Re: [ccp4bb] ALS Colloquium Seminar - starting now!

[James Holton]

Talk on laser plasma x-ray light sources starting in 5 min!

Here's the zoom link. Open to all.

https://lbnl.zoom.us/j/95338327083



On 9/29/2021 12:24 PM, James Holton wrote:

Greetings all,

This year I have the honor of co-organizing the ALS Colloquium Seminar 
series. This is normally a local but broad-audience forum for users of 
the Advanced Light Source to learn more about what other users are 
doing. But, now that its gone virtual you can all join in and listen 
to what I think will be some very interesting talks. Maybe even ask a 
question? Its not easy finding speakers that appeal to a broad range 
of scientist ranging from biologists to gravel monkeys and chemists, 
but what we have in common is we all need light.  Today's speaker at 
3pm California time is LBL's own Jeroen van Tilborg talking about his 
Laser Plasma Accelerators. Yes, those are a real thing, and 
potentially could be ultra-compact light sources in the future. He 
will tell you about the latest developments.

Zoom links on this page:
https://als.lbl.gov/news-events/seminars/

Coming soon are many other exciting speakers I am proud to have 
brought to this series, including two of my users:
Jennifer Dounda, will be on at 3pm Oct 27, 2021, talking about her 
Nobel Prize winning research on CRISPR.
Erica Saphire will be on at 3pm Dec 8, 2021, talking about bringing 
antibody technology from all over the world together to fight SARS-CoV-2.


I think we've got a pretty good lineup!

-James Holton
MAD Scientist





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/

[ccp4bb] Security blockage: CCP4 installation on macOS Big Sur

[Yong Tang]

Dear all,

I downloaded the latest mac version of CCP4 suite for installation on a new
Mac (macOS Big Sur Version 11.5.2). The package was downloaded using
Chrome. After unpacking and moving the folder to its destination
/Applications/ccp4-7.1, the set up using

./BINARY.setup

gives error messages that the app was downloaded via Chrome and that "macOS
cannot verify that this app is free from malware".

I tried using "sudo" but that didn't help.

Do you have a quick pointer for me?

Many thanks, -yong



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/

[ccp4bb] ALS Colloquium Seminar today! - in 2.5 hours

[James Holton]

Greetings all,

This year I have the honor of co-organizing the ALS Colloquium Seminar 
series. This is normally a local but broad-audience forum for users of 
the Advanced Light Source to learn more about what other users are 
doing. But, now that its gone virtual you can all join in and listen to 
what I think will be some very interesting talks. Maybe even ask a 
question? Its not easy finding speakers that appeal to a broad range of 
scientist ranging from biologists to gravel monkeys and chemists, but 
what we have in common is we all need light.  Today's speaker at 3pm 
California time is LBL's own Jeroen van Tilborg talking about his Laser 
Plasma Accelerators. Yes, those are a real thing, and potentially could 
be ultra-compact light sources in the future. He will tell you about the 
latest developments.

Zoom links on this page:
https://als.lbl.gov/news-events/seminars/

Coming soon are many other exciting speakers I am proud to have brought 
to this series, including two of my users:
Jennifer Dounda, will be on at 3pm Oct 27, 2021, talking about her Nobel 
Prize winning research on CRISPR.
Erica Saphire will be on at 3pm Dec 8, 2021, talking about bringing 
antibody technology from all over the world together to fight SARS-CoV-2.


I think we've got a pretty good lineup!

-James Holton
MAD Scientist



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/

Re: [ccp4bb] Add hydrogens

[Sam Tang]

Have just tried out some of the options -- done within minutes! Many thanks
for the numerous input!

All the best

Sam


On Wed, 29 Sept 2021 at 19:03, Sam Tang  wrote:

> Dear community
>
> This may appear to be a silly question -- I am trying to add hydrogens to
> the structure in PDB 1CDW. My initial thought is to run a single run of
> refinement with a refinement program. It happens that I cannot locate the
> map coefficients under the entry (am I missing something?) So... is there
> an easy way to do what I want in this case?
>
> Warm regards
>
> Sam
>



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/

Re: [ccp4bb] Add hydrogens

[Paul Emsley]

On 29/09/2021 12:03, Sam Tang wrote:



This may appear to be a silly question -- I am trying to add hydrogens 
to the structure in PDB 1CDW. My initial thought is to run a single 
run of refinement with a refinement program.[...] So... is there an 
easy way to do what I want in this case?




Calculate -> Modelling -> Add Hydrogen Atoms

(using Coot)

Paul



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/

Re: [ccp4bb] [External] [ccp4bb] Add hydrogens

[Srivastava, Dhiraj]

Even pymol and chimera can add hydrogen. Sorry I understand it’s ccp4bb forum 
and i am talking about chimera and pymol.
Depending on you need, you can do energy minimization in chimera as well.

Dhiraj


From: CCP4 bulletin board  on behalf of Sam Tang 

Sent: Wednesday, September 29, 2021 6:03 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] [ccp4bb] Add hydrogens

Dear community

This may appear to be a silly question -- I am trying to add hydrogens to the 
structure in PDB 1CDW. My initial thought is to run a single run of refinement 
with a refinement program. It happens that I cannot locate the map coefficients 
under the entry (am I missing something?) So... is there an easy way to do what 
I want in this case?

Warm regards

Sam



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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/

Re: [ccp4bb] Add hydrogens

[Tim Gruene]

Dear Sam,

refmac5 has the option of 'geometry optimisation', which doesn't
require data. I would assume that you can ask refmac5 to write out the
hydrogen atoms for the resulting PDB file.

Best regards,
Tim

On Wed, 29 Sep 2021 19:03:47 +0800 Sam Tang 
wrote:

> Dear community
> 
> This may appear to be a silly question -- I am trying to add
> hydrogens to the structure in PDB 1CDW. My initial thought is to run
> a single run of refinement with a refinement program. It happens that
> I cannot locate the map coefficients under the entry (am I missing
> something?) So... is there an easy way to do what I want in this case?
> 
> Warm regards
> 
> Sam
> 
> 
> 
> 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/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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/


pgpKgCsmgnogX.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] Add hydrogens

[Marcin Wojdyr]

Dear Sam,

if you want to add hydrogens on "riding" positions in the same way that
Refmac adds them, here is a command that aims to do exactly the same thing:

gemmi h 1cdw.pdb output.pdb

Otherwise, a program called reduce from MolProbity (distributed with both
Phenix and CCP4) is probably the most popular one for adding hydrogens. I
don't know if there are any newer and better programs than reduce as of
today.

Best,
Marcin


On Wed, 29 Sept 2021 at 13:04, Sam Tang  wrote:

> Dear community
>
> This may appear to be a silly question -- I am trying to add hydrogens to
> the structure in PDB 1CDW. My initial thought is to run a single run of
> refinement with a refinement program. It happens that I cannot locate the
> map coefficients under the entry (am I missing something?) So... is there
> an easy way to do what I want in this case?
>
> Warm regards
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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/

Re: [ccp4bb] Add hydrogens

[Wim Burmeister]

Hello, there is for exemple the "addh" command in chimerax to add hydrogens to 
a structure. Wim 


De: "Mark J. van Raaij"  
À: "CCP4BB"  
Envoyé: Mercredi 29 Septembre 2021 13:11:24 
Objet: Re: [ccp4bb] Add hydrogens 

Dear Sam, 

1CDW is from 1996, when it was not obligatory (or common practice) to upload 
structure factors to the PDB. 
So I think you can't do any refinement, just perhaps some optimisation. 

Mark J van Raaij 
Dpto de Estructura de Macromoleculas, lab 20B 
Centro Nacional de Biotecnologia - CSIC 
calle Darwin 3 
E-28049 Madrid, Spain 
tel. +34 91 585 4616 (internal 432092) 
Section Editor Acta Crystallographica F 
[ https://journals.iucr.org/f/ | https://journals.iucr.org/f/ ] 




On 29 Sep 2021, at 13:03, Sam Tang < [ mailto:samtys0...@gmail.com | 
samtys0...@gmail.com ] > wrote: 

Dear community 

This may appear to be a silly question -- I am trying to add hydrogens to the 
structure in PDB 1CDW. My initial thought is to run a single run of refinement 
with a refinement program. It happens that I cannot locate the map coefficients 
under the entry (am I missing something?) So... is there an easy way to do what 
I want in this case? 

Warm regards 

Sam 




To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 








To unsubscribe from the CCP4BB list, click the following link: 
[ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 ] 

-- 
Wim Burmeister 
Professor 
Institut de Biologie Structurale (IBS) CIBB 
71 avenue des Martyrs / CS 20192 
38044 Grenoble Cedex 9, FRANCE 
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ] 
Mobile: +33 (0) 7 50 49 19 91 
[ 
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
 | website ] 

Changement climatique : «Les autres combats n’ont aucun sens si celui-là est 
perdu» ( Aurélien Barrau ) 



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/

Re: [ccp4bb] Add hydrogens

[Mark J. van Raaij]

Dear Sam,

1CDW is from 1996, when it was not obligatory (or common practice) to upload 
structure factors to the PDB.
So I think you can't do any refinement, just perhaps some optimisation.

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/

> On 29 Sep 2021, at 13:03, Sam Tang  wrote:
> 
> Dear community
> 
> This may appear to be a silly question -- I am trying to add hydrogens to the 
> structure in PDB 1CDW. My initial thought is to run a single run of 
> refinement with a refinement program. It happens that I cannot locate the map 
> coefficients under the entry (am I missing something?) So... is there an easy 
> way to do what I want in this case?
> 
> Warm regards
> 
> Sam
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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/

[ccp4bb] Add hydrogens

[Sam Tang]

Dear community

This may appear to be a silly question -- I am trying to add hydrogens to
the structure in PDB 1CDW. My initial thought is to run a single run of
refinement with a refinement program. It happens that I cannot locate the
map coefficients under the entry (am I missing something?) So... is there
an easy way to do what I want in this case?

Warm regards

Sam



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/

[ccp4bb] MXCuBE3 developer position

[Daniele de Sanctis]

Hi all,

We have an exciting new position for a software developer to participate in
the development of the new feature for serial crystallography experiments
in the MXCuBE3. MXCuBE is the experiment control software to perform data
collection and control the MX beamlines and it is part of a large
collaboration among different synchrotron sources and a software factor  (
https://github.com/mxcube/mxcube3 ; esrf.fr/mxcube3).

The latest version, MXCuBE3, is developed in web technologies and it has
proved to be the perfect companion for remote access experiments.

More information and applications details are available here
https://esrf.gestmax.eu/1545/1/cod-software-ssx/en_US

Best regards

Daniele



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/