[ccp4bb] PhD position available at Leicester/ Diamond Light Source

[Aller, Pierre (DLSLtd,RAL,LSCI)]

Dear all,
We have an exciting PhD project between University of Leicester (Dr Hanna Kwon 
and Prof Peter Moody) and Diamond Light Source (Dr Pierre Aller and Dr Allen 
Orville). The project is to study metalloenzymes with time-resolved serial 
crystallography combined with X-ray emission spectroscopy. The PhD candidate 
will spend about half of their time at Leicester then at Diamond. The closing 
date for the position is the 14th of March 2023 for a starting date of 1st 
October 2023.
To apply and see the full advert here: 
https://le.ac.uk/study/research-degrees/funded-opportunities/mcb-kwon

For any questions on the project please do not hesitate to contact me.
Kind regards,

Pierre

Pierre Aller, PhD
Senior Beamline Scientist XFEL-Hub
Diamond Light Source
Harwell Science and Innovation Campus
Didcot OX11 0DE
UK

pierre.al...@diamond.ac.uk
+44 (0)1235 778183




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[ccp4bb] Refinement of ligand with alternate chemical structure

[Stuart McQuarrie]

I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some 
refinement have noticed partial occupancy of it's hydrolysed form 2x A3, which 
has a cyclic 2'-3' phosphate on the terminal ribose. 

I tried fitting both ligands with 50% occupancy, but refinement doesn't allow 
them to occupy the same space.

I subsequently tried text editing the pdb file, adding altloc identifiers to 
the ca6 and the 2 A3 molecules, making sure they were same chain and residue 
number as per this ccp4bb archive: 
http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html. 
However, before I refined I checked in coot and all the ligand atoms are 
scattered and disconnected.

I have thought about using coot to generate an alt conformation of ca6 and then 
text editing the B conformation to be split and have a 2'-3' cyclic phosphate. 
I am not sure if this is the correct way because it is a different chemical 
structure, so I could use some advice. 

Kind regards,
Stuart



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[ccp4bb] Off topic - 3D models demonstrating drug binding to students

[Edward Snell]

Dear CCP4,

I apologize if this is off topic but I thought this may be a good community to 
ask. Before we re-invent the wheel this end, we are looking for any commercial 
source of three-dimensional macromolecular models that can be used to teach how 
drugs are designed to fit to protein targets. Our audience is mid to advanced 
high-school students and we are looking for materials that can withstand being 
passed around the students and can teach basic concepts of how structure can 
inform ligand binding.

There are commercial sources of these models for macromolecules that we are 
aware of, but few if any that allow us to manipulate a drug and show how it 
fits to the model. We would love to find ones where a student may have name 
recognition of the drug concerned and we can show how it would fit to the 
target of that drug.

Any experience in this area and a source of such models would be greatly 
appreciated. We enjoy our interactions with these students and have the 
advantage of a professional high-school science teacher/science curriculum 
developer on staff with Nicole Terranova (copied on the email). Our program 
related to this is being developed and if anyone has any experiences with this 
nature of teaching, any offline feedback would be appreciated.

Thank you,

Eddie

Edward Snell Ph.D.

President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
Professor, Materials Design and Innovation | University at Buffalo, SUNY
Fellow of the American Crystallographic Association - The Structural Science 
Society

p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu
skype: eddie.snell

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu


[hwi-logo-primary-horizontal]





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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Pavel Afonine]

Hi Stuart,
the answer, I think, is here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Pavel


On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:

> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
> refinement have noticed partial occupancy of it's hydrolysed form 2x A3,
> which has a cyclic 2'-3' phosphate on the terminal ribose.
>
> I tried fitting both ligands with 50% occupancy, but refinement doesn't
> allow them to occupy the same space.
>
> I subsequently tried text editing the pdb file, adding altloc identifiers
> to the ca6 and the 2 A3 molecules, making sure they were same chain and
> residue number as per this ccp4bb archive:
> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
> However, before I refined I checked in coot and all the ligand atoms are
> scattered and disconnected.
>
> I have thought about using coot to generate an alt conformation of ca6 and
> then text editing the B conformation to be split and have a 2'-3' cyclic
> phosphate. I am not sure if this is the correct way because it is a
> different chemical structure, so I could use some advice.
>
> Kind regards,
> Stuart
>
> 
>
> 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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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Eleanor Dodson]

I thought that REFMAC tolerated dual occupancies if the sum of the two
conformers was <= 1.0?
Eleanor
Will test..

On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:

> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
> refinement have noticed partial occupancy of it's hydrolysed form 2x A3,
> which has a cyclic 2'-3' phosphate on the terminal ribose.
>
> I tried fitting both ligands with 50% occupancy, but refinement doesn't
> allow them to occupy the same space.
>
> I subsequently tried text editing the pdb file, adding altloc identifiers
> to the ca6 and the 2 A3 molecules, making sure they were same chain and
> residue number as per this ccp4bb archive:
> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
> However, before I refined I checked in coot and all the ligand atoms are
> scattered and disconnected.
>
> I have thought about using coot to generate an alt conformation of ca6 and
> then text editing the B conformation to be split and have a 2'-3' cyclic
> phosphate. I am not sure if this is the correct way because it is a
> different chemical structure, so I could use some advice.
>
> Kind regards,
> Stuart
>
> 
>
> 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
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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Nigel Moriarty]

One may need to set a preference in Coot to allow such a situation to be
viewed. Paul helped me but I can't find the email.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Wed, Feb 15, 2023 at 12:37 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> I thought that REFMAC tolerated dual occupancies if the sum of the two
> conformers was <= 1.0?
> Eleanor
> Will test..
>
> On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie <
> 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
>> refinement have noticed partial occupancy of it's hydrolysed form 2x A3,
>> which has a cyclic 2'-3' phosphate on the terminal ribose.
>>
>> I tried fitting both ligands with 50% occupancy, but refinement doesn't
>> allow them to occupy the same space.
>>
>> I subsequently tried text editing the pdb file, adding altloc identifiers
>> to the ca6 and the 2 A3 molecules, making sure they were same chain and
>> residue number as per this ccp4bb archive:
>> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
>> However, before I refined I checked in coot and all the ligand atoms are
>> scattered and disconnected.
>>
>> I have thought about using coot to generate an alt conformation of ca6
>> and then text editing the B conformation to be split and have a 2'-3'
>> cyclic phosphate. I am not sure if this is the correct way because it is a
>> different chemical structure, so I could use some advice.
>>
>> Kind regards,
>> Stuart
>>
>> 
>>
>> 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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>



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Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

[Dias, Joao M.]

Hi Ed,
The future is already here... and virtual reality is your friend.
This is a field that will likely be revolutionized in the near future, and your 
students would get an advantage by being exposed to these new technologies.
You could check the following:
https://www.labcompare.com/10-Featured-Articles/577506-VR-for-Science-Drug-Discovery-and-More-in-the-Virtual-World/

https://nanome.ai/
I wonder how they will respond to an academic collaboration, but you might be 
very surprised.
Let me know if you need more info or if you want me to make the introduction.

Good luck,
Joao

Joao M. Dias, Ph.D.
Principal Scientist
Pfizer
Structural and Molecular Sciences
Building 220/ room 3263, MS-8220-3224
445 Eastern Point Rd.
Groton, CT 06340



From: CCP4 bulletin board  On Behalf Of Edward Snell
Sent: Wednesday, February 15, 2023 3:13 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Off topic - 3D models demonstrating drug binding 
to students

Dear CCP4,

I apologize if this is off topic but I thought this may be a good community to 
ask. Before we re-invent the wheel this end, we are looking for any commercial 
source of three-dimensional macromolecular models that can be used to teach how 
drugs are designed to fit to protein targets. Our audience is mid to advanced 
high-school students and we are looking for materials that can withstand being 
passed around the students and can teach basic concepts of how structure can 
inform ligand binding.

There are commercial sources of these models for macromolecules that we are 
aware of, but few if any that allow us to manipulate a drug and show how it 
fits to the model. We would love to find ones where a student may have name 
recognition of the drug concerned and we can show how it would fit to the 
target of that drug.

Any experience in this area and a source of such models would be greatly 
appreciated. We enjoy our interactions with these students and have the 
advantage of a professional high-school science teacher/science curriculum 
developer on staff with Nicole Terranova (copied on the email). Our program 
related to this is being developed and if anyone has any experiences with this 
nature of teaching, any offline feedback would be appreciated.

Thank you,

Eddie

Edward Snell Ph.D.
President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
Professor, Materials Design and Innovation | University at Buffalo, SUNY
Fellow of the American Crystallographic Association - The Structural Science 
Society
p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu
skype: eddie.snell
Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu

[hwi-logo-primary-horizontal]





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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Georg Mlynek]

Dear Stuart,

you have to add

  allow_duplicate_sequence_numbers()

to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).

Try with crambin (pdbcode 1EJG).This should give an error without 
allow_duplicate_sequence_numbers() but coot should start when added.


Br, Georg.


Am 15.02.2023 um 21:47 schrieb Nigel Moriarty:
One may need to set a preference in Coot to allow such a situation to 
be viewed. Paul helped me but I can't find the email.


Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov 
ORCID : orcid.org/-0001-8857-9464 




On Wed, Feb 15, 2023 at 12:37 PM Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:


I thought that REFMAC tolerated dual occupancies if the sum of the
two conformers was <= 1.0?
Eleanor
Will test..

On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie
<974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:

I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and
after some refinement have noticed partial occupancy of it's
hydrolysed form 2x A3, which has a cyclic 2'-3' phosphate on
the terminal ribose.

I tried fitting both ligands with 50% occupancy, but
refinement doesn't allow them to occupy the same space.

I subsequently tried text editing the pdb file, adding altloc
identifiers to the ca6 and the 2 A3 molecules, making sure
they were same chain and residue number as per this ccp4bb
archive:
http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
However, before I refined I checked in coot and all the ligand
atoms are scattered and disconnected.

I have thought about using coot to generate an alt
conformation of ca6 and then text editing the B conformation
to be split and have a 2'-3' cyclic phosphate. I am not sure
if this is the correct way because it is a different chemical
structure, so I could use some advice.

Kind regards,
Stuart



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Re: [ccp4bb] Off topic - 3D models demonstrating drug binding to students

[Bryan Lepore]

These magnetically-linking atomically accurate single-atom models look interesting - but I understand they might be too detailed or might shift around inadvertently :Snatoms Online Store - Magnetic Molecular Models for Educationsnatoms.comI also cannot say I used them (but I am always looking for an excuse to get some!).-Bryan W. Lepore

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[ccp4bb] a reminder

[Tom Peat]

Hello All,

We have less than one week before the abstract deadline comes to an end for the 
IUCr 2023 meeting this year in Melbourne.
This is a second, and possibly last reminder...
For those that would like to present their work at the meeting, it is time to 
pull everything together.
https://www.iucr.org/iucr/cong/2023-iucr-xxvi
https://iucr2023.org/

cheers, tom

Tom Peat, PhD
one of many on the committee...



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