[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland

[Humberto Fernandes]

Dear all

A second postdoctoral position in the Integrated Structural Biology lab at The 
International Center for Translational Eye Research (ICTER) in Warsaw, Poland, 
is available for highly motivated biologists, biochemists, or structural 
biologists, funded until the end of 2023. The position involves cloning, 
protein production, purification, characterization, and structural elucidation 
of proteins of the phototransduction pathway and the visual cycle.

For details and how to apply, until the 11th of August, see:
https://ichf.edu.pl/en/job/mcbo-63-2022-international-centre-for-translational-eye-research-mcbo-63-2022

Feel free to spread this information at your institutes and to interested 
colleagues. And please do not hesitate to contact me if you have any questions.

Thank you, and have a great day,

Humberto



[cid:44557680-2f0c-4987-b4d6-b01cb3d577b8]

ul. Kasprzaka 44/52   www.icter.pl

01-224 Warszawa  email: 
hfernan...@ichf.edu.pl


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Re: [ccp4bb] find clashes

[Eleanor Dodson]

Sorry to go back in time but distang is useful.
You set radii
Example:

 distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb

RADI CA 1

end

will give all CA withion 2A of each other

 distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb

end

Will give all C N O S within VDW contact. -


On Thu, 14 Jul 2022 at 17:28, Kay Diederichs 
wrote:

> Hi Henrike,
>
> I use CCP4's "contact" program:
>
> #!/bin/bash
> # find bad contacts: list all CA-CA distances < 3.8A between non-adjacent
> residues
> # in a well-folded protein, these should be very rare (1 contact in 1000
> residues)
> # KD 20.12.21
> grep CA $1 > /tmp/temp.pdb
> contact xyzin /tmp/temp.pdb < COLOR/{print}' | grep -v FONT
> MODE IRES
> LIMIT 0 3.8
> EOF
> rm /tmp/temp.pdb
>
> If you are interested in non-CA atoms, modify accordingly. But this should
> give you the idea.
>
> HTH,
> Kay
>
>
> On Thu, 14 Jul 2022 17:52:40 +0200, Henrike Wagler <
> henrike.wag...@studium.uni-hamburg.de> wrote:
>
> >Dear all,
> >
> >
> >We are looking into a way to find clashes / bumps between protein chains
> >(closer than van der Waals contacts).
> >
> >Ideally, we would like to that with a script, for example, reading in a
> >pdb file, and giving back the number of clashes.
> >Of course, this is possible within Coot or PyMol, but maybe there is a
> >software as part of CCP4 that we can directly use with a script.
> >
> >Apologies if there an obvious solution that we are currently not aware of.
> >
> >Many thanks
> >
> >Best,
> >Henrike Wagler
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
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> 
>
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Re: [ccp4bb] find clashes

[Kay Diederichs]

Hi Henrike,

I use CCP4's "contact" program:

#!/bin/bash
# find bad contacts: list all CA-CA distances < 3.8A between non-adjacent 
residues
# in a well-folded protein, these should be very rare (1 contact in 1000 
residues)
# KD 20.12.21
grep CA $1 > /tmp/temp.pdb
contact xyzin /tmp/temp.pdb < wrote:

>Dear all,
>
>
>We are looking into a way to find clashes / bumps between protein chains
>(closer than van der Waals contacts).
>
>Ideally, we would like to that with a script, for example, reading in a
>pdb file, and giving back the number of clashes.
>Of course, this is possible within Coot or PyMol, but maybe there is a
>software as part of CCP4 that we can directly use with a script.
>
>Apologies if there an obvious solution that we are currently not aware of.
>
>Many thanks
>
>Best,
>Henrike Wagler
>
>
>
>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] find clashes

[Henrike Wagler]

Dear all,


We are looking into a way to find clashes / bumps between protein chains 
(closer than van der Waals contacts).


Ideally, we would like to that with a script, for example, reading in a 
pdb file, and giving back the number of clashes.
Of course, this is possible within Coot or PyMol, but maybe there is a 
software as part of CCP4 that we can directly use with a script.


Apologies if there an obvious solution that we are currently not aware of.

Many thanks

Best,
Henrike Wagler



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[ccp4bb] CCPBioSim Training Week

[Sarah Fegan - STFC UKRI]

Hi all,

We are pleased to announce that applications are now open (until 15 August) for 
the CCPBioSim Training Week. The training will take place 19-23 September 2022 
as a hybrid event in Leeds (UK) and online. The target audience is Masters and 
PhD students, but everyone is welcome to apply including industrial researchers.

Details and the registration link can be found at 
www.ccpbiosim.ac.uk/training2022.

Please feel free to forward the information to anyone who might be interested.

Best wishes,
Sarah



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[ccp4bb] Exonuclease resistant ssRNA

[Srinivasan Rengachari]

Dear all,
I am trying to reconstitute a 5' to 3' exonuclease bound to substrate RNA for 
structural studies. For this, I would like to synthesize a 40nt ssRNA 
containing a modified residue will inhibit the exonuclease activity eg: at 
position 20. I could find from the literature that using phosphorothioate or 
thiophosphate, it can be achieved. 


But, it would be very helpful to know if someone has a working strategy to 
arrest an exonuclease in this way and could share from where we can get such 
RNA synthesized. 

Many thanks in advance for all your inputs. 

Kind regards,Srinivasan







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Re: [ccp4bb] Help with One dimensional electron density calculation

[Paul Emsley]

On 13/07/2022 19:18, Ravikumar wrote:


I would like to calculate One-dimension electron density profiles of 
the different number of ions bound to an ion channel. Are there any 
programs in CCP4/ Phenix which can do the same job as the MAPMAN 
(UPPSALA electron density server) program to extract the electron 
density values to plot electron density values versus pore axis? I 
have attached an example figure.





Here's how to do it in Coot (see attached).


Paul.





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from __future__ import print_function
import math

imol = read_pdb('pdb6qkc.ent')
imol_map = read_ccp4_map('emd_4572.map', 0)
n_steps = 250

start_point = [154, 154, 133]
end_point   = [154, 154, 180]



imol_map_smooth = sharpen_blur_map_with_resampling(imol_map, 0.0, 2.3)
delta = [x - y for x, y in zip(end_point, start_point)]
delta_step = [ x/float(n_steps) for x in delta]
delta_step_size = math.sqrt(sum([x*x for x in delta_step]))

print(delta)
print(delta_step)
print(delta_step_size)

with open('line-of-density.table', 'w') as f:
for i_step in range(n_steps + 1):
p = [x + i_step * y for x, y in zip(start_point, delta_step)]
r = density_at_point(imol_map_smooth, p[0], p[1], p[2])
d = delta_step_size * i_step
f.write('{} {} {} {} {}\n'.format(p[0], p[1], p[2], d, r))

Re: [ccp4bb] Help with One dimensional electron density calculation

[Martyn Winn - STFC UKRI]

Hi,

It’s not clear why you don’t use MAPMAN if that does what you want. If 
availability is the problem, it is still here 
https://github.com/martynwinn/Uppsala-Software-Factory

If you are prepared to do some Python, then 2 other options:

https://mrcfile.readthedocs.io/en/latest/readme.html  allows you to read in MRC 
file to a numpy array, and then you can you can average, interpolate, plot as 
you wish.  If your pore axis is aligned along Z and you want to average over 
the cross section, then this would be relatively straightforward.

https://gemmi.readthedocs.io/en/latest/grid.html  will also read in maps and 
manipulate.  It understands crystal symmetry, if that is what you have. It also 
has functions for interpolation.

HTH
Martyn

From: CCP4 bulletin board  On Behalf Of Ravikumar
Sent: 13 July 2022 19:18
To: ccp4bb 
Subject: [ccp4bb] Help with One dimensional electron density calculation


Dear all,

I would like to calculate One-dimension electron density profiles of the 
different number of ions bound to an ion channel. Are there any programs in 
CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron density 
server) program to extract the electron density values to plot electron density 
values versus pore axis? I have attached an example figure.

Thank you,
Ravikumar.



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