

* Profound experience and hands-on expertise in biochemical assays, 
enzyme kinetics and substrate binding assays

* Experience in recombinant protein production using different 
expression systems, including construct design and optimization

* Experience in using biophysical assays (SPR, ITC, DSF, etc.) for 
probing protein-ligand interactions

* Expertise in X-ray protein crystallography would be an asset

* First author publication in a relevant journal is required

* Flexible, proactive, efficient, and able to work independently with a 
problem-solving attitude

* Strong team player, high-energy and positive personality

* Fluent in written and spoken English



The successful candidate will be an enthusiastic, self-driven individual who is 
flexible and responsive to the changing needs of a dynamic entrepreneurial 
organization, has the ability to communicate effectively, is an excellent fit 
to an agile and growing biotech team, and has the ambition to perform 
outstandingly.



FoRx Therapeutics encourages and supports a diverse work environment as an 
Equal Opportunity Employer, offering a stimulating work environment and a 
competitive compensation package.



Interested candidates should send a cover letter describing research interests 
and career goals, along with a Curriculum Vitae to:



  h...@forxtherapeutics.com



Kind regards,

Sotirios



- - -

Sotirios K. Sotiriou, PhD

Head of Biology, FoRx Therapeutics AG

WSJ350.3.05, Lichtstrasse 35

4056 Basel, Switzerland

www.forxtherapeutics.com





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Re: [ccp4bb] Coot crashes on CentOS 7.9

[Kay Diederichs]

Dear Karthik,

your processor came out in 2008, and it seems that Paul Emsley used compiler 
options that require newer capabilities than this processor has, likely in an 
attempt to speed up coot. Wikipedia says that AVX came out in 2011 and AVX2 in 
2013, so your processor supports neither extension.

Do you still get

*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.

?

The way to debug this is to run
glxinfo
in a terminal and to compare the output (it is 1078 lines for my machine ...) with that from a machine where the NVidia graphics works well. The 
start of the output is most important and should agree; this is the output for my machine:


name of display: :0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:
...

Later it talks about the specific card and driver version; this will of course 
differ from yours:
...
Memory info (GL_NVX_gpu_memory_info):
Dedicated video memory: 8192 MB
Total available memory: 8192 MB
Currently available dedicated video memory: 7763 MB
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: Quadro P4000/PCIe/SSE2
OpenGL core profile version string: 4.6.0 NVIDIA 460.56
OpenGL core profile shading language version string: 4.60 NVIDIA
OpenGL core profile context flags: (none)
OpenGL core profile profile mask: core profile
OpenGL core profile extensions:
GL_AMD_multi_draw_indirect, GL_AMD_seamless_cubemap_per_texture,
...

The ElRepo NVidia driver has worked well for us, but the driver directly from 
NVidia should also be fine - but needs manual work after updating the kernel 
IIRC.

Best wishes,
Kay

Am 22.04.2021 um 14:13 schrieb Karthikeyan Subramanian:

Dear Kay,

Thanks for the suggestions.

The model name for the computer is "Intel(R) Xeon(R) CPU E5440  @ 2.83GHz".

As suggested, I downloaded and installed the latest ccp4 (7.1) which bundles 
with coot 0.9.5. The coot works just fine with the latest ccp4 bundle.

I used the graphic driver from Nvidia package. I will try to use NVidia 

driver from ELRepo.


Time being I will use the one bundled with CCP4-7.1.

Once again thanks for the help.

With regards

Karthik



On 22-04-2021 02:18 pm, Kay Diederichs wrote:

Dear Karthikeyan Subramanian,

which processor does your computer have? Look at the output of e.g. "head -20 
/proc/cpuinfo". What is "model name"?

To my understanding, the main problem is


*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin

This means that the compiler, when producing the coot binary, used instructions that your 
processor does not understand (in the /proc/cpuinfo output, some flags would be missing). 
This happens on old AMD processors (unless such an old processor is also used when 
compiling), and is the reason why CCP4 has its own distribution for these: go to 
http://www.ccp4.ac.uk/download/#os=linux and scroll down to "Legacy systems". 
If you indeed have an old AMD, just install CCP4 from there - CCP4 currently (at least 
the non-legacy distribution) has coot 0.9.5 .

The other problem is

*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.
which points to the graphics driver; it is not properly installed. Are 

you using the NVidia driver from ElRepo? If not, you should try that.


hope this helps,
Kay

On Thu, 22 Apr 2021 13:27:39 +0530, Karthikeyan Subramanian 
 wrote:


Dear CCP4 members,

I am trying to install the
coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with
Nvidia Quadro FX 4800 graphics card.

Coot crashes soon after launching the window.  The log file is shown
below. Not sure what is missing. The only error I can see is

*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin
"$@"".
*

The older version of coot (0.8.9.2) is working fine on the same machine.

Thanks for the help.

With regards

Karthik

IMTECH, Chandigarh


==

xray6 <1:14pm> 8% pwd
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin
xray6 <1:14pm> 9% ./coot

(coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004:
g_object_set_is_valid_property: object class 'GtkSettings' has no
property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/home/programs/linux/ccp4-7.0/lib/data/monomers/
There are 153 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in

[ccp4bb] PhD position in structural biology of RNA viruses

[moshe dessau]

Dear CCP4 community,
We are looking for enthusiastic team members that want to pursue their PhD in 
the field of structural biology of RNA viruses. Our main interest is the 
mechanism of various processes in RNA viruses infection cycle. Understanding 
virus infection on the molecular and atomic level is fundamental for 
strategizing new counter measures against these viruses. In the lab we are 
using X-ray crystallography, cryoEM, biophysics, biochemistry, cell biology and 
molecular biology methods to understand viruses entry to their host cell, 
membrane fusion, assembly, evasion and more.
If you are passionate about high resolution mechanistic understanding, you 
belong with us!
Our state-of-the-art lab and facilities (Part of the new Azrieli’s Faculty of 
Medicine, Bar Ilan University) are located in the beautiful northern district 
of Israel (the Galilee).
To apply for a position please send an E-mail to: 
moshe.des...@biu.ac.il  and attach your CV and a 
short statement describing your motivation.
We look forward to hearing from you,
Moshe Dessau, PhD.

_
Moshe Dessau, Ph.D.Tel: +972-72-264-4905
Head, The Laboratory of Structural Biology of Infectious Diseases
The Azrieli Faculty of Medicine
Bar-Ilan University
8 Henrietta Szold St.
Safed, 1311502
Israel
E-mail:moshe.des...@biu.ac.il
Website: http://www.dessaulab.com
Skype: dessaumo




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Re: [ccp4bb] Coot crashes on CentOS 7.9

[Karthikeyan Subramanian]

Dear Kay,

Thanks for the suggestions.

The model name for the computer is "Intel(R) Xeon(R) CPU E5440  @ 2.83GHz".

As suggested, I downloaded and installed the latest ccp4 (7.1) which 
bundles with coot 0.9.5. The coot works just fine with the latest ccp4 
bundle.


I used the graphic driver from Nvidia package. I will try to use NVidia 
driver from ELRepo.


Time being I will use the one bundled with CCP4-7.1.

Once again thanks for the help.

With regards

Karthik



On 22-04-2021 02:18 pm, Kay Diederichs wrote:

Dear Karthikeyan Subramanian,

which processor does your computer have? Look at the output of e.g. "head -20 
/proc/cpuinfo". What is "model name"?

To my understanding, the main problem is


*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin

This means that the compiler, when producing the coot binary, used instructions that your 
processor does not understand (in the /proc/cpuinfo output, some flags would be missing). 
This happens on old AMD processors (unless such an old processor is also used when 
compiling), and is the reason why CCP4 has its own distribution for these: go to 
http://www.ccp4.ac.uk/download/#os=linux and scroll down to "Legacy systems". 
If you indeed have an old AMD, just install CCP4 from there - CCP4 currently (at least 
the non-legacy distribution) has coot 0.9.5 .

The other problem is

*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.

which points to the graphics driver; it is not properly installed. Are you 
using the NVidia driver from ElRepo? If not, you should try that.

hope this helps,
Kay

On Thu, 22 Apr 2021 13:27:39 +0530, Karthikeyan Subramanian 
 wrote:


Dear CCP4 members,

I am trying to install the
coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with
Nvidia Quadro FX 4800 graphics card.

Coot crashes soon after launching the window.  The log file is shown
below. Not sure what is missing. The only error I can see is

*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin
"$@"".
*

The older version of coot (0.8.9.2) is working fine on the same machine.

Thanks for the help.

With regards

Karthik

IMTECH, Chandigarh


==

xray6 <1:14pm> 8% pwd
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin
xray6 <1:14pm> 9% ./coot

(coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004:
g_object_set_is_valid_property: object class 'GtkSettings' has no
property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/home/programs/linux/ccp4-7.0/lib/data/monomers/
There are 153 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in 

[ccp4bb] Instruct-ERIC Landscape Survey

[Claudia Alén Amaro]

Dear All

Instruct-ERIC is a European Research Infrastructure, providing researchers with 
access to high-end structural biology technologies and expertise, as well as 
enabling access to this equipment and expertise through an infrastructure 
distributed throughout Europe, with 15 members across the continent.



Structural Biology is currently in the middle of a revolution enabled by 
significant technology advances in recent years (direct electron detectors in 
EM, advances in synchrotron sources and detectors, XFELs, ultra-high field NMR, 
super-resolution cryo-light microscopy etc). For this reason, Instruct-ERIC is 
reviewing the structural biology capabilities within Europe to individuate 
possible updates in order to fully respond to the needs of the structural 
biology community.



It is thus important for us to have your feedback to support this activity: 
please fill in this short survey, and 
circulate it to your structural biology colleagues.



[https://instruct-eric.eu/upload/43sOqLXHCPI20ahXolUu3nhxBZkIu1ml.png]



Thank you for providing your feedback!



Instruct-ERIC Landscape Working Group



Dr Claudia Alén Amaro
Senior Project Manager

[instructlogo]

Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, 
UK.
Telephone: +44 (0) 1865 987629 +44 (0) 7494060412
Website: instruct-eric.org
Twitter: @instructhub



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Re: [ccp4bb] Coot crashes on CentOS 7.9

[Kay Diederichs]

Dear Karthikeyan Subramanian,

which processor does your computer have? Look at the output of e.g. "head -20 
/proc/cpuinfo". What is "model name"?

To my understanding, the main problem is

> >*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin

This means that the compiler, when producing the coot binary, used instructions 
that your processor does not understand (in the /proc/cpuinfo output, some 
flags would be missing). This happens on old AMD processors (unless such an old 
processor is also used when compiling), and is the reason why CCP4 has its own 
distribution for these: go to http://www.ccp4.ac.uk/download/#os=linux and 
scroll down to "Legacy systems". If you indeed have an old AMD, just install 
CCP4 from there - CCP4 currently (at least the non-legacy distribution) has 
coot 0.9.5 .

The other problem is
>*** Cannot find the double-buffered visual.
>*** Trying single-buffered visual.
which points to the graphics driver; it is not properly installed. Are you 
using the NVidia driver from ElRepo? If not, you should try that.

hope this helps,
Kay

On Thu, 22 Apr 2021 13:27:39 +0530, Karthikeyan Subramanian 
 wrote:

>Dear CCP4 members,
>
>I am trying to install the
>coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with
>Nvidia Quadro FX 4800 graphics card.
>
>Coot crashes soon after launching the window.  The log file is shown
>below. Not sure what is missing. The only error I can see is
>
>*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin
>"$@"".
>*
>
>The older version of coot (0.8.9.2) is working fine on the same machine.
>
>Thanks for the help.
>
>With regards
>
>Karthik
>
>IMTECH, Chandigarh
>
>
> ==
>
>xray6 <1:14pm> 8% pwd
>/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin
>xray6 <1:14pm> 9% ./coot
>
>(coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004:
>g_object_set_is_valid_property: object class 'GtkSettings' has no
>property named 'gtk-application-prefer-dark-theme'
>INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
>/home/programs/linux/ccp4-7.0/lib/data/monomers/
>There are 153 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif
>There are 2 data in
>/home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/C.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/G.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/u/U.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DA.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DC.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DG.cif
>There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DT.cif

[ccp4bb] Last day to apply: Scientific Coordinator Coronavirus Structural Task Force

[Andrea Thorn]

Dear colleagues,
We are looking for a scientific coordinator for the Coronavirus
Structural Task Force (www.insidecorona.de).
The position is 50% part-time, can mostly be done remotely, and requires
German and English language skills as well as a Masters degree or
comparable in a relevant subject. The salary is 50% TVL-13 with
appropriate qualification.
If you are - or know - someone who is interested, you can find more
infos here:

uhh.de/cst-coordinator

Best wishes,


Andrea.

--
Dr. Andrea Thorn | group leader
andrea.th...@uni-hamburg.de

HARBOR (Institute for Nanostructure and Solid State Physics),
Universität Hamburg
Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany
Tel. +49 (0)40 42838 3651



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[ccp4bb] Coot crashes on CentOS 7.9

[Karthikeyan Subramanian]

Dear CCP4 members,

I am trying to install the 
coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with 
Nvidia Quadro FX 4800 graphics card.


Coot crashes soon after launching the window.  The log file is shown 
below. Not sure what is missing. The only error I can see is


*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin 
"$@"".

*

The older version of coot (0.8.9.2) is working fine on the same machine.

Thanks for the help.

With regards

Karthik

IMTECH, Chandigarh


===

xray6 <1:14pm> 8% pwd
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin
xray6 <1:14pm> 9% ./coot

(coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004: 
g_object_set_is_valid_property: object class 'GtkSettings' has no 
property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: 
/home/programs/linux/ccp4-7.0/lib/data/monomers/
There are 153 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif

There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in 
/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HOH.cif

There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/n/NA.cif
Spacegroup: P 1

*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.

(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported
INFO:: coot_python initialized
Running python script 
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py

Good Afternoon Person with no name, Welcome to Coot version 0.9.5
(set-display-intro-string "Good Afternoon Person with no name, Welcome 
to Coot version 0.9.5")

Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
(use-graphics-interface-state)
Running python script /home/skarthik/.coot-preferences/0-coot-history.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-display-intro-string "Good Afternoon Person with no name, Welcome 
to Coot version 0.8.9.2")

(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)

[ccp4bb] Positions in time-resolved structural biology at the Paul Scherrer Institut

[PSI]

Excited about following protein movements using the latest large-scale X-ray 
facilities in Switzerland? Please take a minute to look into our open positions 
for postdocs and a tenure-track scientist. Separate PhD applications are also 
welcome through the Life Science Zurich Graduate school or directly to me.

PhD candidates interested to learn structural biology in an interdisciplinary 
environment
https://www.bsm.uzh.ch/application/

Postdoc interested in expression and crystallization of GPCRs
https://www.psi.ch/en/pa/job-opportunities/44148-postdoctoral-fellow

Postdoc interested in serial crystallographic data processing and structure 
interpretation
https://www.psi.ch/en/pa/job-opportunities/44151-postdoctoral-fellow

Tenure-track scientist with focus on sample injection and instrumentation
https://www.psi.ch/en/pa/job-opportunities/44632-scientist-tenure-track

All the best,
Joerg

__
Dr. Jörg Standfuss
Time-resolved Crystallography
Paul Scherrer Institute
CH-5232 Villigen PSI
+41-56-310-2586
www.psi.ch/lbr/standfuss-joerg




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