Re: [ccp4bb] Workshop on "Temperature in macromolecular crystallo

[Dominik Oberthuer]

Dear CCP4 community,

of course I got the date wrong:

The workshop will happen on Monday, September 23rd 2024...

At least you won't have to travel back in time to be able to attend this 
awesome workshop.


Cheers, Dominik

Dear CCP4 community,


I am excited to announce an upcoming workshop on 
Temperature-Controlled Crystallography, where we will explore the 
latest techniques, applications, and advancements, including 
time-resolved methods and multidimensional serial crystallography 
approaches. This workshop is an excellent opportunity to discuss 
challenges and opportunities of macromolecular crystallography at room 
temperature and beyond, learn from leading experts and engage with 
cutting-edge research in the field.


Speakers include:

Marius Schmidt, Gisela Branden, Eike C. Schulz, Alessandra Henkel, 
Sebastian Günther, Chia-Ying Huan, Daniel Keedy, Michael Thompson and 
Silvia Russi.


The workshop is part of this years SSRL/LCLS Users' Meeting 
(https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/summary) 
and will take place on Monday, September 9th 2024 from 8 am to 12 pm 
(PDT).


Apart from the exciting workshop the Users' Meeting features a bunch 
of other very interesting workshops on e.g. data analysis, Application 
of Cryo-EM in Molecular and Cell Biology, Computational Methods in 
Structural Biology, Metals in Structural Biology and MFX-HE: 
Opportunities for High-Throughput Multimodal Structural Studies and 
Their Computational Challenges, that should be very relevant for this 
community.


If you haven't done so, you can still register here:

https://web.cvent.com/event/8c2bdf8d-08a1-41c5-b24e-390d039d9be2/register

Looking forward to seeing you all at SLAC in the end of September!

Cheers, Dominik


--
Dr. Dominik Oberthür

CFEL - Center for Free-Electron Laser Science - DESY
Coherent Imaging Division

Notkestrasse 85
22607 Hamburg
Germany

phone: +49 (0)40 8998 6394
dominik.oberth...@cfel.de



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Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

[John R Helliwell]

Dear Tim, and Arpita and Doeke,
Basically structure is not affected (as evidenced by our Fisher and Helliwell 
database survey in Acta Cryst) but kinetics is affected ie everything is slower 
in D2O and can thereby be toxic.
Greetings 
John 
Emeritus Professor John R Helliwell DSc

> On 6 Sep 2024, at 16:02, Tim Grüne  wrote:
> 
> Hi Doeke,
> if I remember correctly, D2O is poisonous and bacteria grow with reduced 
> growth rate.
> The effect of the greater mass may not be totally insignificant.
> Best,
> Tim
> Am 06.09.2024 15:25, schrieb Hekstra, Doeke Romke:
>> Hi Arpita,
>> H and D have the same number of electrons (1). The D nucleus has an
>> extra neutron, changing its mass and therefore its vibrational energy
>> levels. That can affect hydrogen bonding patterns, although I would
>> expect the effect to be relatively minor (see e.g. Fisher and
>> Helliwell, Acta Cryst A A64: 359-367 (2008)).
>> Best, Doeke
>> From: CCP4 bulletin board  On Behalf Of Arpita
>> Goswami
>> Sent: Thursday, September 5, 2024 11:12 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Studying hydrogen bonding network by neutron
>> diffraction in sample with D2O
>> Dear all,
>> Good morning, Sorry for the off-topic question.
>> There is a protein crystal sample in which water bonding networks by
>> certain species to be studied by neutron diffraction, not exactly
>> within the protein. But between the subunits of the protein. Now it is
>> mandatory to use some D2O for the preparation of samples. Now my
>> question is will there be drastic differences between the hydration
>> patterns of this sample and original sample without D2O? For example,
>> some change in positions and interacting partners of the hydrated
>> species of interest with respect to the protein surface? Since
>> deuterium has 2 electrons instead of one as in protium?
>> We know D2O is regularly used for such experiments in Neutron
>> diffraction and in NMR as well. Please let me know your expert
>> opinions.
>> Thank you.
>> Best Regards,
>> Arpita
>> -
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> 
> --
> --
> 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
> 
> 
> 
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Re: [ccp4bb] PCD 2024 - Registration extended to Sept 6!

[Jeney Wierman]

Gentle reminder that registration for PDC 2024 at Cornell U closes today.

Register here: 
https://web.cvent.com/event/f63b17b8-5582-4590-a22a-e6554d119009/register



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Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Xu, Qingping]

There are still a few spots available for additional students in our workshop, 
we have extended the application deadline. If you are interested in joining, 
please submit your application as soon as possible.

Thanks.

Charles, Andrey, Garib and Qingping



From: CCP4 bulletin board  on behalf of Qingping Xu 
<292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, April 8, 2024 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
details can be found at the school website:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$.
 This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. The daily schedule
will be organized in three sections – lectures, tutorials, and hands-on
(interactive trouble-shooting of the technical difficulties the
participants face in their projects). We have had considerable success
resolving these problems in past years, attested by resulting
publications (see
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$).
 A draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. Graduate
students, postdoctoral researchers and early-career faculty, along with
commercial/industrial researchers are encouraged to apply. Only about 20
applicants will be selected for participation.

Application: Application deadline is  August 31st, 2024. To apply,
visit  
https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. The students will be responsible for their
transportation and lodging. The workshop organizers can assist in making
lodging reservations at the Argonne Guest House. The workshop will cover
all other expenses (including meals).


We hope to see you at the school.

Charles, Andrey, Garib and Qingping



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From: CCP4 bulletin board  on behalf of Qingping Xu 
<292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, April 8, 2024 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collec

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

[Tim Grüne]

Hi Doeke,
if I remember correctly, D2O is poisonous and bacteria grow with reduced 
growth rate.

The effect of the greater mass may not be totally insignificant.
Best,
Tim
Am 06.09.2024 15:25, schrieb Hekstra, Doeke Romke:

Hi Arpita,

H and D have the same number of electrons (1). The D nucleus has an
extra neutron, changing its mass and therefore its vibrational energy
levels. That can affect hydrogen bonding patterns, although I would
expect the effect to be relatively minor (see e.g. Fisher and
Helliwell, Acta Cryst A A64: 359-367 (2008)).

Best, Doeke

From: CCP4 bulletin board  On Behalf Of Arpita
Goswami
Sent: Thursday, September 5, 2024 11:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Studying hydrogen bonding network by neutron
diffraction in sample with D2O

Dear all,

Good morning, Sorry for the off-topic question.

There is a protein crystal sample in which water bonding networks by
certain species to be studied by neutron diffraction, not exactly
within the protein. But between the subunits of the protein. Now it is
mandatory to use some D2O for the preparation of samples. Now my
question is will there be drastic differences between the hydration
patterns of this sample and original sample without D2O? For example,
some change in positions and interacting partners of the hydrated
species of interest with respect to the protein surface? Since
deuterium has 2 electrons instead of one as in protium?

We know D2O is regularly used for such experiments in Neutron
diffraction and in NMR as well. Please let me know your expert
opinions.

Thank you.

Best Regards,

Arpita

-

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--
--
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



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Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

[Hekstra, Doeke Romke]

Hi Arpita,

H and D have the same number of electrons (1). The D nucleus has an extra 
neutron, changing its mass and therefore its vibrational energy levels. That 
can affect hydrogen bonding patterns, although I would expect the effect to be 
relatively minor (see e.g. Fisher and Helliwell, Acta Cryst A A64: 359-367 
(2008)).

Best, Doeke

From: CCP4 bulletin board  On Behalf Of Arpita Goswami
Sent: Thursday, September 5, 2024 11:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in 
sample with D2O

Dear all,

Good morning, Sorry for the off-topic question.

There is a protein crystal sample in which water bonding networks by certain 
species to be studied by neutron diffraction, not exactly within the protein. 
But between the subunits of the protein. Now it is mandatory to use some D2O 
for the preparation of samples. Now my question is will there be drastic 
differences between the hydration patterns of this sample and original sample 
without D2O? For example, some change in positions and interacting partners of 
the hydrated species of interest with respect to the protein surface? Since 
deuterium has 2 electrons instead of one as in protium?

We know D2O is regularly used for such experiments in Neutron diffraction and 
in NMR as well. Please let me know your expert opinions.

Thank you.
Best Regards,
Arpita



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Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

[Arpita Goswami]

Hello Dr. Mathew,

Good day!

Thank you for the explanation and for correcting the sloppy mistake for
Deuterium electron numbers!

Regarding pKa, will there be differences then in the hydrogen bonding
patterns between H2O and D2O enriched solutions for pH 6 to 7 range?

Best regards,
Arpita

On Fri, Sep 6, 2024, 11:15 Matthew Merski  wrote:

> Deuterium only has one electron, like hydrogen. It has a neutron and a
> proton making it an isotope of hydrogen. There will be a difference in
> hydrogen bonding depending on pH as water and D2O have slightly different
> pKa behaviour, but far from the pKa this will not be noticeable.
>
> On Fri, 6 Sept 2024, 04:12 Arpita Goswami,  wrote:
>
>> Dear all,
>>
>> Good morning, Sorry for the off-topic question.
>>
>> There is a protein crystal sample in which water bonding networks by
>> certain species to be studied by neutron diffraction, not exactly within
>> the protein. But between the subunits of the protein. Now it is mandatory
>> to use some D2O for the preparation of samples. Now my question is will
>> there be drastic differences between the hydration patterns of this sample
>> and original sample without D2O? For example, some change in positions and
>> interacting partners of the hydrated species of interest with respect to
>> the protein surface? Since deuterium has 2 electrons instead of one as in
>> protium?
>>
>> We know D2O is regularly used for such experiments in Neutron diffraction
>> and in NMR as well. Please let me know your expert opinions.
>>
>> Thank you.
>> Best Regards,
>> Arpita
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] Job opportunities at SARomics Biostructures

[Karla J. F. Satchell]

Hi Muneer,

You can try the 3D Proteome Viewer at Coronavirus3d.org
https://coronavirus3d.org/#/3dproteomeviewer

Use Google Chrome as does not work well in other browsers.

On the link, hover over and click Nsp6
Scroll down and you will see all mutations in Nsp6 mapped to the alphafold 
model and a list of all mutations back to 2020 with the frequency.
You can export the data as a .cvs file to sort as you choose.
The data are automatically updated once a month. There is lots of other good 
data on this site so look around.
Here is the publication on this database 
(https://pubmed.ncbi.nlm.nih.gov/32470119/)

When I find a specific mutation I am interested in, I use Nextstrain.org and 
label the tree by genotype to colorize on the lineage map.
https://nextstrain.org/ncov/gisaid/global/6m
You will need to translate the nsp6 mutation location to the exact position on 
Orf1A as nsp1-11 are a single protein on nextstrain.
Nextstrain is now mapping mpox and other emerging infections so useful also in 
the future.

Good luck.

Karla Satchell



From: CCP4 bulletin board  on behalf of Muneer Ahmad 

Date: Wednesday, September 4, 2024 at 10:45 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Job opportunities at SARomics Biostructures

Dear All,

I'm hoping someone can assist me with accessing or searching for data related 
to Sara CoV 2 variants. Specifically, I'm interested in the NSP6 protein and 
would like to identify variants that have been found in different species.

If anyone has recommendations for databases, repositories, or specific search 
terms, I would be very grateful.

Thank you,

Muneer Ahmad

On Thu, Sep 5, 2024, 1:24 AM Derek Logan 
<ac2332bb2871-dmarc-requ...@jiscmail.ac.uk<mailto:ac2332bb2871-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Dear all,

Just a reminder that job opportunities are available at SARomics Biostructures 
in Lund, Sweden, a rapidly growing CRO in structural biology for the pharma and 
biotech sectors. SARomics are looking to recruit several scientists in protein 
expression and purification, as well as crystallography, to join their highly 
international team. The company is in an exciting expansion phase and just 
moved into brand new tailor-made labs at the lively life science hub Medicon 
Village a couple of weeks ago.

See here for more details of the positions:

Positions at SARomics 
Biostructures<https://urldefense.com/v3/__https:/www.saromics.com/about/career/__;!!Dq0X2DkFhyF93HkjWTBQKhk!VmUSnTrQ3B0_jBcVYuS1XKe6teuIssjdqVk9UhM6b5DLofcqm21CRz54EHv3YfVbslD78KTTJoPpJkW6-DaoFQYAj_f37R1ka_s$>
saromics.com<https://urldefense.com/v3/__https:/www.saromics.com/about/career/__;!!Dq0X2DkFhyF93HkjWTBQKhk!VmUSnTrQ3B0_jBcVYuS1XKe6teuIssjdqVk9UhM6b5DLofcqm21CRz54EHv3YfVbslD78KTTJoPpJkW6-DaoFQYAj_f37R1ka_s$>
[cid:C90C84C1-7FE5-476A-9FDE-E310050B5327]<https://urldefense.com/v3/__https:/www.saromics.com/about/career/__;!!Dq0X2DkFhyF93HkjWTBQKhk!VmUSnTrQ3B0_jBcVYuS1XKe6teuIssjdqVk9UhM6b5DLofcqm21CRz54EHv3YfVbslD78KTTJoPpJkW6-DaoFQYAj_f37R1ka_s$>

The deadline is 9th September. Please note, as before, the requirement to be 
already legally entitled to work in Sweden.

/Derek
_
Derek Logan
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se<https://urldefense.com/v3/__http:/www.cmps.lu.se__;!!Dq0X2DkFhyF93HkjWTBQKhk!VmUSnTrQ3B0_jBcVYuS1XKe6teuIssjdqVk9UhM6b5DLofcqm21CRz54EHv3YfVbslD78KTTJoPpJkW6-DaoFQYAj_f3lnPtyHY$>














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Re: [ccp4bb] Job opportunities at SARomics Biostructures

[Muneer Ahmad]

Dear All,

I'm hoping someone can assist me with accessing or searching for data
related to Sara CoV 2 variants. Specifically, I'm interested in the NSP6
protein and would like to identify variants that have been found in
different species.

If anyone has recommendations for databases, repositories, or specific
search terms, I would be very grateful.

Thank you,

Muneer Ahmad

On Thu, Sep 5, 2024, 1:24 AM Derek Logan <
ac2332bb2871-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> Just a reminder that job opportunities are available at SARomics
> Biostructures in Lund, Sweden, a rapidly growing CRO in structural biology
> for the pharma and biotech sectors. SARomics are looking to recruit several
> scientists in protein expression and purification, as well as
> crystallography, to join their highly international team. The company is in
> an exciting expansion phase and just moved into brand new tailor-made labs
> at the lively life science hub Medicon Village a couple of weeks ago.
>
> See here for more details of the positions:
>
> Positions at SARomics Biostructures
> 
> saromics.com 
> [image: large.png] 
> 
>
> The deadline is 9th September. Please note, as before, the requirement to
> be already legally entitled to work in Sweden.
>
> /Derek
> _
> *Derek Logan*
> Professor | Biochemistry and Structural Biology
>
> Centre for Molecular Protein Science
> Lund University, Box 124, 221 00 Lund, Sweden
> www.cmps.lu.se
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Marcin Wojdyr]

On Fri, Aug 30, 2024 at 10:33 PM Dr. Kevin M Jude  wrote:
>
> Thanks Jon, these PDB files do have the atom type in column 78. The message 
> in the output that “Atoms of all types will be used” makes me think that 
> either my HEXCLUDE keyword is ignored or that I’m using it incorrectly.

It's an old program that has a hardcoded list of hydrogen names:
https://ccp4forge.rc-harwell.ac.uk/ccp4/ccp4-progs/-/blob/977b01d64807b176a887286e39b0709114495df7/src/contact.f#L557-563
It worked in the 90s, but since then the naming of hydrogens in the
PDB has changed (2HB -> HB2).



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Dr. Kevin M Jude]

Thanks Jon, these PDB files do have the atom type in column 78. The message in 
the output that “Atoms of all types will be used” makes me think that either my 
HEXCLUDE keyword is ignored or that I’m using it incorrectly. I went ahead and 
removed hydrogens from the pdb inputs as a workaround. I’m measuring 
intermolecular contacts in the ASU.

Best wishes
Kevin

From: Jon Cooper 
Date: Friday, August 30, 2024 at 1:06 PM
To: Dr. Kevin M Jude 
Cc: CCP4BB 
Subject: Re: [ccp4bb] Contact: Hexclude doesn't work?

Another thing could be if the atom type field is missing in the pdb file. It's 
the optional one on the far right.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 30/08/2024 20:04, Dr. Kevin M Jude wrote:
I’m trying to run contact on a protonated pdb file and want to ignore 
hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. 
Is it a bug, or am I doing it wrong? Pasting the top of the log file below.

Thanks
Kevin

###
###
###
### CCP4 8.0.017: CONTACT  version 8.0.017 : ##
###
User: kjude  Run date: 30/ 8/2024 Run time: 12:02:24


Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.


** PROGRAM CONTACT *
Data line---   mode isub
Data line---   limits 0 4.0
Data line---   HEXCLUDE
Data line---   from residue all chain A 1 to 60
Data line---   to residue all chain B 1 to 60
Data line---   end

Atoms of all types will be used.


Intersubunit contacts will be printed

Atom-atom search will be done within the limits of  0.00 to  4.00 angstroms


  Logical name: XYZIN  File name: 8da3.pdb1
  PDB file is being opened on unit 1 for INPUT.

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


 RF  RO

0.028  -0.000  -0.000  -0.000   35.546   0.000   0.000  -0.000
   -0.000   0.024  -0.000   0.0000.000  42.449   0.000   0.000
0.000  -0.000   0.013  -0.0000.000   0.000  74.288  -0.000
   -0.000   0.000  -0.000   1.000   -0.000   0.000  -0.000   1.000


Xmin Xmax Ymin Ymax Zmin Zmax :7.32   40.92   -8.96   33.26   29.29   77.18
NX NY NZ boxes 8  11  10

LIST OF CONTACTS :
==


   source atomstarget atoms distance   angle

Asn 3A  C ...   Phe32B  CZ ...   3.74
Asn 3A  O ...   Phe32B  CZ ...   3.71
   ...   Phe32B  CE1...   3.77
Asn 3A  ND2   ...   Trp35B  CZ3...   3.91
   ...   Trp35B  CH2...   3.84
Asn 3A  HB2   ...   Phe32B  CZ ...   3.96
Asn 3A  HB3   ...   Phe32B  CZ ...   3.30
   ...   Phe32B  CE1...   3.18
   ...   Trp35B  CZ3...   3.86
Asn 3A  HD21  ...   Trp35B  CH2...   3.85
Asn 3A  HD22  ...   Asp36B  OD1...   3.80
   ...   Trp35B  CZ3...   3.54
   ...   Trp35B  CH2...   3.72


Etc…
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Jon Cooper]

Another thing could be if the atom type field is missing in the pdb file. It's 
the optional one on the far right.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 30/08/2024 20:04, Dr. Kevin M Jude  wrote:

> I’m trying to run contact on a protonated pdb file and want to ignore 
> hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. 
> Is it a bug, or am I doing it wrong? Pasting the top of the log file below.
>
> Thanks
>
> Kevin
>
> ###
>
> ###
>
> ###
>
> ### CCP4 8.0.017: CONTACT version 8.0.017 : ##
>
> ###
>
> User: kjude Run date: 30/ 8/2024 Run time: 12:02:24
>
> Please reference: Collaborative Computational Project, Number 4. 2011.
>
> "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
> 235-242.
>
> as well as any specific reference in the program write-up.
>
> 
>
> ** PROGRAM CONTACT *
>
> Data line--- mode isub
>
> Data line--- limits 0 4.0
>
> Data line--- HEXCLUDE
>
> Data line--- from residue all chain A 1 to 60
>
> Data line--- to residue all chain B 1 to 60
>
> Data line--- end
>
> Atoms of all types will be used.
>
> Intersubunit contacts will be printed
>
> Atom-atom search will be done within the limits of 0.00 to 4.00 angstroms
>
> Logical name: XYZIN File name: 8da3.pdb1
>
> PDB file is being opened on unit 1 for INPUT.
>
> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
>
> RF RO
>
> 0.028 -0.000 -0.000 -0.000 35.546 0.000 0.000 -0.000
>
> -0.000 0.024 -0.000 0.000 0.000 42.449 0.000 0.000
>
> 0.000 -0.000 0.013 -0.000 0.000 0.000 74.288 -0.000
>
> -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
>
> Xmin Xmax Ymin Ymax Zmin Zmax : 7.32 40.92 -8.96 33.26 29.29 77.18
>
> NX NY NZ boxes 8 11 10
>
> LIST OF CONTACTS :
>
> ==
>
> source atoms target atoms distance angle
>
> Asn 3A C ... Phe 32B CZ ... 3.74
>
> Asn 3A O ... Phe 32B CZ ... 3.71
>
> ... Phe 32B CE1 ... 3.77
>
> Asn 3A ND2 ... Trp 35B CZ3 ... 3.91
>
> ... Trp 35B CH2 ... 3.84
>
> Asn 3A HB2 ... Phe 32B CZ ... 3.96
>
> Asn 3A HB3 ... Phe 32B CZ ... 3.30
>
> ... Phe 32B CE1 ... 3.18
>
> ... Trp 35B CZ3 ... 3.86
>
> Asn 3A HD21 ... Trp 35B CH2 ... 3.85
>
> Asn 3A HD22 ... Asp 36B OD1 ... 3.80
>
> ... Trp 35B CZ3 ... 3.54
>
> ... Trp 35B CH2 ... 3.72
>
> Etc…
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Contact: Hexclude doesn't work?

[Jon Cooper]

Hello, you could run pdbset with the "exclude hydrogens" card or pdbcur with 
"delhydrogen". What contacts are you looking for e.g. crystallographic or 
intramolecular?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 30/08/2024 20:04, Dr. Kevin M Jude  wrote:

> I’m trying to run contact on a protonated pdb file and want to ignore 
> hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts. 
> Is it a bug, or am I doing it wrong? Pasting the top of the log file below.
>
> Thanks
>
> Kevin
>
> ###
>
> ###
>
> ###
>
> ### CCP4 8.0.017: CONTACT version 8.0.017 : ##
>
> ###
>
> User: kjude Run date: 30/ 8/2024 Run time: 12:02:24
>
> Please reference: Collaborative Computational Project, Number 4. 2011.
>
> "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
> 235-242.
>
> as well as any specific reference in the program write-up.
>
> 
>
> ** PROGRAM CONTACT *
>
> Data line--- mode isub
>
> Data line--- limits 0 4.0
>
> Data line--- HEXCLUDE
>
> Data line--- from residue all chain A 1 to 60
>
> Data line--- to residue all chain B 1 to 60
>
> Data line--- end
>
> Atoms of all types will be used.
>
> Intersubunit contacts will be printed
>
> Atom-atom search will be done within the limits of 0.00 to 4.00 angstroms
>
> Logical name: XYZIN File name: 8da3.pdb1
>
> PDB file is being opened on unit 1 for INPUT.
>
> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
>
> RF RO
>
> 0.028 -0.000 -0.000 -0.000 35.546 0.000 0.000 -0.000
>
> -0.000 0.024 -0.000 0.000 0.000 42.449 0.000 0.000
>
> 0.000 -0.000 0.013 -0.000 0.000 0.000 74.288 -0.000
>
> -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
>
> Xmin Xmax Ymin Ymax Zmin Zmax : 7.32 40.92 -8.96 33.26 29.29 77.18
>
> NX NY NZ boxes 8 11 10
>
> LIST OF CONTACTS :
>
> ==
>
> source atoms target atoms distance angle
>
> Asn 3A C ... Phe 32B CZ ... 3.74
>
> Asn 3A O ... Phe 32B CZ ... 3.71
>
> ... Phe 32B CE1 ... 3.77
>
> Asn 3A ND2 ... Trp 35B CZ3 ... 3.91
>
> ... Trp 35B CH2 ... 3.84
>
> Asn 3A HB2 ... Phe 32B CZ ... 3.96
>
> Asn 3A HB3 ... Phe 32B CZ ... 3.30
>
> ... Phe 32B CE1 ... 3.18
>
> ... Trp 35B CZ3 ... 3.86
>
> Asn 3A HD21 ... Trp 35B CH2 ... 3.85
>
> Asn 3A HD22 ... Asp 36B OD1 ... 3.80
>
> ... Trp 35B CZ3 ... 3.54
>
> ... Trp 35B CH2 ... 3.72
>
> Etc…
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] CCP49.0 i2run problem

[Stuart McNicholas]

Dear Xin,
  Sorry, I was wrong in the last reply, the command line argument
problem was just bad result of cut and paste from the email.

However, I have found a couple of issues which are hopefully addressed
in the two attached files.

1) A change to ProvideAsuContents.py to work without a database. This
should replace the file:
/home/programs/ccp4-9/lib/python3.9/site-packages/ccp4i2/wrappers/ProvideAsuContents/script/ProvideAsuContents.py

2) i2run was simply not exiting properly after finishing. The attached
CCP4I2Runner.py should fix this. This belongs in:
/home/programs/ccp4-9/lib/python3.9/site-packages/ccp4i2/core/CCP4I2Runner.py

Please let me know if these do or not fix the problem.

Best wishes,
Stuart

On Fri, 30 Aug 2024 at 08:26, Stuart McNicholas
 wrote:
>
> Dear Xin,
>   It appears that the command line arguments are not being parsed
> properly. I am looking into this right now. I hope to have a fix for
> you very shortly.
>
> Best wishes,
> Stuart
>
> On Fri, 30 Aug 2024 at 06:30, zx2...@connect.hku.hk
>  wrote:
> >
> > Hi all,
> >
> > I am experiencing some issues with i2run command after updating CCP4 to 
> > version 9.0.
> >
> > The command I used is as follows:
> >
> > $CCP4/lib/python3.9/site-packages/ccp4i2/bin/i2run ProvideAsuContents \
> > --ASU_CONTENT \
> > sequence=${sequence} \
> >  nCopies=1 \
> >  polymerType=PROTEIN \
> > --noDb > ASU.log
> >
> > However, I am receiving the following error message:
> >
> > Traceback (most recent call last):
> > File 
> > "/home/programs/ccp4-9/lib/python3.9/site-packages/ccp4i2/core/CCP4I2Runner.py",
> >  line 740, in 
> > threads = app.findChildren(QtCore.QThread)
> > AttributeError: 'NoneType' object has no attribute 'findChildren'
> >
> > I was wondering if you could provide some suggestions on how to solve this 
> > problem.
> >
> > Thank you very much for your time and assistance.
> >
> > Best regards,
> > Xin
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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from core.CCP4PluginScript import CPluginScript
from core import CCP4ModelData
import os,sys
import shutil
from lxml import etree

class ProvideAsuContents(CPluginScript):

TASKNAME = 'ProvideAsuContents'# Task name - should be same as class name
RUNEXTERNALPROCESS=False
   
def startProcess(self, command, **kw):
  asuFileObject = self.container.outputData.ASUCONTENTFILE
  asuFileObject.fileContent.seqList.set(self.container.inputData.ASU_CONTENT)
  if self._dbHandler:
  asuFileObject.saveFile(  { 'projectName': self._dbHandler.projectName,
  'projectId' : self._dbHandler.projectId,
  'jobId' : None,
  'jobNumber' : None } )

  xmlroot = etree.Element('ASUCONTENTMATTHEWS')
  totWeight = 0.0
  if len(self.container.inputData.ASU_CONTENT) > 0:
  entries = etree.SubElement(xmlroot,"entries")
  polymerMode = ""
  for seqObj in self.container.inputData.ASU_CONTENT:
  if seqObj.nCopies > 0:
  if seqObj.polymerType == "PROTEIN":
  if polymerMode == "D":
  polymerMode = "C"
  elif polymerMode == "":
  polymerMode = "P"
  if seqObj.polymerType in ["DNA","RNA"]:
  if polymerMode == "P":
  polymerMode = "C"
  elif polymerMode == "":
  polymerMode = "D"
  totWeight = totWeight + seqObj.molecularWeight(seqObj.polymerType)
  entry = etree.SubElement(entries,"entry")
  nCopies = etree.SubElement(entry,"copies")
  name = etree.SubElement(entry,"name")
  weight = etree.SubElement(entry,"weight")
  sequence = etree.SubElement(entry,"sequence")
  nCopies.text = str(seqObj.nCopies)
  name.text = str(seqObj.name)
  weight.text = "{0:.1f}".format(float(seqObj.molecularWeight(seqObj.polymerType)))
  sequence.text = str(seqObj.sequence)
  totalWeightTag = etree.SubElement(xmlroot,"totalWeight")
  totalWeightTag.text = str(totWeight)

  if self.container.inputData.HKLIN.isSet() and len(self.container.inputData.ASU_CONTENT) > 0:
  if totWeight > 1e

Re: [ccp4bb] CCP49.0 i2run problem

[Stuart McNicholas]

Dear Xin,
  It appears that the command line arguments are not being parsed
properly. I am looking into this right now. I hope to have a fix for
you very shortly.

Best wishes,
Stuart

On Fri, 30 Aug 2024 at 06:30, zx2...@connect.hku.hk
 wrote:
>
> Hi all,
>
> I am experiencing some issues with i2run command after updating CCP4 to 
> version 9.0.
>
> The command I used is as follows:
>
> $CCP4/lib/python3.9/site-packages/ccp4i2/bin/i2run ProvideAsuContents \
>   --ASU_CONTENT \
> sequence=${sequence} \
>    nCopies=1 \
>    polymerType=PROTEIN \
>   --noDb > ASU.log
>
> However, I am receiving the following error message:
>
> Traceback (most recent call last):
> File 
> "/home/programs/ccp4-9/lib/python3.9/site-packages/ccp4i2/core/CCP4I2Runner.py",
>  line 740, in 
> threads = app.findChildren(QtCore.QThread)
> AttributeError: 'NoneType' object has no attribute 'findChildren'
>
> I was wondering if you could provide some suggestions on how to solve this 
> problem.
>
> Thank you very much for your time and assistance.
>
> Best regards,
> Xin
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Coot 1.* in CCP4 9

[David J. Schuller]

Thanks for the guidance.

If I replace two occurrences of  "Coot" with "coot-1" in .../coot_py3/bin/coot
it works.


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: Paul Emsley 
Sent: Wednesday, August 28, 2024 6:32 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



Hello David,


One need not change anything. Just run it from where it is (for now probably 
best not to override the path while other programs expect coot to be coot 0.9.x)


.../ccp4-9/coot_py3/bin/coot


Paul.



On 8/28/24 22:05, David J. Schuller wrote:
Thank you for the response.

My installation claims to be up-to-date, so any modifications have not yet been 
released.

I looked in the .../ccp4-9/bin/coot file and changed coot_py2 to coot_py3.
When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No such file 
or directory
Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 
schul...@cornell.edu<mailto:schul...@cornell.edu>

From: Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>
Sent: Wednesday, August 28, 2024 4:54 PM
To: David J. Schuller <mailto:schul...@cornell.edu>; 
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.

How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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Re: [ccp4bb] Coot 1.* in CCP4 9

[Paul Emsley]

Hello David,


One need not change anything. Just run it from where it is (for now 
probably best not to override the path while other programs expect coot 
to be coot 0.9.x)



.../ccp4-9/coot_py3/bin/coot


Paul.



On 8/28/24 22:05, David J. Schuller wrote:

Thank you for the response.

My installation claims to be up-to-date, so any modifications have not 
yet been released.


I looked in the .../ccp4-9/bin/coot file and changed coot/_py2 to 
coot/_py3.

When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No 
such file or directory

Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
schul...@cornell.edu

*From:* Paul Emsley 
*Sent:* Wednesday, August 28, 2024 4:54 PM
*To:* David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 


*Subject:* Re: [ccp4bb] Coot 1.* in CCP4 9


On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.


How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.





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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>






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Re: [ccp4bb] Coot 1.* in CCP4 9

[David J. Schuller]

Thank you for the response.

My installation claims to be up-to-date, so any modifications have not yet been 
released.

I looked in the .../ccp4-9/bin/coot file and changed coot_py2 to coot_py3.
When next I try to execute I get:
""
$ coot
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/bin/coot: line 196: 
/nfs/chess/sw/macchess/ccp4_master/ccp4-9/coot_py3/libexec/Coot: No such file 
or directory
Coot crashed.
""


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: Paul Emsley 
Sent: Wednesday, August 28, 2024 4:54 PM
To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] Coot 1.* in CCP4 9



On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.

How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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Re: [ccp4bb] Coot 1.* in CCP4 9

[Paul Emsley]

On 8/28/24 21:53, David J. Schuller wrote:
I installed CCP4 9 on Alma 9 Linux. I requested installation of both 
Coot-0.9.8.95 and Coot-1.1.08.


How do I execute the latter?



It's in the coot_py3 directory after installation.

I believe that Charles has recently made a binary update to 1.1.10.


Paul.




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Re: [ccp4bb] error in error message

[David J. Schuller]

During the installation process, at the bottom of the installer:

"*Un)istallation in progress ..."

istallation => installation


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: CCP4 bulletin board  on behalf of David J. 
Schuller 
Sent: Wednesday, August 28, 2024 1:49 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] error in error message

I am attempting to install CCP4 9.0 from the launcher, downloaded 2024-08-28. I 
get an error message about a missing dependency. One sentence is "Setup cannot 
proceed further until these components are not installed..."

Clearly the "not" is erroneous.


===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu



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Re: [ccp4bb] Multiple binding model in BLI

[Nikolay Dobrev]

Dear Mintu,
this seems to be quite a particular case.
Just a side question before we jump on the octet fitting of the 1:3 model.
Do you have any other evidence that your binding partners are binding
in 1:3 stoichiometry? Like a biological mechanism for that or any
other experimental assay like SEC?
You might try to swap the location of the ligand and analyte and do
the reverse experiment.
Also did you perform NSB control?
Kind regards,
Nikolay

On Wed, Aug 28, 2024 at 5:37 PM Mintu Chandra  wrote:
>
> Dear Perrakis,
> Yes, with a 1:3 binding model, I mean stoichiometry with a sequential binding 
> model. The sensogram profile that I am getting clearly suggests that neither 
> it is a 1:1 nor 1:2 stoichiometric binding (at least R-square and RSS values 
> suggest that it might be a 1:3 stoichiometric binding). I can certainly try 
> KINTEK but am currently not familiar with that software.
>
> Thanks.
> M Chandra
>
>
> On Wed, Aug 28, 2024 at 10:23 AM  wrote:
>>
>> Dear Chandra,
>>
>> What exactly do you mean by 1:3 or 1:2 binding mode? Is that stoichiometry? 
>> Do you need/want to fit a simple binding model with that stoichiometry, a 
>> sequential model, or a co-operative model?
>>
>> Graphpad can get you a long way with existing equations when you define the 
>> exact problem, but I am personally very find of the KINTEK software (you can 
>> get a student and trial license for it) which can do anything you ever want 
>> to do with transit and equilibrium kinetics analysis.
>>
>> A.
>>
>>
>>
>>
>> On 28 Aug 2024, at 17:16, Mintu Chandra  wrote:
>>
>> LET OP: Deze e-mail is afkomstig van buiten de organisatie. Open alleen 
>> links of bijlagen als je de afzender kent en weet dat de inhoud veilig is.
>>
>> CAUTION: This email originated from outside of the organization. Do not 
>> click links or open attachments unless you recognize the sender and know the 
>> content is safe.
>>
>> Hello everyone,
>> I am trying to fit a BLI sensogram curve into a 1:3 binding model but there 
>> is limited scope in the software package (limited to 1:2 binding model) and 
>> therefore not able to fit the curve to get the accurate KD value. I am 
>> trying graphpad prism but not getting enough information on which particular 
>> equation I need to use to fit the BLI curve into a 1:3 binding model.
>>
>> Any help or suggestion from the community in this matter would be highly 
>> appreciated.
>>
>> Thank you,
>> M Chandra
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>
>
>
> --
>
> Mintu Chandra, PhD
>
> Research Assistant Professor
>
> Department of Biological Sciences & Biochemistry
>
> Vanderbilt University
>
> Nashville, TN, USA - 37235
>
> Mobile : 615-947-9274
>
> Email : mintu.chan...@vanderbilt.edu
>
> ORCID : https://orcid.org/-0003-2382-5024
>
> Google Scholar : 
> https://scholar.google.com.au/citations?user=xYytyGAJ&hl=en
>
> Linkedin : https://www.linkedin.com/in/dr-mintu-chandra-584a8b2b/
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Multiple binding model in BLI

[Mintu Chandra]

Dear Perrakis,
Yes, with a 1:3 binding model, I mean stoichiometry with a sequential
binding model. The sensogram profile that I am getting clearly suggests
that neither it is a 1:1 nor 1:2 stoichiometric binding (at least R-square
and RSS values suggest that it might be a 1:3 stoichiometric binding). I
can certainly try KINTEK but am currently not familiar with that software.

Thanks.
M Chandra


On Wed, Aug 28, 2024 at 10:23 AM  wrote:

> Dear Chandra,
>
> What exactly do you mean by 1:3 or 1:2 binding mode? Is that
> stoichiometry? Do you need/want to fit a simple binding model with that
> stoichiometry, a sequential model, or a co-operative model?
>
> Graphpad can get you a long way with existing equations when you define
> the exact problem, but I am personally very find of the KINTEK software
> (you can get a student and trial license for it) which can do anything you
> ever want to do with transit and equilibrium kinetics analysis.
>
> A.
>
>
>
>
> On 28 Aug 2024, at 17:16, Mintu Chandra  wrote:
>
> *LET OP:* Deze e-mail is afkomstig van buiten de organisatie. Open alleen
> links of bijlagen als je de afzender kent en weet dat de inhoud veilig is.
>
> *CAUTION:* This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe.
> Hello everyone,
> I am trying to fit a BLI sensogram curve into a 1:3 binding model but
> there is limited scope in the software package (limited to 1:2 binding
> model) and therefore not able to fit the curve to get the accurate KD
> value. I am trying graphpad prism but not getting enough information on
> which particular equation I need to use to fit the BLI curve into a 1:3
> binding model.
>
> Any help or suggestion from the community in this matter would be highly
> appreciated.
>
> Thank you,
> M Chandra
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>

-- 

*Mintu Chandra*, PhD

Research Assistant Professor

Department of Biological Sciences & Biochemistry

Vanderbilt University

Nashville, TN, USA - 37235

Mobile : 615-947-9274

*Email* : mintu.chan...@vanderbilt.edu

*ORCID* : https://orcid.org/-0003-2382-5024

*Google Scholar* :
https://scholar.google.com.au/citations?user=xYytyGAJ&hl=en

Linkedin : https://www.linkedin.com/in/dr-mintu-chandra-584a8b2b/



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Re: [ccp4bb] Multiple binding model in BLI

[a . perrakis]

Dear Chandra,

What exactly do you mean by 1:3 or 1:2 binding mode? Is that stoichiometry? Do 
you need/want to fit a simple binding model with that stoichiometry, a 
sequential model, or a co-operative model?

Graphpad can get you a long way with existing equations when you define the 
exact problem, but I am personally very find of the KINTEK software (you can 
get a student and trial license for it) which can do anything you ever want to 
do with transit and equilibrium kinetics analysis.

A.




On 28 Aug 2024, at 17:16, Mintu Chandra  wrote:

LET OP: Deze e-mail is afkomstig van buiten de organisatie. Open alleen links 
of bijlagen als je de afzender kent en weet dat de inhoud veilig is.
CAUTION: This email originated from outside of the organization. Do not click 
links or open attachments unless you recognize the sender and know the content 
is safe.
Hello everyone,
I am trying to fit a BLI sensogram curve into a 1:3 binding model but there is 
limited scope in the software package (limited to 1:2 binding model) and 
therefore not able to fit the curve to get the accurate KD value. I am trying 
graphpad prism but not getting enough information on which particular equation 
I need to use to fit the BLI curve into a 1:3 binding model.

Any help or suggestion from the community in this matter would be highly 
appreciated.

Thank you,
M Chandra



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Re: [ccp4bb] malware in ccp4?

[Andy Purkiss]

Hi Andrea,

I would suggest that this is probably a false positive down to the way your 
anti-virus software detects threats. Searching for this particular threat gives 
several similar examples from even very simple Python code.

On my home PC, a scan of the CCP4 installation with Windows Defender doesn't 
report any issues.

Hope that helps,

Andy


From: CCP4 bulletin board  on behalf of Andrea Smith 

Sent: 28 August 2024 12:05
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] malware in ccp4?


External Sender: Use caution.


Hi,



I updated to ccp4-9 a couple of days ago (windows, package manager) and today 
my antivirus moved one of the ccp4 files to a quarantine. It was:

CCP4-9/WinCoot1/lib/python.3.11/site-packages/rdkit/Chem/rdDistGeom.pyd


It claims the threat is Win64:Evo-gen [Trj].



Is this an issue or did my antivirus just delete an actual part of a software?



Thank you,

Andrea



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The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



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Re: [ccp4bb] Terminating a protein:cmpd covalent adduction using DTT

[Artem Evdokimov]

Dear Yong,

I've used both BME and DTT (as well as CoA, Cys, or GSH, etc.) to
terminate/exhaust covalent chemistry on Cys residues. It's relatively
speaking 'a piece of cake' however one has to keep in mind that if the
particular covalent reagent is very highly specific towards a Cys residue
in a protein's targeted microenvironment, that reagent may not be reactive
enough to effectively quench with BME or DTT. In other terms, the 'warhead'
reactivity may be dialed down so much that it does not react readily with
free thiols. You may want to confirm your outcome somehow (e.g. by small
molecule MS).

It's not like this reaction is hard to set up, or requires massive
optimization of conditions - generally speaking, as long as you have 'much
more' of DTT or BME than you have of the covalent agent, given some time
the reaction will go to completion.

All the best,

Artem

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410814/
"*Excess alkylating compound was quenched with 1 mM DTT*"

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310217/
"*...useful post-reaction to quench any remaining maleimide after achieving
the desired conjugation levels.*"

https://pubmed.ncbi.nlm.nih.gov/26387744/
"*...N-acetyl cysteine (21 μL of 100 mM stock in water, 2.2 μmol, 40 eq)
was added to quench unreacted maleimide.*"

- Cosmic Cats approve of this message


On Tue, Aug 27, 2024 at 3:17 PM Yong Tang  wrote:

> Dear all, happy summer!
>
> I searched in many ways but could not find relevant references easily
> so I'm hoping you could help.
>
> For TSA assays on a Cys-containing protein (drug target) that has just
> gone through a covalent adduction reaction with a compound carrying a
> Michael acceptor covalent warhead, we would like to stop the further
> progression of the covalent adduction before subjecting the reaction
> mixture to TSA analysis. It is my understanding that people usually use DTT
> to deplete the excess covalent compound - do you happen to come across such
> a scientific reference?
>
> Thank you so much in advance, -yong
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Showing Stick Representation In Coot

[Firdous Tarique]

Thanks Parijat

This is exactly what I wanted.

Best wishes

Firdous

On Tue, Aug 27, 2024 at 3:00 PM Parijat Das  wrote:

> You can use the Draw>Additional representation to do that in coot.
>
> Regards,
>
> Parijat
>
>
> On Tue, Aug 27, 2024 at 6:22 PM Firdous Tarique <
> kahkashantari...@gmail.com> wrote:
>
>> Hello everyone.
>>
>> Is there any way to show stick representation of the selected amino acid
>> residues in Coot while everything else is represented in the form of
>> C-alphas/Backbone. I want to show the amino acids of the catalytic centre
>> in the stick form and not alter the C-alphas/Backbone conformation for the
>> rest of the molecule. Just curious if it can be done in Coot or not.
>>
>> Best
>>
>> Firdous
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] Showing Stick Representation In Coot

[Firdous Tarique]

That makes sense.

Thanks

On Tue, Aug 27, 2024 at 2:46 PM Edwin Pozharski 
wrote:

> I don't know the explicit answer to your question, but you can always copy
> active site residues into a separate model and use different representation
> for that.
>
> On Tue, Aug 27, 2024 at 8:52 AM Firdous Tarique <
> kahkashantari...@gmail.com> wrote:
>
>> Hello everyone.
>>
>> Is there any way to show stick representation of the selected amino acid
>> residues in Coot while everything else is represented in the form of
>> C-alphas/Backbone. I want to show the amino acids of the catalytic centre
>> in the stick form and not alter the C-alphas/Backbone conformation for the
>> rest of the molecule. Just curious if it can be done in Coot or not.
>>
>> Best
>>
>> Firdous
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] Showing Stick Representation In Coot

[Edwin Pozharski]

I don't know the explicit answer to your question, but you can always copy
active site residues into a separate model and use different representation
for that.

On Tue, Aug 27, 2024 at 8:52 AM Firdous Tarique 
wrote:

> Hello everyone.
>
> Is there any way to show stick representation of the selected amino acid
> residues in Coot while everything else is represented in the form of
> C-alphas/Backbone. I want to show the amino acids of the catalytic centre
> in the stick form and not alter the C-alphas/Backbone conformation for the
> rest of the molecule. Just curious if it can be done in Coot or not.
>
> Best
>
> Firdous
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Mini map aide updates

[Jon Cooper]

A couple of updates to Mini Map Aide (https://minimapai.de), if anyone likes 
the idea of looking at maps on mobile phones, although I know many people look 
at their phones to get away from maps ;-

It can now draw symmetry-related molecules based on the space group symbol 
given in the CRYST1 card in the PDB file. At least one expert (Ian Tickle) was 
not very impressed with my method for generating the symmetry-mates, so do not 
expect the world's fastest performance! Still it should work for all of the 65 
enantio-morphic/genic space groups, except for R3 and R32 which are handled as 
H3 and H32. A few of the more common non-standard ones also work. It should 
handle about 99.89 % of the crystal structures in the PDB!

I also spotted recently that it was not displaying many (probably most) of the 
CCP4 maps which are downloadable from the EBI PDBe but that is now fixed, I 
think. At some stage they switched from storing maps which cover the deposited 
coordinates to storing the map for exactly one complete unit cell, which is 
quite elegant because the electron density values for a molecule that happens 
to be outside the cell can still be read on the fly quite easily.
Do let me know of any problems.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.

On Sunday, 12 March 2023 at 00:11, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> I am cautiously optimistic that there have been some improvements to my Mini 
> Map Aide (a basic map viewer mainly for mobile devices): http://minimapai.de
>
> - The browser does not accidentally 'go back' on scrolling upwards in the 
> graphics window.
> - Atom selection is now more accurate i.e. it almost works reliably, unlike 
> before.
> -
>
> Better memory management - it can go through several hundred residues without 
> crashing!
>
> -
>
> New virtual server!
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent with [Proton Mail](https://proton.me/) secure email.
>
> --- Original Message ---
> On Wednesday, November 9th, 2022 at 00:30, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> For info, or more likely amusement, the Mini Map Aide website which I put 
>> together a few months ago for looking at electron density maps, primarily on 
>> mobile devices:
>>
>> http://minimapai.de
>>
>> now allows tweaks to be made to individual amino acids and basic 
>> regularisation to be done, so there definitely is no excuse to shrink from 
>> building, or at least tweaking, models. It is still a bit harebrained and 
>> I'm not sure how the results of my geometry minimiser would stand up in any 
>> validation tests but, used cautiously, it seems to give better rmsd's than 
>> the 1974 lysozyme models ;-0
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent with [Proton Mail](https://proton.me/) secure email.
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

[John R Helliwell]

Dear Medhanjali,In case of difficulty with the weblink in our J Appl Cryst Online DPI paper that I mentioned, Prof Sekar provides this one:-Diffraction Precision Index (DPI)physics.iisc.ac.inBest wishes,John Emeritus Professor John R Helliwell DScOn 23 Aug 2024, at 21:53, Medhanjali Dasgupta  wrote:Thank you all for the help!MOn Fri, Aug 23, 2024, 1:32 PM Pavel Afonine  wrote:Hi,phenix.refine reports it in the log file (coordinate error estimate, not DPI).PavelOn Fri, Aug 23, 2024 at 12:45 AM John R Helliwell  wrote:Dear Medhanjali,I imagine you would find this useful:-Online_DPI: a web server to calculate the diffraction precision index for a protein structurejournals.iucr.orgSee also:-sciencedirect.comBest wishes,John Emeritus Professor John R Helliwell DScOn 22 Aug 2024, at 19:08, Medhanjali Dasgupta  wrote:Hello,I am looking to estimate coordinate errors in my models before depositing them. Is there anything that automatically generates Luzzati plots for the pdb models and estimate coordinate errors?Thanks in advance!Medhanjali


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Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

[Medhanjali Dasgupta]

Thank you all for the help!

M

On Fri, Aug 23, 2024, 1:32 PM Pavel Afonine  wrote:

> Hi,
>
> phenix.refine reports it in the log file (coordinate error estimate, not
> DPI).
>
> Pavel
>
> On Fri, Aug 23, 2024 at 12:45 AM John R Helliwell 
> wrote:
>
>> Dear Medhanjali,
>> I imagine you would find this useful:-
>> Online_DPI: a web server to calculate the diffraction precision index for
>> a protein structure
>> 
>> journals.iucr.org
>> 
>> [image: apple-touch-icon-precomposed.png]
>> 
>> 
>> See also:-
>> sciencedirect.com
>> 
>> 
>> 
>>
>> Best wishes,
>> John
>>
>> Emeritus Professor John R Helliwell DSc
>>
>>
>>
>>
>> On 22 Aug 2024, at 19:08, Medhanjali Dasgupta <
>> medhanjalidasgu...@gmail.com> wrote:
>>
>> 
>> Hello,
>>
>> I am looking to estimate coordinate errors in my models before depositing
>> them. Is there anything that automatically generates Luzzati plots for the
>> pdb models and estimate coordinate errors?
>>
>>
>> Thanks in advance!
>> Medhanjali
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>
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>>
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>
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Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

[Pavel Afonine]

Hi,

phenix.refine reports it in the log file (coordinate error estimate, not
DPI).

Pavel

On Fri, Aug 23, 2024 at 12:45 AM John R Helliwell 
wrote:

> Dear Medhanjali,
> I imagine you would find this useful:-
> Online_DPI: a web server to calculate the diffraction precision index for
> a protein structure
> 
> journals.iucr.org
> 
> [image: apple-touch-icon-precomposed.png]
> 
> 
> See also:-
> sciencedirect.com
> 
> 
> 
>
> Best wishes,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 22 Aug 2024, at 19:08, Medhanjali Dasgupta <
> medhanjalidasgu...@gmail.com> wrote:
>
> 
> Hello,
>
> I am looking to estimate coordinate errors in my models before depositing
> them. Is there anything that automatically generates Luzzati plots for the
> pdb models and estimate coordinate errors?
>
>
> Thanks in advance!
> Medhanjali
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
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Re: [ccp4bb] HERCULES 2025 - European School

[giorgio schiro]

Hi all,

off course there is a mistake in the deadline: it is of course 6 October 
2024, not 2023.



Best wishes,

giorgio


On 23/08/2024 11:02, giorgio schiro wrote:



*HERCULES 2025**- European School*
/Neutron & Synchrotron Radiation Science since 1991/

*2025 **session**:**/9th March - 12th April, 2025/*
DEADLINE FOR APPLICATION: 6 October 2023

HERCULES is a European course for PhD students and young researchers 
using *Neutrons* *and **Synchrotron Radiation* for applications in 
*Biology*, *Chemistry*, *Physics*, *Hard & Soft Condensed Matter*.


The 5-week school includes *lectures* (60%), *hands-on practicals, 
labs &* *tutorials* (30%), visits, a poster session, group work 
sessions, ...
/*P*//*articipants will spend one week in a partner institution*//in 
Europe among/:


  * *ALBA* in Barcelona, Spain
  * *PETRA III and EU-XFEL* in Hambourg, Germany
  * *KIT light source *in Karlsruhe, Germany
  * *SOLEIL *in Saint-Aubin, France

This comes in addition to practicals, labs, and tutorials which will 
take place in Grenoble at *ILL*, *ESRF* and Grenoble Laboratories 
(*CNRS*, *IBS*).


The school  includes a common part and two parallel sessions:
- /*Physics and chemistry of condensed matter (session A)*/
- /*Biomolecular and soft condensed matter (session B)*/
The school will be held in an hybrid format. Thus, a part-time online 
participation is also possible, consisting only in following online 
the lectures held in Grenoble during weeks 1, 2, 3 and 5.


*_/Why join Hercules/_/?/*
- to *learn new techniques using neutron and synchrotron radiation*
- to expand your *theoretical *and*practical *knowledge, /not only for 
your present research but also for your scientific career/

- to *experiment these techniques* on world-class instruments & beamlines
- to *build a network of relations* with fellow young researchers and 
experienced teachers from all over the World


/*Bursaries/reduced costs*/
- A limited number of fellowship grants will be available to reduce 
registration fees


  * Full list of lectures:
https://hercules-school.eu/general-programme (with links to the
dedicated pages)
  * Download the full 2023 Booklet (lectures, practicals...)





*Contact email*: hercu...@hercules-school.eu





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Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

[John R Helliwell]

Dear Medhanjali,I imagine you would find this useful:-Online_DPI: a web server to calculate the diffraction precision index for a protein structurejournals.iucr.orgSee also:-sciencedirect.comBest wishes,John Emeritus Professor John R Helliwell DScOn 22 Aug 2024, at 19:08, Medhanjali Dasgupta  wrote:Hello,I am looking to estimate coordinate errors in my models before depositing them. Is there anything that automatically generates Luzzati plots for the pdb models and estimate coordinate errors?Thanks in advance!Medhanjali


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Re: [ccp4bb] CIF file Cannot Open by Coot

[Martin Hu]

Dear All,

I sincerely appreciate everyone’s contributions and suggestions—the issue has 
now been resolved!

Following Oliver's instructions, I used the Grad Web Server to obtain the 
coordinates and restraint files for input, then adjusted the conformation using 
real-space refinement in Coot. The input ligand now has restraints and can be 
refined via Refmac.

Thank you all again for your invaluable support.

Best regards,
Martin



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Re: [ccp4bb] current non-commercial version of XDS will expire at end of August

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

Rather unsurprisingly xia2 will stop working with this version due to some 
rather inelegant parsing of the INTEGRATE.LP file - the fix is an easy one and 
will come out in the next-but-one release of dials as the next release was 
already in progress. An extra couple of spaces and slightly wider columns mean 
the text scraping was broken (astonishing that it survived until now)

If anyone needs a quick fix I can send out a simple set of instructions for an 
in-place change.

The overall behaviour seems unaffected but I have not yet checked in detail.

Best wishes Graeme

> On 20 Aug 2024, at 12:20, Kay Diederichs  
> wrote:
>
> CAUTION: This email is from outside of the organisation and has a suspicious 
> subject or content. This might likely be a phishing email. Do not click links 
> or open attachments unless you recognise the sender and know the content is 
> safe. If in doubt, contact IT Helpdesk.
>
>
> Dear XDS users,
>
> just a heads-up: non-commercial users of XDS should update their binaries; 
> download link and release notes are at https://xds.mr.mpg.de/ .
>
> A few little things have changed so you may have to adapt your scripts.
>
> Best wishes,
> Kay
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
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Re: [ccp4bb] CIF file Cannot Open by Coot

[Oliver Smart]

Hi Martin,

I hope you are getting on well with one of the restraints for your molecule. 
But if choose
to tweak the restraints to agree with a CSD small molecule structure for 
BODIPY, then
I thought I should let you know that the structure you have downloaded YOWVOW 
has a high R-factor 10.29%

> On 19 Aug 2024, at 12:42, Martin Hu  wrote:
> 
> _refine_ls_R_factor_gt   0.1029

There is a better-determined structure in the CSD YOWVOW01 that has an R-factor
of 3.09% that can be accessed from

https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=YOWVOW01

You can download a MOL2 file from there (use the button in the 3D viewer).

If you want to tweak ideal bond lengths etc. then it would be much more 
sensible to use
YOWVOW01 than YOWVOW as a source of information.

Best regards,

Oliver





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Re: [ccp4bb] CIF file Cannot Open by Coot

[Fei Long]

Hi,

Sorry. One correction in the restraint or dictionary file. There are 
three rings in the molecules. Two rings (without B1 atom) are aromatic 
and the ring with B1 is not. That might not affect the result of 
refinement too much. Anyway, the new restraint file is attached again.


Best wishes,

Fei

On 2024-08-19 14:42, Hu, Wenhao wrote:

Dear Jon,

Thank you so much for all your effort! I really appreciate it. I’ve
just tried to load the files, but unfortunately, it still won’t open
and continues to show the error message I’ve attached here.

Thanks again for your help.

Best regards,

Martin

From: CCP4 bulletin board  on behalf of Jon
Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot

⚠ Caution: External sender

I made your cif into a pdb (attached) which looks OK. Maybe worth
trying with that.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 19/08/2024 12:42, Martin Hu  wrote:


 Dear All,

 Thank you all for your help. I’ve tried several approaches to

input this file, including changing the format to mmCIF, importing it
as coordinates, and checking the restraints in the file. However, I am
still unable to install the experimental ligand structure into the
protein. It seems that COOT or JLigand cannot read the restraints from
the CIF file.


 I’m wondering if anyone has faced a similar problem before, and

if there is a way to input the experimental structure and save its
restraints so that it can be refined with the overall protein
structure in Refmac?


 I’ve attached the original CIF file here for your reference (in

.txt format).


 Sincerely,
 Martin






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###

 #
 # This file contains crystal structure data downloaded from the
 # Cambridge Structural Database (CSD) hosted by the Cambridge
 # Crystallographic Data Centre (CCDC).
 #
 # Full information about CCDC data access policies and citation
 # guidelines are available at

https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccdc.cam.ac.uk%2Faccess%2FV1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623572595%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1UNcBtGEJl2mElc8AyyDvIzhkmQzINthVoWLdUFtKPk%3D&reserved=0
[5]

 #
 # Audit and citation data items may have been added by the CCDC.
 # Please retain this information to preserve the provenance of
 # this file and to allow appropriate attribution of the data.
 #


###


 data_twin5
 _audit_block_doi 10.5517/ccryflp
 _database_code_depnum_ccdc_archive 'CCDC 713483'
 loop_
 _citation_id
 _citation_doi
 _citation_year
 1 

Re: [ccp4bb] CIF file Cannot Open by Coot

[Oliver Smart]

Dear Martin,

My approach to your problem is to download an MOL2 of the small-molecule 
compound from WebCSD rather than the small-molecule CIF file. MOL2 files have 
the advantage that both the coordinates and the CCDC-curated bond orders are 
included in the file. MOL2 files can be read by AceDRG, Grade2, and eLBOW.

I have recorded a YouTube video showing how to download a MOL2 file for your 
ligand from WebCSD, use it in the Grade Web Server to produce restraints and 
use them in COOT.

Please see https://youtu.be/Sx6haYQ3tSY for the YouTube video.

I will send you the Grade Web Server tarball off the bulletin board.

I hope this is useful!

Best regards,

Oliver


> On 19 Aug 2024, at 12:42, Martin Hu  wrote:
> 
> Dear All,
> 
> Thank you all for your help. I’ve tried several approaches to input this 
> file, including changing the format to mmCIF, importing it as coordinates, 
> and checking the restraints in the file. However, I am still unable to 
> install the experimental ligand structure into the protein. It seems that 
> COOT or JLigand cannot read the restraints from the CIF file.
> 
> I’m wondering if anyone has faced a similar problem before, and if there is a 
> way to input the experimental structure and save its restraints so that it 
> can be refined with the overall protein structure in Refmac?
> 
> I’ve attached the original CIF file here for your reference (in .txt format).
> 
> Sincerely,
> Martin
> 
> 
> 
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> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
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> 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/
> ### 
> # 
> # This file contains crystal structure data downloaded from the 
> # Cambridge Structural Database (CSD) hosted by the Cambridge 
> # Crystallographic Data Centre (CCDC).
> # 
> # Full information about CCDC data access policies and citation 
> # guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 
> # 
> # Audit and citation data items may have been added by the CCDC. 
> # Please retain this information to preserve the provenance of 
> # this file and to allow appropriate attribution of the data. 
> # 
> ###
> 
> data_twin5
> _audit_block_doi 10.5517/ccryflp
> _database_code_depnum_ccdc_archive 'CCDC 713483'
> loop_
> _citation_id
> _citation_doi
> _citation_year
> 1 10.1016/j.dyepig.2009.03.001 2009
> _audit_update_record 
> ;
> 2008-12-13 deposited with the CCDC.   2024-08-19 downloaded from the CCDC.
> ;
> 
> 
> 
> _audit_creation_method   SHELXL-97
> 
> _chemical_name_systematic
> ;
> 
> ?
> 
> ;
> 
> _chemical_name_common?
> 
> _chemical_melting_point  ?
> 
> _chemical_formula_moiety 'C9 H7 B F2 N2'
> 
> _chemical_formula_sum'C9 H7 B F2 N2'
> 
> _chemical_formula_weight 191.98
> 
> 
> 
> loop_
> 
> _atom_type_symbol
> 
> _atom_type_description
> 
> _atom_type_scat_dispersion_real
> 
> _atom_type_scat_dispersion_imag
> 
> _atom_type_scat_source
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
> H H 0. 0. 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
> B B 0.0013 0.0007 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
> N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
> F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
> 
> 
> 
> _symmetry_cell_setting   Monoclinic
> 
> _symmetry_space_group_name_H-M   C2/c
> _symmetry_space_group_name_Hall  '-C 2yc'
> 
> 
> 
> loop_
> 
> _symmetry_equiv_pos_as_xyz
> 
> 
> 
> 
> 
> 
> 
> 
> 'x, y, z'
> '-x, y, -z+1/2'
> 'x+1/2, y+1/2, z'
> '-x+1/2, y+1/2, -z+1/2'
> '-x, -y, -z'
> 'x, -y, z-1/2'
> '-x+1/2, -y+1/2, -z'
> 'x+1/2, -y+1/2, z-1/2'
> 
> 
> 
> _cell_length_a   10.126(4)
> 
> _cell_length_b   10.196(4)
> 
> _cell_length_c   17.143(6)
> 
> _cell_angle_alpha90.00
> 
> _cell_angle_beta 102.285(6)
> 
> _cell_angle_gamma90.00
> 
> _cell_volume 1729.5(11)
> 
> _cell_formula_units_Z8
> 
> _cell_measurement_temperature296(2)
> 
> _cell_measurement_reflns_used32
> 
> _cell_measurement_theta_min  2.45
> 
> _cell_measurement_theta_max  12.33
> 
> 
> 
> _exptl_crystal_description   plate
> 
> _exptl_crystal_colourorange
> 
> _exptl_crystal_size_max  0.20
> 
> _exptl_crystal_size_mid  0.20
> 
> _exptl_crystal_size_min  0.04
> 
> _exptl_crystal_density_meas  'not measured'
> 
> _ex

Re: [ccp4bb] CIF file Cannot Open by Coot

[CRAIG A BINGMAN]

If you open the original file with a text editor, you can see that it was 
slightly damaged. I opened the file you posted with a text editor, and the 
problems were easy to find, as they are at the top (and bottom) of the file.  
To be sure, I downloaded the file directly from CCDC.  There are two 
differences.

This stuff was added by the CCP4BB software to the posted file, and people 
downloading it need to remove it for the file to conform to cif format.


< 

<

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The original problem seems to be

# guidelines are available at http://www.ccdc.cam.ac.uk/access/V1

was substituted with

# guidelines are available at 
https://urldefense.com/v3/__http://www.ccdc.cam.ac.uk/access/V1__;!!Mak6IKo!
OV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urJe0f3Kw$<https://urldefense.com/v3/__http:/www.ccdc.cam.ac.uk/access/V1__;!!Mak6IKo!%0bOV_3FThPxaA5qExHRwno08D_kXk6gsRk82GjtYbpPlS2-UxkKj_2PucPWORcGrONc3f5vLk9L3l-uXQ64urJe0f3Kw$>

This caused OV_3… to appear on a new line without a comment.
If you put a “#” character in front of the OV_3, or delete the entire line 
starting with OV_3 (and get rid of the footer tacked on by CCP4BB) the file 
loads into pymol and coot just fine.

Craig


From: CCP4 bulletin board  on behalf of Martin Hu 

Date: Monday, August 19, 2024 at 6:43 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
Dear All,

Thank you all for your help. I’ve tried several approaches to input this file, 
including changing the format to mmCIF, importing it as coordinates, and 
checking the restraints in the file. However, I am still unable to install the 
experimental ligand structure into the protein. It seems that COOT or JLigand 
cannot read the restraints from the CIF file.

I’m wondering if anyone has faced a similar problem before, and if there is a 
way to input the experimental structure and save its restraints so that it can 
be refined with the overall protein structure in Refmac?

I’ve attached the original CIF file here for your reference (in .txt format).

Sincerely,
Martin



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[ccp4bb] Your restraint file from acedrg Re: [ccp4bb] CIF file Cannot Open by Coot

[Fei Long]

Dear all,

The attached is a restraint file generated by aceDRG, using your 
713483.txt as the input file. The latest version of aceDRG, currently 
not released yet and under the final testing, can generate restraint or 
dictionary files of ligands using input files in form of small molecule 
cif files from CSD or COD. The things under testing are deciding 
bond-orders and charges, the rest of the chemistry are already within 
the released version of aceDRG. We will try to release that version, 
which will deal with the molecules with metal as well, as soon as 
possible. Meanwhile, please try that file and tell us (me, Garib, or 
Paul) if you see any problem.


Best wishes,

Fei

On 2024-08-19 15:02, Paul Emsley wrote:

On 19/08/2024 14:42, Hu, Wenhao wrote:


Dear Jon,

Thank you so much for all your effort! I really appreciate it.
I’ve just tried to load the files, but unfortunately, it still
won’t open and continues to show the error message I’ve attached
here.


Martin,

These are not restraints. They are not in mmCIF format (as Philip
Jeffrey says) - which is the format Coot expects for restraints. Coot
- an indeed any other program - will continue to give you error
messages if you read in a small molecule cif files as if they were
restraints.

We, in the CCP4 world, typically use Acedrg to generate restraints.
You will need to generate a suitable input for Acedrg given your cif
file. The author of Acedrg would be in a good place to help you with
that. Have you ever played Street Fighter?

Paul.

-

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--
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk
Tel:+44 1223 4027844




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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
LIG   LIG   "Test_713483_mol_1" NON-POLYMER 21 14 . 
#
data_comp_LIG
_chem_comp.pdbx_typeHETAIN
#

loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
LIG F1  F1  F F0  0.057  1.314 1.644  0.057  1.314 1.644
LIG N2  N2  N NR5  1  0.974  3.504 2.269  0.974  3.504 2.269
LIG B1  B1  B B-1 -0.090 2.690 1.420  -0.090 2.690 1.420
LIG C5  C5  C CR16 0  2.169  4.568 0.423  2.169  4.568 0.423
LIG C6  C6  C CR56 0  1.978  4.340 1.782  1.978  4.340 1.782
LIG C7  C7  C CR15 0  2.676  4.844 2.916  2.676  4.844 2.916
LIG C8  C8  C CR15 0  2.072  4.295 4.049  2.072  4.295 4.049
LIG C9  C9  C CR15 0  1.027  3.474 3.626  1.027  3.474 3.626
LIG F2  F2  F F0  -1.390 3.106 1.740  -1.390 3.106 1.740
LIG N1  N1  N NR5  0  0.294  3.080 -0.067 0.294  3.080 -0.067
LIG C1  C1  C CR15 0  -0.365 2.606 -1.156 -0.365 2.606 -1.156
LIG C2  C2  C CR15 0  0.224  3.143 -2.301 0.224  3.143 -2.301
LIG C3  C3  C CR15 0  1.275  3.971 -1.899 1.275  3.971 -1.899
LIG C4  C4  C CR56 0  1.320  3.930 -0.477 1.320  3.930 -0.477
LIG H5A H5A H H0  2.855  5.138 0.120  2.855  5.138 0.120
LIG H7A H7A H H0  3.408  5.435 2.903  3.408  5.435 2.903
LIG H8A H8A H H0  2.324  4.451 4.939  2.324  4.451 4.939
LIG H9A H9A H H0  0.446  2.974 4.188  0.446  2.974 4.188
LIG H1A H1A H H0  -1.103 2.009 -1.135 -1.103 2.009 -1.135
LIG H2A H2A H H0  -0.040 2.978 -3.187 -0.040 2.978 -3.187
LIG H3A H3A H H0  1.847  4.463 -2.462 1.847  4.463 -2.462

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
LIG F1  F(B[6a]N[5a,6a]2F)
LIG N2  
N[5a,6a](C[5a,6a]C[5a]C[6a])(B[6a]N[5a,6a]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG B1  B[6a](N[5a,6a]C[5a,6a]C[5a])2(F)2{2|H<1>,5|C<3>}
LIG C5  C[6a](C[5a,6a]N[5a,6a]C[5a])2(H){1|B<4>,2|H<1>,4|C<3>}
LIG C6  
C[5a,6a](N[5a,6a]B[6a]C[5a])(C[6a]C[5a,6a]H)(C[5a]C[5a]H){1|C<3>,1|N<3>,2|F<1>,2|H<1>}
LIG C7  C[5a](C[5a,6a]N[5a,6a]C[6a])(C[5a]C[5a]H)(H){1|B<4>,1|C<3>,2|H<1>}
LIG C8  C[5a](C[5a]C[5a,6a]H)(C[5a]N[5a,6a]H)(H){1|B<4>,1|C<3>}
LIG C9  
C[5a](N[5a,6a]C[5a,6a]B[6a])(C[5a]C[5a]H)(H){1|C<3>,1|H<1>,1|N<3>,2|F<1>}
LIG F2  F(B[6a]N[5a,6a]2F)
LIG N1  
N[5a,6a](C[5a,6a]C[5a]C[6a])(B[6a]N[5a,6a]FF)(C[5a]C[5a]H){2|C<3>,3|H<1>}
LIG C1  
C[5a](N[5a,6a]C[5a,6a]B[6a])(C[5a]C[5a]H)(

Re: [ccp4bb] CIF file Cannot Open by Coot

[Jon Cooper]

Can coot read the pdb file? If not it maybe because the space group is "nil". 
Try changing it to exactly "P 1"

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 19/08/2024 14:55, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> 
wrote:

> Hello, the cif file is exactly the same as before and it's not mmcif (as that 
> complaint mentions). I thought there might be some way of generating ligand 
> restraints with a pdb file, these days? Is prodrg still around? Probably not 
> - sorry for being a distraction ;-0 ;-0
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>  Original Message 
> On 19/08/2024 14:42, Hu, Wenhao  wrote:
>
>> Dear Jon,
>>
>> Thank you so much for all your effort! I really appreciate it. I’ve just 
>> tried to load the files, but unfortunately, it still won’t open and 
>> continues to show the error message I’ve attached here.
>>
>> Thanks again for your help.
>>
>> Best regards,
>>
>> Martin
>>
>> From: CCP4 bulletin board  on behalf of Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> Date: Monday, August 19, 2024 at 14:24
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>>
>> ⚠ Caution: External sender
>>
>> I made your cif into a pdb (attached) which looks OK. Maybe worth trying 
>> with that.
>>
>> Best wishes, Jon Cooper.
>> jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail Android
>>
>>  Original Message 
>> On 19/08/2024 12:42, Martin Hu  wrote:
>>
>>> Dear All,
>>>
>>> Thank you all for your help. I’ve tried several approaches to input this 
>>> file, including changing the format to mmCIF, importing it as coordinates, 
>>> and checking the restraints in the file. However, I am still unable to 
>>> install the experimental ligand structure into the protein. It seems that 
>>> COOT or JLigand cannot read the restraints from the CIF file.
>>>
>>> I’m wondering if anyone has faced a similar problem before, and if there is 
>>> a way to input the experimental structure and save its restraints so that 
>>> it can be refined with the overall protein structure in Refmac?
>>>
>>> I’ve attached the original CIF file here for your reference (in .txt 
>>> format).
>>>
>>> Sincerely,
>>> Martin
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] CIF file Cannot Open by Coot

[Paul Emsley]

On 19/08/2024 14:42, Hu, Wenhao wrote:



Dear Jon,

Thank you so much for all your effort! I really appreciate it. I’ve 
just tried to load the files, but unfortunately, it still won’t open 
and continues to show the error message I’ve attached here.




Martin,

These are not restraints. They are not in mmCIF format (as Philip 
Jeffrey says) - which is the format Coot expects for restraints. Coot - 
an indeed any other program - will continue to give you error messages 
if you read in a small molecule cif files as if they were restraints.


We, in the CCP4 world, typically use Acedrg to generate restraints. You 
will need to generate a suitable input for Acedrg given your cif file. 
The author of Acedrg would be in a good place to help you with that. 
Have you ever played Street Fighter?


Paul.




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Re: [ccp4bb] CIF file Cannot Open by Coot

[Jon Cooper]

Hello, the cif file is exactly the same as before and it's not mmcif (as that 
complaint mentions). I thought there might be some way of generating ligand 
restraints with a pdb file, these days? Is prodrg still around? Probably not - 
sorry for being a distraction ;-0 ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 19/08/2024 14:42, Hu, Wenhao  wrote:

> Dear Jon,
>
> Thank you so much for all your effort! I really appreciate it. I’ve just 
> tried to load the files, but unfortunately, it still won’t open and continues 
> to show the error message I’ve attached here.
>
> Thanks again for your help.
>
> Best regards,
>
> Martin
>
> From: CCP4 bulletin board  on behalf of Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> Date: Monday, August 19, 2024 at 14:24
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>
> ⚠ Caution: External sender
>
> I made your cif into a pdb (attached) which looks OK. Maybe worth trying with 
> that.
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>  Original Message 
> On 19/08/2024 12:42, Martin Hu  wrote:
>
>> Dear All,
>>
>> Thank you all for your help. I’ve tried several approaches to input this 
>> file, including changing the format to mmCIF, importing it as coordinates, 
>> and checking the restraints in the file. However, I am still unable to 
>> install the experimental ligand structure into the protein. It seems that 
>> COOT or JLigand cannot read the restraints from the CIF file.
>>
>> I’m wondering if anyone has faced a similar problem before, and if there is 
>> a way to input the experimental structure and save its restraints so that it 
>> can be refined with the overall protein structure in Refmac?
>>
>> I’ve attached the original CIF file here for your reference (in .txt format).
>>
>> Sincerely,
>> Martin
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] CIF file Cannot Open by Coot

[Hu, Wenhao]

Dear Jon,

Thank you so much for all your effort! I really appreciate it. I’ve just tried 
to load the files, but unfortunately, it still won’t open and continues to show 
the error message I’ve attached here.

Thanks again for your help.

Best regards,
Martin

From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
⚠ Caution: External sender


I made your cif into a pdb (attached) which looks OK. Maybe worth trying with 
that.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 19/08/2024 12:42, Martin Hu  wrote:

>  Dear All,
>
>  Thank you all for your help. I’ve tried several approaches to input this 
> file, including changing the format to mmCIF, importing it as coordinates, 
> and checking the restraints in the file. However, I am still unable to 
> install the experimental ligand structure into the protein. It seems that 
> COOT or JLigand cannot read the restraints from the CIF file.
>
>  I’m wondering if anyone has faced a similar problem before, and if there is 
> a way to input the experimental structure and save its restraints so that it 
> can be refined with the overall protein structure in Refmac?
>
>  I’ve attached the original CIF file here for your reference (in .txt format).
>
>  Sincerely,
>  Martin
>
>  
>
>  To unsubscribe from the CCP4BB list, click the following link:
>  
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623540130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=l0Po7pO%2B5QxANPgjMOPRsZzuCyiu1Jx0xQ%2BVH4J08qQ%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
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>  ###
>  #
>  # This file contains crystal structure data downloaded from the
>  # Cambridge Structural Database (CSD) hosted by the Cambridge
>  # Crystallographic Data Centre (CCDC).
>  #
>  # Full information about CCDC data access policies and citation
>  # guidelines are available at 
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccdc.cam.ac.uk%2Faccess%2FV1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623572595%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1UNcBtGEJl2mElc8AyyDvIzhkmQzINthVoWLdUFtKPk%3D&reserved=0<http://www.ccdc.cam.ac.uk/access/V1>
>  #
>  # Audit and citation data items may have been added by the CCDC.
>  # Please retain this information to preserve the provenance of
>  # this file and to allow appropriate attribution of the data.
>  #
>  ###
>
>  data_twin5
>  _audit_block_doi 10.5517/ccryflp
>  _dat

Re: [ccp4bb] CIF file Cannot Open by Coot

[Martin Hu]

Dear All,

Thank you all for your help. I’ve tried several approaches to input this file, 
including changing the format to mmCIF, importing it as coordinates, and 
checking the restraints in the file. However, I am still unable to install the 
experimental ligand structure into the protein. It seems that COOT or JLigand 
cannot read the restraints from the CIF file.

I’m wondering if anyone has faced a similar problem before, and if there is a 
way to input the experimental structure and save its restraints so that it can 
be refined with the overall protein structure in Refmac?

I’ve attached the original CIF file here for your reference (in .txt format).

Sincerely,
Martin



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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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### 
# 
# This file contains crystal structure data downloaded from the 
# Cambridge Structural Database (CSD) hosted by the Cambridge 
# Crystallographic Data Centre (CCDC).
# 
# Full information about CCDC data access policies and citation 
# guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 
# 
# Audit and citation data items may have been added by the CCDC. 
# Please retain this information to preserve the provenance of 
# this file and to allow appropriate attribution of the data. 
# 
###

data_twin5
_audit_block_doi 10.5517/ccryflp
_database_code_depnum_ccdc_archive 'CCDC 713483'
loop_
_citation_id
_citation_doi
_citation_year
1 10.1016/j.dyepig.2009.03.001 2009
_audit_update_record 
;
2008-12-13 deposited with the CCDC. 2024-08-19 downloaded from the CCDC.
;



_audit_creation_method   SHELXL-97

_chemical_name_systematic
;

?

;

_chemical_name_common?

_chemical_melting_point  ?

_chemical_formula_moiety 'C9 H7 B F2 N2'

_chemical_formula_sum'C9 H7 B F2 N2'

_chemical_formula_weight 191.98



loop_

_atom_type_symbol

_atom_type_description

_atom_type_scat_dispersion_real

_atom_type_scat_dispersion_imag

_atom_type_scat_source










C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0. 0. 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
B B 0.0013 0.0007 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'



_symmetry_cell_setting   Monoclinic

_symmetry_space_group_name_H-M   C2/c
_symmetry_space_group_name_Hall  '-C 2yc'



loop_

_symmetry_equiv_pos_as_xyz








'x, y, z'
'-x, y, -z+1/2'
'x+1/2, y+1/2, z'
'-x+1/2, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -y, z-1/2'
'-x+1/2, -y+1/2, -z'
'x+1/2, -y+1/2, z-1/2'



_cell_length_a   10.126(4)

_cell_length_b   10.196(4)

_cell_length_c   17.143(6)

_cell_angle_alpha90.00

_cell_angle_beta 102.285(6)

_cell_angle_gamma90.00

_cell_volume 1729.5(11)

_cell_formula_units_Z8

_cell_measurement_temperature296(2)

_cell_measurement_reflns_used32

_cell_measurement_theta_min  2.45

_cell_measurement_theta_max  12.33



_exptl_crystal_description   plate

_exptl_crystal_colourorange

_exptl_crystal_size_max  0.20

_exptl_crystal_size_mid  0.20

_exptl_crystal_size_min  0.04

_exptl_crystal_density_meas  'not measured'

_exptl_crystal_density_diffrn1.475

_exptl_crystal_density_method'not measured'

_exptl_crystal_F_000 784

_exptl_absorpt_coefficient_mu0.119

_exptl_absorpt_correction_type   multi-scan

_exptl_absorpt_correction_T_min  0.9766

_exptl_absorpt_correction_T_max  0.9953

_exptl_absorpt_process_details   twinabs



_exptl_special_details   
;

?

;



_diffrn_ambient_temperature  296(2)

_diffrn_radiation_wavelength 0.71073

_diffrn_radiation_type   MoK\a

_diffrn_radiation_source 'fine-focus sealed tube'

_diffrn_radiation_monochromator  graphite

_diffrn_measurement_device_type  'CCD area detector'

_diffrn_measurement_method   'phi and omega scans'

_diffrn_detector_area_resol_mean ?

_diffrn_standards_number ?

_diffrn_standards_interval_count ?

_diffrn_standards_interval_time  ?

_diffrn_standards_decay_%?

_diffrn_reflns_number3845

_diffrn_reflns_av_R_equivalents  0.

_diffrn_reflns_av_sigmaI/netI0.2541

_diffrn_reflns_limit_h_min   -11

_diffrn_reflns_li

[ccp4bb] Coot keybinding [was Re: [ccp4bb] libcheck]

[Paul Emsley]

On 15/08/2024 17:14, Petr Pachl wrote:

[And now this part]



Also two off topic questions regarding coot-1 and coot. I tried to
transfer some of my keybindings and settings to coot-1 "language".


The language is Python (well, one of them is).

Unfortunately, there is not a good web resource for the Python API. (I 
should see to that). The current API documentation is based on the C++ 
API. I hope it is not too difficult to translate.



However as I understand not all things are supported.

That's right. I dropped some things in the move.

  Like adding a icon  for example of "split-water" into the main icon menu...

OK, that's a good example for a blog post. (I should write it.)


And to old coot... is it possible to add keybinding for "tandem
refine"?


H? T? It depends on what is n in "tandem."


  I find it very useful.


Yes, me too. I will add some auto-accept functions for Coot 1.


Paul.



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Re: [ccp4bb] libcheck

[Paul Emsley]

On 16/08/2024 09:06, Andrea Smith wrote:


Dear Paul,


Dear Andrea,


my molecule can't be too big for libcheck as I used libcheck 
successfully for molecules of exactly the same size before.


I said "too big" - what libcheck actually says is that your molecule is 
too _complex_ (particularly in the planes department).


Now, only one atom is different, but this atom is a heavy metal and 
therefore Acedrg won't work (also any program I tried to use with 
SMILES code just gives nonsense pdb and cif output because the 
molecule is quite complex).



aha.


I also can't simply rewrite the atom name in the pdb and cif files I 
have for the old molecules, because the heavy metal changes the 
geometry. Maybe I could try to rewrite the files but it would mean 
manually editing a lot of bond lengths and angles which I know can be 
prevented by generating lib file from libcheck because I already did 
it previously for other similar molecules.


well the coot function write_dictionary_from_residue() can do quite 
a lot for you - if you review and edit the bond orders then you can 
create a suitable input to the above programs (I imagine). Or, perish 
the thought, pyrogen even.


So there must be something wrong either with my pdb I use as input in 
libcheck (but I couldn't figure out what) or the way I run libcheck.




I have run out of CCP4-related solutions. Acedrg doesn't do metals. We 
don't do chemistry perception at the moment.


You might like to have a look at Grade2, phenix.elbow, or Prodrg 
(several years ago Prodrg used to do chemistry perception (at least the 
web-server version did), I haven't used it in quite a while).


Paul.



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Re: [ccp4bb] libcheck

[Andrea Smith]

Dear Paul,
 
my molecule can't be too big for libcheck as I used libcheck successfully for 
molecules of exactly the same size before. Now, only one atom is different, but 
this atom is a heavy metal and therefore Acedrg won't work (also any program I 
tried to use with SMILES code just gives nonsense pdb and cif output because 
the molecule is quite complex). I also can't simply rewrite the atom name in 
the pdb and cif files I have for the old molecules, because the heavy metal 
changes the geometry. Maybe I could try to rewrite the files but it would mean 
manually editing a lot of bond lengths and angles which I know can be prevented 
by generating lib file from libcheck because I already did it previously for 
other similar molecules.
 
So there must be something wrong either with my pdb I use as input in libcheck 
(but I couldn't figure out what) or the way I run libcheck.

Andrea


On Thursday, August 15, 2024 17:13 CEST, Paul Emsley 
 wrote:

 
On 8/15/24 09:01, Andrea Smith wrote:
>
> --
>
> Dear all,
>
Dear Andrea,
>
> I successfully used libcheck to generate libraries for my ligands a 
> couple of months ago. Now I wanted to use it again and it is giving me 
> an error. Moreover, even though I select COOR Y and LCOOR N, libcheck 
> uses COOR N and LCOOR Y.
>
That is chemistry-perception mode, it seems to me (it's been a while 
since I've used it).
>
> Can someone tell me what am I doing wrong?
>
You are doing nothing wrong. You have a big molecule.
>
> I attach a prinscreen from my terminal window. I am using Linux 
> Ubuntu, Libcheck vers 5.2.02 (which I used successfully previously).
>
Fascinating. Libcheck is telling you to edit the Fortran code and 
recompile it. But who's up for that?

The alternative is to use Acedrg.

However, the current version of Acedrg doesn't do chemistry perception - 
so you will have to draw the molecule out in 2D (or by some other means 
determine the SMILES string).

Paul.



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Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Xu, Qingping]

Please note that we are still accepting applications, interested students are 
encouraged to apply before the deadline. A draft program is available at the 
course website.

Charles, Andrey and Qingping


From: CCP4 bulletin board  on behalf of Qingping Xu 
<292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, April 8, 2024 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
details can be found at the school website:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$.
 This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. The daily schedule
will be organized in three sections – lectures, tutorials, and hands-on
(interactive trouble-shooting of the technical difficulties the
participants face in their projects). We have had considerable success
resolving these problems in past years, attested by resulting
publications (see
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$).
 A draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. Graduate
students, postdoctoral researchers and early-career faculty, along with
commercial/industrial researchers are encouraged to apply. Only about 20
applicants will be selected for participation.

Application: Application deadline is  August 31st, 2024. To apply,
visit  
https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. The students will be responsible for their
transportation and lodging. The workshop organizers can assist in making
lodging reservations at the Argonne Guest House. The workshop will cover
all other expenses (including meals).


We hope to see you at the school.

Charles, Andrey, Garib and Qingping



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Re: [ccp4bb] CIF file Cannot Open by Coot

[Paul Emsley]

On 8/15/24 16:08, Hu, Wenhao wrote:

Hi Paul,



I’ve attached screenshots that show the error message from Coot, along 
with the contents of the line that the message refers to. Since this 
CIF file contains experimental data and restrains that would be 
difficult to rebuild in other software, I’m seeking solutions to 
successfully import this file into Coot.

Any help you can provide would be greatly appreciated.



Having now looked at the file and poked at it a bit it is (still) not 
clear to me what is causing the parsing problem when read as a dictionary.


However, that is not important because files from WebCSD are not 
dictionaries. They contain coordinates, so use File → Open Coordinates...


Paul.




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Re: [ccp4bb] libcheck

[Paul Emsley]

On 8/15/24 17:14, Petr Pachl wrote:


Hi Paul,
so there is not  way how to generate cif file when we have precise
ideal structure (given from quantum chemistry calculations)?


[This part first]

That's right (if by that you mean that you (only) have coordinates and 
elements) - not in the CCP4 Ecosystem today.




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Re: [ccp4bb] libcheck

[Petr Pachl]

Hi Paul,
so there is not  way how to generate cif file when we have precise
ideal structure (given from quantum chemistry calculations)?

Also two off topic questions regarding coot-1 and coot. I tried to
transfer some of my keybindings and settings to coot-1 "language".
However as I understand not all things are supported. Like adding a
icon  for example of "split-water" into the main icon menu... 

And to old coot... is it possible to add keybinding for "tandem
refine"? I find it very useful.

Thanks a lot,
Petr

Paul Emsley píše v Čt 15. 08. 2024 v 16:13 +0100:
> On 8/15/24 09:01, Andrea Smith wrote:
> > 
> > --
> > 
> > Dear all,
> > 
> Dear Andrea,
> > 
> > I successfully used libcheck to generate libraries for my ligands a
> > couple of months ago. Now I wanted to use it again and it is giving
> > me 
> > an error. Moreover, even though I select COOR Y and LCOOR N,
> > libcheck 
> > uses COOR N and LCOOR Y.
> > 
> That is chemistry-perception mode, it seems to me (it's been a while 
> since I've used it).
> > 
> > Can someone tell me what am I doing wrong?
> > 
> You are doing nothing wrong. You have a big molecule.
> > 
> > I attach a prinscreen from my terminal window. I am using Linux 
> > Ubuntu, Libcheck vers 5.2.02 (which I used successfully
> > previously).
> > 
> Fascinating. Libcheck is telling you to edit the Fortran code and 
> recompile it. But who's up for that?
> 
> The alternative is to use Acedrg.
> 
> However, the current version of Acedrg doesn't do chemistry
> perception - 
> so you will have to draw the molecule out in 2D (or by some other
> means 
> determine the SMILES string).
> 
> Paul.
> 
> #
> ###
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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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Re: [ccp4bb] CIF file Cannot Open by Coot

[Philip D. Jeffrey]

If you have not edited the file, the WebCSD file will contain the contents of 
the asymmetric unit of a small molecule structure, with reported geometry and 
esds, but no restraints, not least of all because small molecule refinements 
are (nearly always) unrestrained.  This would be CIF format.

Coot is probably expecting mmCIF format, related but not the same thing 
(different dictionary/data items), which is consistent with the error messages.

Phil
Princeton

From: CCP4 bulletin board  on behalf of Hu, Wenhao 

Sent: Thursday, August 15, 2024 11:08 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot

Hi Paul,

Thank you for your reply.

I’ve attached screenshots that show the error message from Coot, along with the 
contents of the line that the message refers to. Since this CIF file contains 
experimental data and restrains that would be difficult to rebuild in other 
software, I’m seeking solutions to successfully import this file into Coot.
Any help you can provide would be greatly appreciated.

Best regards,
Martin

From: Paul Emsley 
Sent: Thursday, August 15, 2024 3:09 PM
To: Hu, Wenhao ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] CIF file Cannot Open by Coot

⚠ Caution: External sender


On 8/15/24 14:44, Martin Hu wrote:
> Dear [Recipient's Name],

Dear [Correspondent's Name],

>
> I have downloaded a CIF file of a ligand of interest directly from WebCSD, 
> which was originally obtained from experimental crystallography research, and 
> attempted to import it into Coot. However, Coot indicates that it cannot read 
> the file for some reason.
And what is that reason?
>   I've also tried opening the CIF file in JLigand, but encountered the same 
> issue, with the program stating that it cannot read the file.
At a guess, I'd imagine that it is for the same reason.
>
> I have already checked the file and confirmed that it contains all necessary 
> descriptions about this ligand. Has anyone encountered a similar problem or 
> know how to resolve it?
>
It might be a matter of too much rather than too little. One wonders.
Until you tell us what coot says in the console, we are a bit in the dark.

Regards,

Paul.





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Re: [ccp4bb] libcheck

[Paul Emsley]

On 8/15/24 09:01, Andrea Smith wrote:


--

Dear all,


Dear Andrea,


I successfully used libcheck to generate libraries for my ligands a 
couple of months ago. Now I wanted to use it again and it is giving me 
an error. Moreover, even though I select COOR Y and LCOOR N, libcheck 
uses COOR N and LCOOR Y.


That is chemistry-perception mode, it seems to me (it's been a while 
since I've used it).


Can someone tell me what am I doing wrong?


You are doing nothing wrong. You have a big molecule.


I attach a prinscreen from my terminal window. I am using Linux 
Ubuntu, Libcheck vers 5.2.02 (which I used successfully previously).


Fascinating. Libcheck is telling you to edit the Fortran code and 
recompile it. But who's up for that?


The alternative is to use Acedrg.

However, the current version of Acedrg doesn't do chemistry perception - 
so you will have to draw the molecule out in 2D (or by some other means 
determine the SMILES string).


Paul.



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Re: [ccp4bb] CIF file Cannot Open by Coot

[Hu, Wenhao]

Hi Paul,

Thank you for your reply.

I’ve attached screenshots that show the error message from Coot, along with the 
contents of the line that the message refers to. Since this CIF file contains 
experimental data and restrains that would be difficult to rebuild in other 
software, I’m seeking solutions to successfully import this file into Coot.
Any help you can provide would be greatly appreciated.

Best regards,
Martin

From: Paul Emsley 
Sent: Thursday, August 15, 2024 3:09 PM
To: Hu, Wenhao ; CCP4BB@JISCMAIL.AC.UK 

Subject: Re: [ccp4bb] CIF file Cannot Open by Coot

⚠ Caution: External sender


On 8/15/24 14:44, Martin Hu wrote:
> Dear [Recipient's Name],

Dear [Correspondent's Name],

>
> I have downloaded a CIF file of a ligand of interest directly from WebCSD, 
> which was originally obtained from experimental crystallography research, and 
> attempted to import it into Coot. However, Coot indicates that it cannot read 
> the file for some reason.
And what is that reason?
>   I've also tried opening the CIF file in JLigand, but encountered the same 
> issue, with the program stating that it cannot read the file.
At a guess, I'd imagine that it is for the same reason.
>
> I have already checked the file and confirmed that it contains all necessary 
> descriptions about this ligand. Has anyone encountered a similar problem or 
> know how to resolve it?
>
It might be a matter of too much rather than too little. One wonders.
Until you tell us what coot says in the console, we are a bit in the dark.

Regards,

Paul.





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Re: [ccp4bb] CIF file Cannot Open by Coot

[Paul Emsley]

On 8/15/24 15:01, Tang, Jiazhi wrote:


--

It happens sometimes when you can not open the downloaded cif files 
properly.


One solution is to draw the compound yourself in Chemdraw, copy the 
smiles and generate the cif in Elbow within the phenix suit or other 
ligand software within ccp4. Just be careful if the ligand contains 
ions, which could cause some issues.



While true, this is not The CCP4 Way.

The CCP4 Way is to draw the ligand with Lidia or Layla or Lhasa (part of 
moorhen.org) and feed the output SMILES (or MolFile) to Acedrg.




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Re: [ccp4bb] CIF file Cannot Open by Coot

[Tang, Jiazhi]

It happens sometimes when you can not open the downloaded cif files properly.

One solution is to draw the compound yourself in Chemdraw, copy the smiles and 
generate the cif in Elbow within the phenix suit or other ligand software 
within ccp4. Just be careful if the ligand contains ions, which could cause 
some issues.

Regards,
Jiazhi

发件人: CCP4 bulletin board  代表 Martin Hu 

发送时间: Thursday, August 15, 2024 2:44:46 PM
收件人: CCP4BB@JISCMAIL.AC.UK 
主题: [ccp4bb] CIF file Cannot Open by Coot

Dear [Recipient's Name],

I have downloaded a CIF file of a ligand of interest directly from WebCSD, 
which was originally obtained from experimental crystallography research, and 
attempted to import it into Coot. However, Coot indicates that it cannot read 
the file for some reason. I've also tried opening the CIF file in JLigand, but 
encountered the same issue, with the program stating that it cannot read the 
file.

I have already checked the file and confirmed that it contains all necessary 
descriptions about this ligand. Has anyone encountered a similar problem or 
know how to resolve it?

Thank you in advance

Best regards,
Martin



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Re: [ccp4bb] CIF file Cannot Open by Coot

[Paul Emsley]

On 8/15/24 14:44, Martin Hu wrote:

Dear [Recipient's Name],


Dear [Correspondent's Name],



I have downloaded a CIF file of a ligand of interest directly from WebCSD, 
which was originally obtained from experimental crystallography research, and 
attempted to import it into Coot. However, Coot indicates that it cannot read 
the file for some reason.

And what is that reason?

  I've also tried opening the CIF file in JLigand, but encountered the same 
issue, with the program stating that it cannot read the file.

At a guess, I'd imagine that it is for the same reason.


I have already checked the file and confirmed that it contains all necessary 
descriptions about this ligand. Has anyone encountered a similar problem or 
know how to resolve it?

It might be a matter of too much rather than too little. One wonders. 
Until you tell us what coot says in the console, we are a bit in the dark.


Regards,

Paul.



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Re: [ccp4bb] DLS/CCP4 data analysis workshop 2024

[David Waterman]

Hi folks,

Here's a reminder that applications are open for the 11th joint
Diamond-CCP4 MX workshop, and remain open for just over one more month. But
with holidays, conferences and all the other distractions of summer, why
not get your application in sooner rather than later? :)

Best wishes,
-- David


On Fri, 26 Jul 2024 at 09:59, David Waterman  wrote:

> We are pleased to announce that applications are now open for the 11th
> joint Diamond-CCP4 Workshop on MX data collection and structure solution!
> Bringing together leading experts in the field of MX to teach best practice
> in data collection and analysis, this course is aimed at PhD students,
> postdocs and early career scientists who have a focus on structural biology.
>
> This is an in-person workshop, based at Diamond Light Source in the UK,
> but will be preceded by two remote setup days on Zoom prior to the on-site
> element. We will make use of a Slack workspace through the course.
>
> It is essential that applicants commit to attending the workshop in its
> entirety. Please note below the workshop days and timings involved:
>
> - First online preparation day (before fishing crystals): Tuesday 29
> October
> - Second online preparation day (before data collection): Tuesday 19
> November
> - On-site: Monday 25 November to Monday 2 December
> - Day off: Saturday 30 November
>
> There is no fee to attend this online workshop, however attendance will be
> subject to an application process and a letter of support from the
> attendee's supervisor will be required. Both the application form and
> supervisor's letter of support will need to be submitted by 17:00 (UK time)
> on 16 September.
>
> Some prior experience of crystallography and data collection is expected,
> and those who already have an interesting project (crystals and possibly
> previously collected datasets) will be given priority in selection.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2024/
>
> -- David (on behalf of the organisers)
>



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Re: [ccp4bb] CCP4 database transfer to new computer

[Poland, Brad]

Never mind.  I figured it out.

From: CCP4 bulletin board  On Behalf Of Poland, Brad
Sent: Thursday, August 8, 2024 2:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] CCP4 database transfer to new computer

Hi all. Does anyone know how to transfer my current CCP4 database to a new 
computer? I’m using the gen 1 GUI. Thank you, Brad Brad Poland, PhD Structural 
Biology Lead Corteva Agriscience 7200 NW 62nd Ave Johnston, IA 50131 To 
unsubscribe

Hi all. Does anyone know how to transfer my current CCP4 database to a new 
computer?  I’m using the gen 1 GUI.

Thank you,

Brad


Brad Poland, PhD
Structural Biology Lead
Corteva Agriscience
7200 NW 62nd Ave
Johnston, IA 50131




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Re: [ccp4bb] Phenix real space refine getting lost ...

[Jon Cooper]

A 2 gigabyte map is a very big one. Maybe it needs resampling or cropping down 
to something in the megabyte range. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 07/08/2024 09:24, Klemens Wild  wrote:

>  Dear community
>  
>  small problem running phenix.real_space_refine on a high resolution map
>  via GUI (2.4 A, 2.05 GB) on a MacBook Pro 32 GB M1 ... Never encountered
>  this before, but always used smaller maps:
>  
>  Routine starts and job hangs upon extracting box (see attachment).
>  Separate job on map runs when I do wrapping (thought it might be this),
>  however, when I feed the GUI with this output, again nothing. Not sure
>  what the problem is (no log file indication or error message): some grid
>  things, unit cell issues, map too big?
>  
>  Some input would be helpful, as I am stuck ...
>  
>  Thx
>  
>  Klemens
>  
>  
>  
>  
>  To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Richard Pauptit, 1954-2024

[Patrick Shaw Stewart]

That's a good obituary, but I don't think it quite communicates how funny -
and quirky - Richard was.  I remember him once giving an introduction to an
invited speaker that went on for around 25 mins.  I know he had ambitions
to become a rock star in his 60s - did he also want to be a stand-up
comic?  The explanation was never given.


On Fri, Aug 2, 2024 at 2:18 PM Caitriona Dennis 
wrote:

> Dear colleagues,
>
> With sadness I convey news of the passing of Dr Richard Pauptit, formerly
> Astrazeneca, U.K.
>  Richard was well known in the protein crystallography field, a great
> scientist and inspiring teacher. Many of you will have encountered him at
> meetings, worked with him and enjoyed his hospitality. He was an active
> member of the CCP4 commitee.
> He retired from Astrazeneca in 2014 but still played a role in many
> projects.
> His obituary is published in ActaF
> https://doi.org/10.1107/S2053230X24007064
> 
> Richard Alexander Pauptit 1954–2024
> 
> Richard Pauptit is remembered.
> doi.org
>
>
> Cait Dennis
> Lecturer, HullYork Medical School, University of York, UK.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
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Re: [ccp4bb] Three years postdoc position at University of Kent

[Mohinder Pal]

Dear all, 

As it is the holiday season, I have extended the deadline for the 3-year 
postdoc position in my lab until 21st August. Please see the link to apply and 
share it if you know someone who would be interested. 

https://www.jobs.ac.uk/job/DJA996/research-associate

Best wishes,
Mohinder

> On 17 Jul 2024, at 19:14, Mohinder Pal  wrote:
> 
> Dear CCP4BB members,
> 
> I am delighted to share that a three-year postdoc position is available in my 
> group. We are looking for an enthusiastic individual interested in 
> biochemistry and structural biology, especially single-particle cryo-electron 
> microscopy and X-ray crystallography techniques. The post is for three years 
> and will investigate the assembly and regulation of DNA repair enzymes.
>  
> The successful candidate will work on a cutting-edge experimental research 
> project in the structure-function analysis and regulation of DNA repair 
> enzymes. The project involves a combination of biochemistry, biophysics, and 
> structural biology work. The structural part of the project will involve 
> single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. 
> The role will also include developing research objectives, conducting 
> research, writing research work for publication, and liaising with national 
> and international collaborators.
>  
> Our laboratory, which is newly established in Kent, is growing fast. We are 
> well-equipped with a 120keV electron microscope for single-particle work and 
> have access to eBIC and the University of Leicester for high-end data 
> collection. In addition, the School of Biosciences at Kent houses numerous 
> shared facilities, from NMR and Mass Spectrometry to cell biology and 
> super-resolution imaging. 
>  
> This 3-year research associate position is available from September 2024, but 
> the start date is flexible. The applicants must have or be about to receive a 
> PhD in a relevant science subject. Candidates should also have some 
> experience in electron microscopy (negative staining and cryo-EM), but 
> training will be provided in this field, offering a unique opportunity for 
> growth and learning. For more information or informal enquiries, please 
> contact Mohinder Pal at m@kent.ac.uk .
>  
> For more details and to apply for this position, please follow the link 
> below: https://www.jobs.ac.uk/job/DIT588/research-associate.
> 
> Best wishes
> Mohinder
> 
> ---
> "Whatever you’re meant to do, do it now. The conditions are always 
> impossible.” 
> Doris Lessing
> ---
>  




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Re: [ccp4bb] Off topic: Nobel prize stats

[Bryan Lepore]

Forgot to credit the Nobel Prize website :The Nobel Prize in Chemistry 1946nobelprize.org-BWL

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Re: [ccp4bb] Off topic: Nobel prize stats

[Bryan Lepore]

The Nobel Prize in Chemistry 1946 

James Batcheller Sumner
“for his discovery that enzymes can be crystallized” 
Prize share: 1/2

John Howard Northrop and Wendell Meredith Stanley "for their preparation of 
enzymes and virus proteins in a pure form"
Prize share 1/2 jointly

Thought it might be worth noting specifically Sumner, even though it isn't 
directly a specific protein structure - though in my haste I might have 
overlooked this in the superb reviews shared already - thank you, much 
appreciated!

-Bryan W. Lepore


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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Eleanor Dodson]

Cutting data back is a BAD THING.. If the information is not provided no
refinement program can use it...
Especially for B factor estimation it is the high resolution data that
indicates AlphaHelix1 is better positioned than SurfaceLoop 3...
E



On Fri, 2 Aug 2024 at 17:19, Reza Khayat  wrote:

> With regards to the image that Bohdan sent and Eleanor's statements, I'm
> curious if  the splitting of B-factors in Bohdan's image is due to the
> increased amount of data (which may diminish the extent of uncertainty),
> due to the diminished ensemble of structures within the crystal, or both.
> What happens to the B-factors of a structure that was derived from a
> 1Angstrom data set if you reduce the amount of data to 3Angstrom. In other
> words, you are diminishing the amount of data but not affecting the
> ensemble of structures that define the crystal. Perhaps I'm way off on this
> one
>
> Best wishes,
> Reza
> --
> *From:* CCP4 bulletin board  on behalf of John R
> Helliwell 
> *Sent:* 02 August 2024 11:47 AM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to
> assume a loop is in place, in the AlphaFold era?
>
> Dear Colleagues,
> I think this paper from 1979 is still very interesting:-
> Crystallographic studies of the dynamic properties of lysozyme
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
> nature.com
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
> [image: apple-touch-icon-f39cb19454.png]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
> Have a great weekend,
> John
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 2 Aug 2024, at 16:29, Bohdan Schneider 
> wrote:
>
> Hello:
>
> yes, a great discussion! I second Eleanor's statement that B-factors of
> high resolution structures do carry a message about atom flexibility. I
> attach a screenshot of a figure from our paper (Schneider et al.: Local
> dynamics of proteins and DNA evaluated from crystallographic B factors,
> Acta Cryst. (2014). D70, 2413–2419) that shows clear resolution dependence
> of B factors at protein/protein interface for amino acids and waters. Our
> high resolution group of structures could not be below 1 Å as Eleanor
> suggests but even modest limit to 1.9 Å and then structures at 1.9-2.5 and
> 2.5-3.0 show the effect clearly. We looked at several other groups of atoms
> (backbone/side chains at the protein core, at the protein surface, DNA
> phosphates/bases, waters at the interfaces or bound on the protein surface)
> and saw the same dependence.
>
> Best,
>
> Bohdan, bs.structbio.org
>
> On 2024-08-02 13:26, Eleanor Dodson wrote:
>
> All interesting points.. (And good to see a reference to /" P.A. Machin,
> J.W. Campbell, M. Elder (Eds)
>
> Refinement of Protein Structures, SERC Daresbury Laboratory, Warrington,
> UK (1980)"/
>
> - for those who remember, a super exciting discussion over what was
> feasible for refinement, and how to do it! )
>
> My take - if a crystal diffracts to 1A we can be fairly sure of the
> accurate position of most of the coordinates, see other conformations for
> some regions, and give realistic B values to most atoms.
>
> If the crystal only diffracts to 3A then the lattice is not perfect, and
> there must be multiple conformations for lots of the molecule.
>
> There is not going to be sufficient experimental data to model this
> properly so every parameter assuming a single conformer - coordinate, B
> value, occupancy - is an approximation. Restraints

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Reza Khayat]

With regards to the image that Bohdan sent and Eleanor's statements, I'm 
curious if  the splitting of B-factors in Bohdan's image is due to the 
increased amount of data (which may diminish the extent of uncertainty), due to 
the diminished ensemble of structures within the crystal, or both. What happens 
to the B-factors of a structure that was derived from a 1Angstrom data set if 
you reduce the amount of data to 3Angstrom. In other words, you are diminishing 
the amount of data but not affecting the ensemble of structures that define the 
crystal. Perhaps I'm way off on this one

Best wishes,
Reza

From: CCP4 bulletin board  on behalf of John R Helliwell 

Sent: 02 August 2024 11:47 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a 
loop is in place, in the AlphaFold era?

Dear Colleagues,
I think this paper from 1979 is still very interesting:-
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
Crystallographic studies of the dynamic properties of 
lysozyme<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
nature.com<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
[apple-touch-icon-f39cb19454.png]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_280563a0&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_Me4Xe5QZbbYN_GNBrKXdDe2jPv25n-V7XAp03Qcx-XmE9JutFEcl_X81WALv787&s=jC_Z5R86pF5k_iS5FpD1922HfoZySK0czqxWXOR8Gag&e=>
Have a great weekend,
John

Emeritus Professor John R Helliwell DSc




On 2 Aug 2024, at 16:29, Bohdan Schneider  wrote:

Hello:

yes, a great discussion! I second Eleanor's statement that B-factors of high 
resolution structures do carry a message about atom flexibility. I attach a 
screenshot of a figure from our paper (Schneider et al.: Local dynamics of 
proteins and DNA evaluated from crystallographic B factors, Acta Cryst. (2014). 
D70, 2413–2419) that shows clear resolution dependence of B factors at 
protein/protein interface for amino acids and waters. Our high resolution group 
of structures could not be below 1 Å as Eleanor suggests but even modest limit 
to 1.9 Å and then structures at 1.9-2.5 and 2.5-3.0 show the effect clearly. We 
looked at several other groups of atoms (backbone/side chains at the protein 
core, at the protein surface, DNA phosphates/bases, waters at the interfaces or 
bound on the protein surface) and saw the same dependence.

Best,

Bohdan, bs.structbio.org

On 2024-08-02 13:26, Eleanor Dodson wrote:
All interesting points.. (And good to see a reference to /" P.A. Machin, J.W. 
Campbell, M. Elder (Eds)
Refinement of Protein Structures, SERC Daresbury Laboratory, Warrington, UK 
(1980)"/
- for those who remember, a super exciting discussion over what was feasible 
for refinement, and how to do it! )
My take - if a crystal diffracts to 1A we can be fairly sure of the accurate 
position of most of the coordinates, see other conformations for some regions, 
and give realistic B values to most atoms.
If the crystal only diffracts to 3A then the lattice is not perfect, and there 
must be multiple conformations for lots of the molecule.
There is not going to be sufficient experimental data to model this properly so 
every parameter assuming a single conformer - coordinate, B value, occupancy - 
is an approximation. Restraints help to some extent but they impose prior 
knowledge and do not glean information from the experimental data.
The "trash can" should indicate the degree of uncertainty and interpreting that 
is a bit problematic.  B values twice the overall B ?? Hmm-  do NOT base too 
much faith in that part of the model.. As crystallographers I think maybe we 
need to flag this better for trusting users of the information. Omitting that 
region? I am not sure .. How do others model those floppy lysines? I usually 
make a sort of informed guess but indeed giving a single conformation is not 
the truth, the whole truth, and nothing but the truth..
On Fri, 2 Aug 2024 at 0

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[John R Helliwell]

ts). I have never seen a    macromolecular refinement end up with Rwork = 0.  Have you?    At the end of the day, what we do with our models is look at their    parameters and try to extract the physically meaningful reality they    are trying to capture. Restraints are very helpful in preventing    many types of unrealistic situations, but ultimately it is up to you    to decide if the fitted model makes sense.    -James Holton    MAD Scientist    On 7/30/2024 11:30 AM, Ian Tickle wrote:    Obviously no refined parameters can ever be completely error-free,    it's just that for the co-ordinates we have very accurate    geometric restraints so that the relative uncertainty in the    refined co-ordinates is small (but try refining co-ordinates    without restraints!).  For the B factors we don't have accurate    estimates (if any) for their restraints so their relative    uncertainty after refinement is much greater.    -- Ian    On Tue, Jul 30, 2024 at 6:57 PM Oganesyan, Vaheh  wrote:    Yes, it is and I like the definition of shared “trash bin”. It    will have more physical meaning if we can separate those    contributions into separate bins.    Vaheh    *From:* Pavel Afonine     >    *Sent:* Tuesday, July 30, 2024 1:51 PM    *To:* Oganesyan, Vaheh     >    *Cc:* CCP4BB@jiscmail.ac.uk     *Subject:* Re: [ccp4bb] How high a B factor is too high to    assume a loop is in place, in the AlphaFold era?    Vaheh,    I think coordinates are no different from B factors,    occupancies, f', or f'' in this respect. Coordinates can play    their "trash bin" role by adjusting to the noise at the    expense of violated geometry (bonds, angles, planes, torsions,    etc.). As I mentioned in my previous email, their trash bin    capacity is much smaller (but definitely not zero!) because    the number and strength (confidence) of geometry restraints    are much greater than those of ADP restraints.    I agree that all refined parameters share this trash bin    capacity, but to varying degrees. Isn't this essentially what    we call the error on the refined parameter? All refined    parameters have their error bars, which we have referred to as    the "trash bin" in this thread.    Pavel    On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh     wrote:    Your point is taken, Pavel. However, despite resolution,    you define coordinate of the atom as a geometric point    with no width. Although coordinates are “refineable”, they    have no capacity for “trash”. Their “trash” still goes    into B-factor “trash bin”. At least this is how I see it.    Thank you.    *Vaheh Oganesyan, Ph.D.*    *R&D **| Biologics Engineering*    One Medimmune Way, Gaithersburg, MD 20878    T:  301-398-5851    _vaheh.oganes...@astrazeneca.com    *From:* Pavel Afonine >    *Sent:* Tuesday, July 30, 2024 11:45 AM    *To:* Oganesyan, Vaheh     *Cc:* CCP4BB@jiscmail.ac.uk     *Subject:* Re: [ccp4bb] How high a B factor is too high to    assume a loop is in place, in the AlphaFold era?    From this perspective, all refinable atomic model    parameters can be viewed as trash bins, with the size of    these bins being proportional to the amount of prior    information (restraints) imposed on these parameters. For    example, coordinates have the most restraints and thus are    the smallest trash bins, while B factors have the least    restraints and thus are one of the largest bins.    Pavel    On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh     wrote:    Early in my Crystallography life I was postdoc with    Robert Huber in Munich. We had those gatherings once a    week when in very informal way we can ask and answer    questions. I remember my question about B factors: how    is it possible to have high resolution structure and    average B-factor of 100A^2 . I think it was Robert or    Albrecht Messerschmidt who told that B-factor is a    “trash can” that describes not only loosely positioned    atoms but also all other problems that either you    created during processing, harvesting or crystal had    from the beginning.    *Vaheh Oganesyan, Ph.D.*    *R&D **| Biologics Engineering*    One Medimmune Way, Gaithersburg, MD 20878    T:  301-398-5851    _vaheh.oganes...@astrazeneca.com    *From:* CCP4 bulletin board  *On Behalf Of *James        Holton    *Sent:* Tuesday, July 30, 2024 10:35 AM    *To:* CCP4BB@JISCMAIL.A

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Eleanor Dodson]

nes...@astrazeneca.com> wrote:
>
>> Yes, it is and I like the definition of shared “trash bin”. It will have
>> more physical meaning if we can separate those contributions into separate
>> bins.
>>
>>
>>
>> Vaheh
>>
>>
>>
>>
>>
>>
>>
>> *From:* Pavel Afonine 
>> *Sent:* Tuesday, July 30, 2024 1:51 PM
>> *To:* Oganesyan, Vaheh 
>> *Cc:* CCP4BB@jiscmail.ac.uk
>> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
>> is in place, in the AlphaFold era?
>>
>>
>>
>> Vaheh,
>>
>> I think coordinates are no different from B factors, occupancies, f', or
>> f'' in this respect. Coordinates can play their "trash bin" role by
>> adjusting to the noise at the expense of violated geometry (bonds, angles,
>> planes, torsions, etc.). As I mentioned in my previous email, their trash
>> bin capacity is much smaller (but definitely not zero!) because the number
>> and strength (confidence) of geometry restraints are much greater than
>> those of ADP restraints.
>>
>> I agree that all refined parameters share this trash bin capacity, but to
>> varying degrees. Isn't this essentially what we call the error on the
>> refined parameter? All refined parameters have their error bars, which we
>> have referred to as the "trash bin" in this thread.
>>
>> Pavel
>>
>>
>>
>> On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh <
>> vaheh.oganes...@astrazeneca.com> wrote:
>>
>> Your point is taken, Pavel. However, despite resolution, you define
>> coordinate of the atom as a geometric point with no width. Although
>> coordinates are “refineable”, they have no capacity for “trash”. Their
>> “trash” still goes into B-factor “trash bin”. At least this is how I see it.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> *Vaheh Oganesyan, Ph.D.*
>>
>> *R&D **| Biologics Engineering*
>>
>> One Medimmune Way, Gaithersburg, MD 20878
>>
>> T:  301-398-5851
>>
>> *vaheh.oganes...@astrazeneca.com *
>>
>>
>>
>>
>>
>>
>>
>> *From:* Pavel Afonine 
>> *Sent:* Tuesday, July 30, 2024 11:45 AM
>> *To:* Oganesyan, Vaheh 
>> *Cc:* CCP4BB@jiscmail.ac.uk
>> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
>> is in place, in the AlphaFold era?
>>
>>
>>
>> From this perspective, all refinable atomic model parameters can be
>> viewed as trash bins, with the size of these bins being proportional to the
>> amount of prior information (restraints) imposed on these parameters. For
>> example, coordinates have the most restraints and thus are the smallest
>> trash bins, while B factors have the least restraints and thus are one of
>> the largest bins.
>>
>> Pavel
>>
>>
>>
>>
>>
>> On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh <
>> vaheh.oganes...@astrazeneca.com> wrote:
>>
>> Early in my Crystallography life I was postdoc with Robert Huber in
>> Munich. We had those gatherings once a week when in very informal way we
>> can ask and answer questions. I remember my question about B factors: how
>> is it possible to have high resolution structure and average B-factor of
>> 100A2. I think it was Robert or Albrecht Messerschmidt who told that
>> B-factor is a “trash can” that describes not only loosely positioned atoms
>> but also all other problems that either you created during processing,
>> harvesting or crystal had from the beginning.
>>
>>
>>
>> *Vaheh Oganesyan, Ph.D.*
>>
>> *R&D **| Biologics Engineering*
>>
>> One Medimmune Way, Gaithersburg, MD 20878
>>
>> T:  301-398-5851
>>
>> *vaheh.oganes...@astrazeneca.com *
>>
>>
>>
>>
>>
>>
>>
>> *From:* CCP4 bulletin board  *On Behalf Of *James
>> Holton
>> *Sent:* Tuesday, July 30, 2024 10:35 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
>> is in place, in the AlphaFold era?
>>
>>
>>
>> How high B factors can go depends on the refinement program you are
>> using.
>>
>> In fact, my impression is that the division between the "let the B
>> factors blow up" and "delete the unseen" camps is correlated to their
>> preferred refinement program. You see, phenix.refine is relatively
>> aggressive with B factor refinement, and w

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[James Holton]

I submit that modern B factor restraints make them much less trashy than 
they were in the early days.  As Pavel points out the exact strategies 
differ from program to program, but I don't think anybody does 
unrestrained B factor refinement. Not by default.


Besides, all we are really doing is fitting Gaussian-shaped peaks to the 
"curve" of the data.  These peaks have a width and a height. For 
example, a carbon atom with B=20 has a peak density of 1.6 e-/A^3 and a 
full-width-at-half-max (FWHM) of 1.4 A.  That is it! That is the model 
density being fit. If you increase to B=80 the peak drops to 0.3 e-/A^3 
and the FWHM increases to 2.6 A.  At the largest B you can stuff into a 
PDB file (999.99), the peak height is 0.008 e-/A^3 and the "peak" is 
8.45A wide. Your disordered loop, however, is probably not sampling from 
a symmetric Gaussian distribution like that. This is the real problem 
with large B factors. They can fit better than sharper B atoms, but that 
doesn't mean they fit well.


Occupancy is easy because all it does is scale the height without 
affecting the width.  So, an 0.5 occupancy atom model is half the height 
of a full-occupancy one.  The width is unchanged.  B factors impact both 
width and height because they must preserve the number of electrons in 
the peak.  This is perhaps why they are often confusing and mysterious.  
We should also never forget that bulk solvent gets excluded with exactly 
the same radii rules from every modeled atom, regardless of B factor and 
occupancy.  So, the "change in density" from adding or deleting an atom 
is a little more complicated than adding or subtracting a Gaussian peak.


Nevertheless, if you want to fit peak height and width independently 
(like we do in pretty much every other kind of curve fitting), then you 
should refine occupancy and B factors at the same time.


Over-fitting you say?  Hardly. Polynomials are easy to over-fit, but not 
Gaussians. Observations/parameters is a useful guide for polynomial 
fits, but in general the hallmark of over-fitting is that the prediction 
passes exactly through all the observed points (and not the 
cross-validation or "Rfree" points). I have never seen a macromolecular 
refinement end up with Rwork = 0.  Have you?


At the end of the day, what we do with our models is look at their 
parameters and try to extract the physically meaningful reality they are 
trying to capture. Restraints are very helpful in preventing many types 
of unrealistic situations, but ultimately it is up to you to decide if 
the fitted model makes sense.


-James Holton
MAD Scientist

On 7/30/2024 11:30 AM, Ian Tickle wrote:


Obviously no refined parameters can ever be completely error-free, 
it's just that for the co-ordinates we have very accurate geometric 
restraints so that the relative uncertainty in the refined 
co-ordinates is small (but try refining co-ordinates without 
restraints!).  For the B factors we don't have accurate estimates (if 
any) for their restraints so their relative uncertainty after 
refinement is much greater.


-- Ian


On Tue, Jul 30, 2024 at 6:57 PM Oganesyan, Vaheh 
 wrote:


Yes, it is and I like the definition of shared “trash bin”. It
will have more physical meaning if we can separate those
contributions into separate bins.

Vaheh

*From:* Pavel Afonine 
*Sent:* Tuesday, July 30, 2024 1:51 PM
*To:* Oganesyan, Vaheh 
*Cc:* CCP4BB@jiscmail.ac.uk
*Subject:* Re: [ccp4bb] How high a B factor is too high to assume
a loop is in place, in the AlphaFold era?

Vaheh,

I think coordinates are no different from B factors, occupancies,
f', or f'' in this respect. Coordinates can play their "trash bin"
role by adjusting to the noise at the expense of violated geometry
(bonds, angles, planes, torsions, etc.). As I mentioned in my
previous email, their trash bin capacity is much smaller (but
definitely not zero!) because the number and strength (confidence)
of geometry restraints are much greater than those of ADP restraints.

I agree that all refined parameters share this trash bin capacity,
but to varying degrees. Isn't this essentially what we call the
error on the refined parameter? All refined parameters have their
error bars, which we have referred to as the "trash bin" in this
thread.

Pavel

On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh
 wrote:

Your point is taken, Pavel. However, despite resolution, you
define coordinate of the atom as a geometric point with no
width. Although coordinates are “refineable”, they have no
capacity for “trash”. Their “trash” still goes into B-factor
“trash bin”. At least this is how I see it.

Thank you.

*Vaheh Oganesyan, Ph.D.*

*R&D **| Biologics Engineering*

One M

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Ian Tickle]

Obviously no refined parameters can ever be completely error-free, it's
just that for the co-ordinates we have very accurate geometric restraints
so that the relative uncertainty in the refined co-ordinates is small (but
try refining co-ordinates without restraints!).  For the B factors we don't
have accurate estimates (if any) for their restraints so their relative
uncertainty after refinement is much greater.

-- Ian


On Tue, Jul 30, 2024 at 6:57 PM Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> Yes, it is and I like the definition of shared “trash bin”. It will have
> more physical meaning if we can separate those contributions into separate
> bins.
>
>
>
> Vaheh
>
>
>
>
>
>
>
> *From:* Pavel Afonine 
> *Sent:* Tuesday, July 30, 2024 1:51 PM
> *To:* Oganesyan, Vaheh 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> Vaheh,
>
> I think coordinates are no different from B factors, occupancies, f', or
> f'' in this respect. Coordinates can play their "trash bin" role by
> adjusting to the noise at the expense of violated geometry (bonds, angles,
> planes, torsions, etc.). As I mentioned in my previous email, their trash
> bin capacity is much smaller (but definitely not zero!) because the number
> and strength (confidence) of geometry restraints are much greater than
> those of ADP restraints.
>
> I agree that all refined parameters share this trash bin capacity, but to
> varying degrees. Isn't this essentially what we call the error on the
> refined parameter? All refined parameters have their error bars, which we
> have referred to as the "trash bin" in this thread.
>
> Pavel
>
>
>
> On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
>
> Your point is taken, Pavel. However, despite resolution, you define
> coordinate of the atom as a geometric point with no width. Although
> coordinates are “refineable”, they have no capacity for “trash”. Their
> “trash” still goes into B-factor “trash bin”. At least this is how I see it.
>
>
>
> Thank you.
>
>
>
> *Vaheh Oganesyan, Ph.D.*
>
> *R&D **| Biologics Engineering*
>
> One Medimmune Way, Gaithersburg, MD 20878
>
> T:  301-398-5851
>
> *vaheh.oganes...@astrazeneca.com *
>
>
>
>
>
>
>
> *From:* Pavel Afonine 
> *Sent:* Tuesday, July 30, 2024 11:45 AM
> *To:* Oganesyan, Vaheh 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> From this perspective, all refinable atomic model parameters can be viewed
> as trash bins, with the size of these bins being proportional to the amount
> of prior information (restraints) imposed on these parameters. For example,
> coordinates have the most restraints and thus are the smallest trash bins,
> while B factors have the least restraints and thus are one of the largest
> bins.
>
> Pavel
>
>
>
>
>
> On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
>
> Early in my Crystallography life I was postdoc with Robert Huber in
> Munich. We had those gatherings once a week when in very informal way we
> can ask and answer questions. I remember my question about B factors: how
> is it possible to have high resolution structure and average B-factor of
> 100A2. I think it was Robert or Albrecht Messerschmidt who told that
> B-factor is a “trash can” that describes not only loosely positioned atoms
> but also all other problems that either you created during processing,
> harvesting or crystal had from the beginning.
>
>
>
> *Vaheh Oganesyan, Ph.D.*
>
> *R&D **| Biologics Engineering*
>
> One Medimmune Way, Gaithersburg, MD 20878
>
> T:  301-398-5851
>
> *vaheh.oganes...@astrazeneca.com *
>
>
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *James
> Holton
> *Sent:* Tuesday, July 30, 2024 10:35 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> How high B factors can go depends on the refinement program you are
> using.
>
> In fact, my impression is that the division between the "let the B factors
> blow up" and "delete the unseen" camps is correlated to their preferred
> refinement program. You see, phenix.refine is relatively aggressive with B
> factor refinement, and will allow "missing" atoms to attain very high B
&g

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Oganesyan, Vaheh]

Yes, it is and I like the definition of shared “trash bin”. It will have more 
physical meaning if we can separate those contributions into separate bins.

Vaheh



From: Pavel Afonine 
Sent: Tuesday, July 30, 2024 1:51 PM
To: Oganesyan, Vaheh 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?


Vaheh,

I think coordinates are no different from B factors, occupancies, f', or f'' in 
this respect. Coordinates can play their "trash bin" role by adjusting to the 
noise at the expense of violated geometry (bonds, angles, planes, torsions, 
etc.). As I mentioned in my previous email, their trash bin capacity is much 
smaller (but definitely not zero!) because the number and strength (confidence) 
of geometry restraints are much greater than those of ADP restraints.

I agree that all refined parameters share this trash bin capacity, but to 
varying degrees. Isn't this essentially what we call the error on the refined 
parameter? All refined parameters have their error bars, which we have referred 
to as the "trash bin" in this thread.

Pavel

On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
Your point is taken, Pavel. However, despite resolution, you define coordinate 
of the atom as a geometric point with no width. Although coordinates are 
“refineable”, they have no capacity for “trash”. Their “trash” still goes into 
B-factor “trash bin”. At least this is how I see it.

Thank you.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DAE288.40D743D0]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com>



From: Pavel Afonine mailto:pafon...@gmail.com>>
Sent: Tuesday, July 30, 2024 11:45 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?


From this perspective, all refinable atomic model parameters can be viewed as 
trash bins, with the size of these bins being proportional to the amount of 
prior information (restraints) imposed on these parameters. For example, 
coordinates have the most restraints and thus are the smallest trash bins, 
while B factors have the least restraints and thus are one of the largest bins.

Pavel



On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
Early in my Crystallography life I was postdoc with Robert Huber in Munich. We 
had those gatherings once a week when in very informal way we can ask and 
answer questions. I remember my question about B factors: how is it possible to 
have high resolution structure and average B-factor of 100A2. I think it was 
Robert or Albrecht Messerschmidt who told that B-factor is a “trash can” that 
describes not only loosely positioned atoms but also all other problems that 
either you created during processing, harvesting or crystal had from the 
beginning.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DAE288.40D743D0]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com>



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of James Holton
Sent: Tuesday, July 30, 2024 10:35 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?

How high B factors can go depends on the refinement program you are using.

In fact, my impression is that the division between the "let the B factors blow 
up" and "delete the unseen" camps is correlated to their preferred refinement 
program. You see, phenix.refine is relatively aggressive with B factor 
refinement, and will allow "missing" atoms to attain very high B factors. 
Refmac, on the other hand, has restraints that try to make B factor 
distributions look like those found in the PDB, and so tends to keep nearby B 
factors similar. As a result, you may get "red density" for disordered regions 
from refmac, inviting you to delete the offending atoms, but not from phenix, 
which will raise the B factor until the density fits.

Then there are programs like VagaBond that don't formally have B factors, but 
rather let an ensemble of chains spread out in the loopy regions you are 
concerned about.  This might be the way to go?

You can also do ensemble refinement in the latest Amber.  That is, you run an 
MD simulation of a unit cell (or more) and gradually increase structure factor 
restraints. This would probably result in the "fan" of loops you have in mind?

-James Holton
MAD Scientist
On 7/2

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Pavel Afonine]

Vaheh,

I think coordinates are no different from B factors, occupancies, f', or
f'' in this respect. Coordinates can play their "trash bin" role by
adjusting to the noise at the expense of violated geometry (bonds, angles,
planes, torsions, etc.). As I mentioned in my previous email, their trash
bin capacity is much smaller (but definitely not zero!) because the number
and strength (confidence) of geometry restraints are much greater than
those of ADP restraints.

I agree that all refined parameters share this trash bin capacity, but to
varying degrees. Isn't this essentially what we call the error on the
refined parameter? All refined parameters have their error bars, which we
have referred to as the "trash bin" in this thread.

Pavel

On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> Your point is taken, Pavel. However, despite resolution, you define
> coordinate of the atom as a geometric point with no width. Although
> coordinates are “refineable”, they have no capacity for “trash”. Their
> “trash” still goes into B-factor “trash bin”. At least this is how I see it.
>
>
>
> Thank you.
>
>
>
> *Vaheh Oganesyan, Ph.D.*
>
> *R&D* *| Biologics Engineering*
>
> One Medimmune Way, Gaithersburg, MD 20878
>
> T:  301-398-5851
>
> *vaheh.oganes...@astrazeneca.com *
>
>
>
>
>
>
>
> *From:* Pavel Afonine 
> *Sent:* Tuesday, July 30, 2024 11:45 AM
> *To:* Oganesyan, Vaheh 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> From this perspective, all refinable atomic model parameters can be viewed
> as trash bins, with the size of these bins being proportional to the amount
> of prior information (restraints) imposed on these parameters. For example,
> coordinates have the most restraints and thus are the smallest trash bins,
> while B factors have the least restraints and thus are one of the largest
> bins.
>
> Pavel
>
>
>
>
>
> On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh <
> vaheh.oganes...@astrazeneca.com> wrote:
>
> Early in my Crystallography life I was postdoc with Robert Huber in
> Munich. We had those gatherings once a week when in very informal way we
> can ask and answer questions. I remember my question about B factors: how
> is it possible to have high resolution structure and average B-factor of
> 100A2. I think it was Robert or Albrecht Messerschmidt who told that
> B-factor is a “trash can” that describes not only loosely positioned atoms
> but also all other problems that either you created during processing,
> harvesting or crystal had from the beginning.
>
>
>
> *Vaheh Oganesyan, Ph.D.*
>
> *R&D **| Biologics Engineering*
>
> One Medimmune Way, Gaithersburg, MD 20878
>
> T:  301-398-5851
>
> *vaheh.oganes...@astrazeneca.com *
>
>
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *James
> Holton
> *Sent:* Tuesday, July 30, 2024 10:35 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> How high B factors can go depends on the refinement program you are
> using.
>
> In fact, my impression is that the division between the "let the B factors
> blow up" and "delete the unseen" camps is correlated to their preferred
> refinement program. You see, phenix.refine is relatively aggressive with B
> factor refinement, and will allow "missing" atoms to attain very high B
> factors. Refmac, on the other hand, has restraints that try to make B
> factor distributions look like those found in the PDB, and so tends to keep
> nearby B factors similar. As a result, you may get "red density" for
> disordered regions from refmac, inviting you to delete the offending atoms,
> but not from phenix, which will raise the B factor until the density fits.
>
> Then there are programs like VagaBond that don't formally have B factors,
> but rather let an ensemble of chains spread out in the loopy regions you
> are concerned about.  This might be the way to go?
>
> You can also do ensemble refinement in the latest Amber.  That is, you run
> an MD simulation of a unit cell (or more) and gradually increase structure
> factor restraints. This would probably result in the "fan" of loops you
> have in mind?
>
> -James Holton
> MAD Scientist
>
> On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
>
> Dear CCP4bb,
>
>
>
> I'm refining the ~3A crystal structure of a big protein, largely composed
> of alpha helices conn

Re: [ccp4bb] Questions about PanDDA modelling and refining

[Aline Dias da Purificacao]

**Question:**

After step 11 in my pandda-export folder I have the following files:


File name:

Remarks:

1

ensemble-model.log

2

ensemble-model.pdb

Contains both bound and ground-state

3

ensemble-model-restraints.log

4

ensemble-model-restraints.phenix.params

5

ensemble-model-restraints.refmac.params

6

pandda-input.mtz

Does not contain the "event density" of ligand

7

pandda-input.pdb

Does not contain ligand

8

pandda-model.pdb

Contains bound state of ligand

9

pandda-output.mtz

Does not contain the "event density" of ligand

10

pandda-output-event-001.mtz

Contains the "event density" of ligand


In the file ensemble-model.pdb I see water and ligand on the same spot. My
protein normally has water in that site but if the ligand is bound - there
is no water.

**Answer:**


Hello, I recently went through several challenges with ligand
identification using PanDDA, but I hope I can now help you.

Firstly, explaining your files after pandda.export:

1. The ensemble model is the file that contains a combination of the
unbound file (pandda-input) and the file you modeled during the
pandda.inspect step (pandda-model). In the final step of pandda.export, it
automatically runs giant.merge_conformations, which generates the ensemble
model, the restraints, and their respective logs.

2. The pandda-input files are those you submitted to pandda.analyse, so
they are the inputs for pandda.

3. The pandda model is the file you modeled and saved during the
pandda.inspect step.

The only thing I don't understand about your pandda export output files is
that your event map “pandda-output-event-001.mtz” is in mtz format when it
should be in .native.ccp4 format. Additionally, the z-map was not extracted
by pandda.export, and it is crucial for analyzing blobs in the event map. I
also can't understand what this output.mtz refers to.

These were my output files (very similar to yours except for the
differences I pointed out). Notice that I have the event map and the z-map
in .native.ccp4 format:


The first question then is: what version of PanDDA and CCP4 are you using?
This might help us understand why these differences were observed.

---

**Question:**

Further modeling is required for my structures, and thus I move on to step
13 where I get confused. I have highlighted in bold the instructions of the
tutorial.

Generation of restraints for refinement (giant.make_restraints) It says:
"...The output restraint files can then be fed to giant.quick_refine which
then either runs phenix or refmac (see below)." Should I skip this step as
I already have the phenix.params and refmac.params files?

**Answer:**


Yes, the output files from pandda.export already contain the restraints you
will need for refinement.

---

**Question:**

Quick-and-easy refinement (giant.quick_refine) To make refinement more
straightforward giant.quick_refine can be used to refine the models. A
normal refinement will look like

giant.quick_refine input.pdb input.mtz ligand.cif restraints.params

Which files should I use here? The pandda-input.pdb pandda-input.mtz
ligand.cif and ensemble-model-refmac.params? If the .params file is for the
ensemble, should I rather use the ensemble-model.pdb
pandda-output-event-001.mtz ligand.cif and ensemble-model-refmac-params?

**Answer:**


In the first refinement cycle using giant.refine, you should use the files:
ensemble-model.pdb, pandda-input.mtz, ligand.cif, and either
ensemble-model-refmac.params or ensemble-model-phenix.params.

---

**Question:**

If I want to include additional parameterization for the refmac, do I
manually add instructions in the .params file? For example, if I want to
increase the weight parameter?

**Answer:**


I don't know. If anyone else can clarify this question, it would be greatly
appreciated.

---

**Question:**

Splitting the ensemble model (giant.split_conformations) Should it be done
on the output of step 13.2?

**Answer:**


After the first refinement cycle, a folder “refine001” will be created with
the following files:


This output.pdb is the refined ensemble model. If adjustments to the ligand
are necessary, it is advisable to split the ensemble into bound and unbound
models because working with the ensemble model can be confusing due to the
multiple alternate conformations it contains. After the split, you can
separately model the unbound state using the output mtz normally, and the
bound state using the event map.

---

**Question:**

(Re-)modelling of the bound-/ground-states (coot) The ground-state
conformations should be modeled into a ground-state ("reference")
dataset/map (e.g., "*-ground-state-average-map.native.ccp4" from
pandda.analyse). I do not have any file in the format native.ccp4
Should I do it with the file pandda-input.pdb with pandda-input.mtz? The
bound-state conformations of the protein are modeled into the appropriate
event maps as in pandda.inspect. Should I use the files pandda-model.pdb
with pandda-ouput-event-001.mtz? 

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Oganesyan, Vaheh]

Your point is taken, Pavel. However, despite resolution, you define coordinate 
of the atom as a geometric point with no width. Although coordinates are 
“refineable”, they have no capacity for “trash”. Their “trash” still goes into 
B-factor “trash bin”. At least this is how I see it.

Thank you.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DAE281.A8E8D260]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com>



From: Pavel Afonine 
Sent: Tuesday, July 30, 2024 11:45 AM
To: Oganesyan, Vaheh 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?


From this perspective, all refinable atomic model parameters can be viewed as 
trash bins, with the size of these bins being proportional to the amount of 
prior information (restraints) imposed on these parameters. For example, 
coordinates have the most restraints and thus are the smallest trash bins, 
while B factors have the least restraints and thus are one of the largest bins.

Pavel



On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:
Early in my Crystallography life I was postdoc with Robert Huber in Munich. We 
had those gatherings once a week when in very informal way we can ask and 
answer questions. I remember my question about B factors: how is it possible to 
have high resolution structure and average B-factor of 100A2. I think it was 
Robert or Albrecht Messerschmidt who told that B-factor is a “trash can” that 
describes not only loosely positioned atoms but also all other problems that 
either you created during processing, harvesting or crystal had from the 
beginning.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DAE281.A8E8D260]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com>



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of James Holton
Sent: Tuesday, July 30, 2024 10:35 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?

How high B factors can go depends on the refinement program you are using.

In fact, my impression is that the division between the "let the B factors blow 
up" and "delete the unseen" camps is correlated to their preferred refinement 
program. You see, phenix.refine is relatively aggressive with B factor 
refinement, and will allow "missing" atoms to attain very high B factors. 
Refmac, on the other hand, has restraints that try to make B factor 
distributions look like those found in the PDB, and so tends to keep nearby B 
factors similar. As a result, you may get "red density" for disordered regions 
from refmac, inviting you to delete the offending atoms, but not from phenix, 
which will raise the B factor until the density fits.

Then there are programs like VagaBond that don't formally have B factors, but 
rather let an ensemble of chains spread out in the loopy regions you are 
concerned about.  This might be the way to go?

You can also do ensemble refinement in the latest Amber.  That is, you run an 
MD simulation of a unit cell (or more) and gradually increase structure factor 
restraints. This would probably result in the "fan" of loops you have in mind?

-James Holton
MAD Scientist
On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
Dear CCP4bb,

I'm refining the ~3A crystal structure of a big protein, largely composed of 
alpha helices connected by poorly-resolved loops.
In the old pre-AlphaFold (AF) days I used to simply remove those loops/regions 
with too high B factors, because there was little to none density at 1 sigma in 
a 2Fo-Fc map.
However, considering that the quality of a readily-computable AF model is 
comparable to a 3A experimental structure, and that the UniProt database is 
flooded with noodle-like AF models, I was considering depositing a combined 
model in the PDB.
Once R/Rfree reach a minimum for the model truncated in poorly resolved loops, 
I would calculate an augmented model with AF calculated missing regions 
(provided they have an acceptable pLDDT value), assign them zero occupancy, and 
run only one cycle of refinement to calculate the formal refinement statistics.
Would that be acceptable? Has anyone tried a similar approach?
I'd rather do that instead of depositing a counterintuitive model with 
truncated regions that few people would find useful!!

Thank you for your comments,

Javier

--
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
Ema

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Phil Jeffrey]

“That which is not restricted will take its liberties”
(Wayne Hendrickson)
https://www.sciencedirect.com/science/article/pii/S0969212601001873

in turn, apparently from one of the older CCP4 workshops
P.A. Machin, J.W. Campbell, M. Elder (Eds)
Refinement of Protein Structures, SERC Daresbury Laboratory, Warrington, 
UK (1980)


Phil Jeffrey


On 7/30/24 11:44 AM, Pavel Afonine wrote:
 From this perspective, all refinable atomic model parameters can be 
viewed as trash bins, with the size of these bins being proportional to 
the amount of prior information (restraints) imposed on these 
parameters. For example, coordinates have the most restraints and thus 
are the smallest trash bins, while B factors have the least restraints 
and thus are one of the largest bins.


Pavel



On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh 
> wrote:


Early in my Crystallography life I was postdoc with Robert Huber in
Munich. We had those gatherings once a week when in very informal
way we can ask and answer questions. I remember my question about B
factors: how is it possible to have high resolution structure and
average B-factor of 100A^2 . I think it was Robert or Albrecht
Messerschmidt who told that B-factor is a “trash can” that describes
not only loosely positioned atoms but also all other problems that
either you created during processing, harvesting or crystal had from
the beginning.

__ __

*Vaheh Oganesyan, Ph.D.*



*R&D| Biologics Engineering***

One Medimmune Way, Gaithersburg, MD 20878

T:  301-398-5851

_vaheh.oganes...@astrazeneca.com _





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

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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Pavel Afonine]

>From this perspective, all refinable atomic model parameters can be viewed
as trash bins, with the size of these bins being proportional to the amount
of prior information (restraints) imposed on these parameters. For example,
coordinates have the most restraints and thus are the smallest trash bins,
while B factors have the least restraints and thus are one of the largest
bins.

Pavel



On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> Early in my Crystallography life I was postdoc with Robert Huber in
> Munich. We had those gatherings once a week when in very informal way we
> can ask and answer questions. I remember my question about B factors: how
> is it possible to have high resolution structure and average B-factor of
> 100A2. I think it was Robert or Albrecht Messerschmidt who told that
> B-factor is a “trash can” that describes not only loosely positioned atoms
> but also all other problems that either you created during processing,
> harvesting or crystal had from the beginning.
>
>
>
> *Vaheh Oganesyan, Ph.D.*
>
> *R&D* *| Biologics Engineering*
>
> One Medimmune Way, Gaithersburg, MD 20878
>
> T:  301-398-5851
>
> *vaheh.oganes...@astrazeneca.com *
>
>
>
>
>
>
>
> *From:* CCP4 bulletin board  * On Behalf Of *James
> Holton
> *Sent:* Tuesday, July 30, 2024 10:35 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop
> is in place, in the AlphaFold era?
>
>
>
> How high B factors can go depends on the refinement program you are
> using.
>
> In fact, my impression is that the division between the "let the B factors
> blow up" and "delete the unseen" camps is correlated to their preferred
> refinement program. You see, phenix.refine is relatively aggressive with B
> factor refinement, and will allow "missing" atoms to attain very high B
> factors. Refmac, on the other hand, has restraints that try to make B
> factor distributions look like those found in the PDB, and so tends to keep
> nearby B factors similar. As a result, you may get "red density" for
> disordered regions from refmac, inviting you to delete the offending atoms,
> but not from phenix, which will raise the B factor until the density fits.
>
> Then there are programs like VagaBond that don't formally have B factors,
> but rather let an ensemble of chains spread out in the loopy regions you
> are concerned about.  This might be the way to go?
>
> You can also do ensemble refinement in the latest Amber.  That is, you run
> an MD simulation of a unit cell (or more) and gradually increase structure
> factor restraints. This would probably result in the "fan" of loops you
> have in mind?
>
> -James Holton
> MAD Scientist
>
> On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
>
> Dear CCP4bb,
>
>
>
> I'm refining the ~3A crystal structure of a big protein, largely composed
> of alpha helices connected by poorly-resolved loops.
>
> In the old pre-AlphaFold (AF) days I used to simply remove those
> loops/regions with too high B factors, because there was little to none
> density at 1 sigma in a 2Fo-Fc map.
>
> However, considering that the quality of a readily-computable AF model is
> comparable to a 3A experimental structure, and that the UniProt database is
> flooded with noodle-like AF models, I was considering depositing a combined
> model in the PDB.
>
> Once R/Rfree reach a minimum for the model truncated in poorly resolved
> loops, I would calculate an augmented model with AF calculated missing
> regions (provided they have an acceptable pLDDT value), assign them zero
> occupancy, and run only one cycle of refinement to calculate the formal
> refinement statistics.
>
> Would that be acceptable? Has anyone tried a similar approach?
>
> I'd rather do that instead of depositing a counterintuitive model with
> truncated regions that few people would find useful!!
>
>
>
> Thank you for your comments,
>
>
>
> Javier
>
>
> --
>
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
>
> Tel: +54-(0385)-4238352
>
> Email  Twitter <https://twitter.com/_biojmg>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following l

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Oganesyan, Vaheh]

Early in my Crystallography life I was postdoc with Robert Huber in Munich. We 
had those gatherings once a week when in very informal way we can ask and 
answer questions. I remember my question about B factors: how is it possible to 
have high resolution structure and average B-factor of 100A2. I think it was 
Robert or Albrecht Messerschmidt who told that B-factor is a “trash can” that 
describes not only loosely positioned atoms but also all other problems that 
either you created during processing, harvesting or crystal had from the 
beginning.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01DAE273.3470B910]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com>



From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Tuesday, July 30, 2024 10:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in 
place, in the AlphaFold era?

How high B factors can go depends on the refinement program you are using.

In fact, my impression is that the division between the "let the B factors blow 
up" and "delete the unseen" camps is correlated to their preferred refinement 
program. You see, phenix.refine is relatively aggressive with B factor 
refinement, and will allow "missing" atoms to attain very high B factors. 
Refmac, on the other hand, has restraints that try to make B factor 
distributions look like those found in the PDB, and so tends to keep nearby B 
factors similar. As a result, you may get "red density" for disordered regions 
from refmac, inviting you to delete the offending atoms, but not from phenix, 
which will raise the B factor until the density fits.

Then there are programs like VagaBond that don't formally have B factors, but 
rather let an ensemble of chains spread out in the loopy regions you are 
concerned about.  This might be the way to go?

You can also do ensemble refinement in the latest Amber.  That is, you run an 
MD simulation of a unit cell (or more) and gradually increase structure factor 
restraints. This would probably result in the "fan" of loops you have in mind?

-James Holton
MAD Scientist
On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
Dear CCP4bb,

I'm refining the ~3A crystal structure of a big protein, largely composed of 
alpha helices connected by poorly-resolved loops.
In the old pre-AlphaFold (AF) days I used to simply remove those loops/regions 
with too high B factors, because there was little to none density at 1 sigma in 
a 2Fo-Fc map.
However, considering that the quality of a readily-computable AF model is 
comparable to a 3A experimental structure, and that the UniProt database is 
flooded with noodle-like AF models, I was considering depositing a combined 
model in the PDB.
Once R/Rfree reach a minimum for the model truncated in poorly resolved loops, 
I would calculate an augmented model with AF calculated missing regions 
(provided they have an acceptable pLDDT value), assign them zero occupancy, and 
run only one cycle of refinement to calculate the formal refinement statistics.
Would that be acceptable? Has anyone tried a similar approach?
I'd rather do that instead of depositing a counterintuitive model with 
truncated regions that few people would find useful!!

Thank you for your comments,

Javier

--
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
Email<mailto:bio...@gmail.com> Twitter<https://twitter.com/_biojmg>




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




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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Pavel Afonine]

The reason why phenix.refine allows B factors to grow until they fit the
map is that it uses restraints that do not only require the similarity of B
factors of covalently bonded atoms, but rather the similarity of B factors
of atoms located within a sphere of radius R (around 5Å). This is to
account for the fact that atomic B factors arise not only from atomic
vibrations but also from other sources of motion, such as side chain
librations and more. Additionally, atoms with higher B factors contribute
less to the restraints target. This concept is encoded into the restraints
formula 6 here:

https://journals.iucr.org/d/issues/2012/04/00/ba5180/index.html

Other refinement programs may restrain the ΔB between bonded atoms to be as
small as the data allows (Hirshfeld's rigid bond) or restrain these ΔB to
match expected distributions (TNT).

Regarding B factors versus ensembles: my understanding is that B factors
model the spread of a single peak of density, whereas alternative
conformations (ensembles) model distinct peaks of density. Essentially, the
difference between B factors and occupancy is the size of the motion
(disorder) you are trying to model. With this in mind, I'd question the
validity of using an ensemble of point scatterers to model a single peak.
Pavel


On Tue, Jul 30, 2024 at 7:35 AM James Holton  wrote:

> How high B factors can go depends on the refinement program you are
> using.
>
> In fact, my impression is that the division between the "let the B factors
> blow up" and "delete the unseen" camps is correlated to their preferred
> refinement program. You see, phenix.refine is relatively aggressive with B
> factor refinement, and will allow "missing" atoms to attain very high B
> factors. Refmac, on the other hand, has restraints that try to make B
> factor distributions look like those found in the PDB, and so tends to keep
> nearby B factors similar. As a result, you may get "red density" for
> disordered regions from refmac, inviting you to delete the offending atoms,
> but not from phenix, which will raise the B factor until the density fits.
>
> Then there are programs like VagaBond that don't formally have B factors,
> but rather let an ensemble of chains spread out in the loopy regions you
> are concerned about.  This might be the way to go?
>
> You can also do ensemble refinement in the latest Amber.  That is, you run
> an MD simulation of a unit cell (or more) and gradually increase structure
> factor restraints. This would probably result in the "fan" of loops you
> have in mind?
>
> -James Holton
> MAD Scientist
>
> On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
>
>
>
> Dear CCP4bb,
>
> I'm refining the ~3A crystal structure of a big protein, largely composed
> of alpha helices connected by poorly-resolved loops.
> In the old pre-AlphaFold (AF) days I used to simply remove those
> loops/regions with too high B factors, because there was little to none
> density at 1 sigma in a 2Fo-Fc map.
> However, considering that the quality of a readily-computable AF model is
> comparable to a 3A experimental structure, and that the UniProt database is
> flooded with noodle-like AF models, I was considering depositing a combined
> model in the PDB.
> Once R/Rfree reach a minimum for the model truncated in poorly resolved
> loops, I would calculate an augmented model with AF calculated missing
> regions (provided they have an acceptable pLDDT value), assign them zero
> occupancy, and run only one cycle of refinement to calculate the formal
> refinement statistics.
> Would that be acceptable? Has anyone tried a similar approach?
> I'd rather do that instead of depositing a counterintuitive model with
> truncated regions that few people would find useful!!
>
> Thank you for your comments,
>
> Javier
>
> --
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
> Tel: +54-(0385)-4238352
> Email  Twitter 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Daniel M. Himmel, Ph. D.]

If it hasn't already been mentioned, I would humbly like to remind everyone
that a high B-factor on an atom causes it to have a small or negligible
contribution to a fourier transform.  Therefore, beware that modelling
atoms with high B-factors could be introducing model bias by inserting
atoms that really aren't there or atoms that are so mobile or have so much
vibrational energy that their probable position(s) cannot be modelled with
any certainty.

Be careful.  Be skeptical before running to build in atoms with high
B-factors (regardless of which software you use for refinement).

Daniel



Daniel M. Himmel, Ph. D.

Principal, Himmel Sci Med Com, LLC

E-mail:  danielmhim...@gmail.com

URL   :  https://himmelscimedcom.com
Member, American Medical Writers Association

You can also find me at https://www.talusfreelance.com


On Tue, Jul 30, 2024 at 10:35 AM James Holton  wrote:

> How high B factors can go depends on the refinement program you are
> using.
>
> In fact, my impression is that the division between the "let the B factors
> blow up" and "delete the unseen" camps is correlated to their preferred
> refinement program. You see, phenix.refine is relatively aggressive with B
> factor refinement, and will allow "missing" atoms to attain very high B
> factors. Refmac, on the other hand, has restraints that try to make B
> factor distributions look like those found in the PDB, and so tends to keep
> nearby B factors similar. As a result, you may get "red density" for
> disordered regions from refmac, inviting you to delete the offending atoms,
> but not from phenix, which will raise the B factor until the density fits.
>
> Then there are programs like VagaBond that don't formally have B factors,
> but rather let an ensemble of chains spread out in the loopy regions you
> are concerned about.  This might be the way to go?
>
> You can also do ensemble refinement in the latest Amber.  That is, you run
> an MD simulation of a unit cell (or more) and gradually increase structure
> factor restraints. This would probably result in the "fan" of loops you
> have in mind?
>
> -James Holton
> MAD Scientist
>
> On 7/28/2024 8:13 AM, Javier Gonzalez wrote:
>
>
>
> Dear CCP4bb,
>
> I'm refining the ~3A crystal structure of a big protein, largely composed
> of alpha helices connected by poorly-resolved loops.
> In the old pre-AlphaFold (AF) days I used to simply remove those
> loops/regions with too high B factors, because there was little to none
> density at 1 sigma in a 2Fo-Fc map.
> However, considering that the quality of a readily-computable AF model is
> comparable to a 3A experimental structure, and that the UniProt database is
> flooded with noodle-like AF models, I was considering depositing a combined
> model in the PDB.
> Once R/Rfree reach a minimum for the model truncated in poorly resolved
> loops, I would calculate an augmented model with AF calculated missing
> regions (provided they have an acceptable pLDDT value), assign them zero
> occupancy, and run only one cycle of refinement to calculate the formal
> refinement statistics.
> Would that be acceptable? Has anyone tried a similar approach?
> I'd rather do that instead of depositing a counterintuitive model with
> truncated regions that few people would find useful!!
>
> Thank you for your comments,
>
> Javier
>
> --
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
> Tel: +54-(0385)-4238352
> Email  Twitter 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[James Holton]

How high B factors can go depends on the refinement program you are using.

In fact, my impression is that the division between the "let the B 
factors blow up" and "delete the unseen" camps is correlated to their 
preferred refinement program. You see, phenix.refine is relatively 
aggressive with B factor refinement, and will allow "missing" atoms to 
attain very high B factors. Refmac, on the other hand, has restraints 
that try to make B factor distributions look like those found in the 
PDB, and so tends to keep nearby B factors similar. As a result, you may 
get "red density" for disordered regions from refmac, inviting you to 
delete the offending atoms, but not from phenix, which will raise the B 
factor until the density fits.


Then there are programs like VagaBond that don't formally have B 
factors, but rather let an ensemble of chains spread out in the loopy 
regions you are concerned about.  This might be the way to go?


You can also do ensemble refinement in the latest Amber.  That is, you 
run an MD simulation of a unit cell (or more) and gradually increase 
structure factor restraints. This would probably result in the "fan" of 
loops you have in mind?


-James Holton
MAD Scientist

On 7/28/2024 8:13 AM, Javier Gonzalez wrote:




Dear CCP4bb,

I'm refining the ~3A crystal structure of a big protein, largely 
composed of alpha helices connected by poorly-resolved loops.
In the old pre-AlphaFold (AF) days I used to simply remove those 
loops/regions with too high B factors, because there was little to 
none density at 1 sigma in a 2Fo-Fc map.
However, considering that the quality of a readily-computable AF model 
is comparable to a 3A experimental structure, and that the UniProt 
database is flooded with noodle-like AF models, I was considering 
depositing a combined model in the PDB.
Once R/Rfree reach a minimum for the model truncated in poorly 
resolved loops, I would calculate an augmented model with AF 
calculated missing regions (provided they have an acceptable pLDDT 
value), assign them zero occupancy, and run only one cycle of 
refinement to calculate the formal refinement statistics.

Would that be acceptable? Has anyone tried a similar approach?
I'd rather do that instead of depositing a counterintuitive model with 
truncated regions that few people would find useful!!


Thank you for your comments,

Javier

--
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
Email  Twitter 




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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Javier Gonzalez]

Thank you all for your thoughtful answers.

I'll stick to the crystallographic data and model as much as I can with
reasonable occupancy and B factors, even if the result is a truncated model.

I don't believe in the zero occupancy trick either. I just thought the PDB
was more flexible these days, since the community of structural biologists
seems to have accepted the highly accurate and highly imprecise coordinates
of AF-generated noodle-like loops in the UniProt database.

It sounds like the PDB-DEV database is the right place to deposit those
hybrid models I had in mind, and leave the genuine crystallographic models
for the PDB.

Best wishes,
Javier

On Sun, Jul 28, 2024 at 2:52 PM Guillaume Gaullier <
guillaume.gaull...@kemi.uu.se> wrote:

> Hello Javier,
>
> Placing atoms implies that you know they are present somewhere (possibly
> with some uncertainty on exactly where), but setting their occupancies to
> zero implies that you know they are nowhere at all. This is a paradox.
>
> I think atoms with zero occupancy make no sense in a final deposited model
> (they could be useful as a working intermediate to exclude the bulk solvent
> model, but this is unrelated to what you describe).
> So in this particular case, partial occupancies only make sense for
> multiple conformations (and should add up to 1), as Pavel describes.
>
> If you can’t resolve more than one conformation, maybe a better approach
> is to fix the coordinates to what AlphaFold suggested (which is often
> reasonable, but check their pLDDT to assess this) and refine to let the
> B-factors of these atoms rise. This will convey the large uncertainty on
> their positions. I think it is a valid approach because you know these
> residues are there somewhere (in other words, to me you would need evidence
> of their absence to justify truncating these loops: SDS-PAGE showing that
> the protein is cleaved, for example).
>
> I hope this helps,
>
> Guillaume
>
> On 28 Jul 2024, at 17:32, Pavel Afonine  wrote:
>
> 
>
> Javier,
>
> Flexible loops may be better modeled with ensembles of N models, meaning
> the occupancy of each-one would be 1/N, and the map contours to visualize
> them should be chosen as 1/N sigma (not 1 sigma). While model prediction
> tools such as AlphaFold are helpful, they don't suddenly lift the
> requirement for the atomic model you release to the world to fit the
> experimental data! With this premise in mind, the approaches to validate
> your model geometry and model-to-data fit quality have not changed before
> and after the AlphaFold era.
>
> Whether you truncate residue side chains/loops that you don't see or keep
> them with zero occupancy is a perennial question on this list that has been
> coming up for decades, and I have yet to see an answer that everyone agrees
> on!
>
> All the best,
> Pavel
>
>
> On Sun, Jul 28, 2024 at 8:13 AM Javier Gonzalez  wrote:
>
>>
>>
>> Dear CCP4bb,
>>
>> I'm refining the ~3A crystal structure of a big protein, largely composed
>> of alpha helices connected by poorly-resolved loops.
>> In the old pre-AlphaFold (AF) days I used to simply remove those
>> loops/regions with too high B factors, because there was little to none
>> density at 1 sigma in a 2Fo-Fc map.
>> However, considering that the quality of a readily-computable AF model is
>> comparable to a 3A experimental structure, and that the UniProt database is
>> flooded with noodle-like AF models, I was considering depositing a combined
>> model in the PDB.
>> Once R/Rfree reach a minimum for the model truncated in poorly resolved
>> loops, I would calculate an augmented model with AF calculated missing
>> regions (provided they have an acceptable pLDDT value), assign them zero
>> occupancy, and run only one cycle of refinement to calculate the formal
>> refinement statistics.
>> Would that be acceptable? Has anyone tried a similar approach?
>> I'd rather do that instead of depositing a counterintuitive model with
>> truncated regions that few people would find useful!!
>>
>> Thank you for your comments,
>>
>> Javier
>>
>> --
>> Dr. Javier M. González
>> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
>> Universidad Nacional de Santiago del Estero (UNSE)
>> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
>> Santiago del Estero. Argentina
>> Tel: +54-(0385)-4238352
>> Email  Twitter 
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
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> igen avsändaren och vet att innehållet är säkert.
> CAUTION: Do not click on links or open attachments unless you recognise
> the sender and know the content is safe.
>
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>
> När du ha

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Guillaume Gaullier]

Hello Javier,

Placing atoms implies that you know they are present somewhere (possibly with 
some uncertainty on exactly where), but setting their occupancies to zero 
implies that you know they are nowhere at all. This is a paradox.

I think atoms with zero occupancy make no sense in a final deposited model 
(they could be useful as a working intermediate to exclude the bulk solvent 
model, but this is unrelated to what you describe).
So in this particular case, partial occupancies only make sense for multiple 
conformations (and should add up to 1), as Pavel describes.

If you can’t resolve more than one conformation, maybe a better approach is to 
fix the coordinates to what AlphaFold suggested (which is often reasonable, but 
check their pLDDT to assess this) and refine to let the B-factors of these 
atoms rise. This will convey the large uncertainty on their positions. I think 
it is a valid approach because you know these residues are there somewhere (in 
other words, to me you would need evidence of their absence to justify 
truncating these loops: SDS-PAGE showing that the protein is cleaved, for 
example).

I hope this helps,

Guillaume

On 28 Jul 2024, at 17:32, Pavel Afonine  wrote:



Javier,

Flexible loops may be better modeled with ensembles of N models, meaning the 
occupancy of each-one would be 1/N, and the map contours to visualize them 
should be chosen as 1/N sigma (not 1 sigma). While model prediction tools such 
as AlphaFold are helpful, they don't suddenly lift the requirement for the 
atomic model you release to the world to fit the experimental data! With this 
premise in mind, the approaches to validate your model geometry and 
model-to-data fit quality have not changed before and after the AlphaFold era.

Whether you truncate residue side chains/loops that you don't see or keep them 
with zero occupancy is a perennial question on this list that has been coming 
up for decades, and I have yet to see an answer that everyone agrees on!

All the best,
Pavel


On Sun, Jul 28, 2024 at 8:13 AM Javier Gonzalez 
mailto:bio...@gmail.com>> wrote:



Dear CCP4bb,

I'm refining the ~3A crystal structure of a big protein, largely composed of 
alpha helices connected by poorly-resolved loops.
In the old pre-AlphaFold (AF) days I used to simply remove those loops/regions 
with too high B factors, because there was little to none density at 1 sigma in 
a 2Fo-Fc map.
However, considering that the quality of a readily-computable AF model is 
comparable to a 3A experimental structure, and that the UniProt database is 
flooded with noodle-like AF models, I was considering depositing a combined 
model in the PDB.
Once R/Rfree reach a minimum for the model truncated in poorly resolved loops, 
I would calculate an augmented model with AF calculated missing regions 
(provided they have an acceptable pLDDT value), assign them zero occupancy, and 
run only one cycle of refinement to calculate the formal refinement statistics.
Would that be acceptable? Has anyone tried a similar approach?
I'd rather do that instead of depositing a counterintuitive model with 
truncated regions that few people would find useful!!

Thank you for your comments,

Javier

--
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
Email Twitter




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Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

[Pavel Afonine]

Javier,

Flexible loops may be better modeled with ensembles of N models, meaning
the occupancy of each-one would be 1/N, and the map contours to visualize
them should be chosen as 1/N sigma (not 1 sigma). While model prediction
tools such as AlphaFold are helpful, they don't suddenly lift the
requirement for the atomic model you release to the world to fit the
experimental data! With this premise in mind, the approaches to validate
your model geometry and model-to-data fit quality have not changed before
and after the AlphaFold era.

Whether you truncate residue side chains/loops that you don't see or keep
them with zero occupancy is a perennial question on this list that has been
coming up for decades, and I have yet to see an answer that everyone agrees
on!

All the best,
Pavel


On Sun, Jul 28, 2024 at 8:13 AM Javier Gonzalez  wrote:

>
>
> Dear CCP4bb,
>
> I'm refining the ~3A crystal structure of a big protein, largely composed
> of alpha helices connected by poorly-resolved loops.
> In the old pre-AlphaFold (AF) days I used to simply remove those
> loops/regions with too high B factors, because there was little to none
> density at 1 sigma in a 2Fo-Fc map.
> However, considering that the quality of a readily-computable AF model is
> comparable to a 3A experimental structure, and that the UniProt database is
> flooded with noodle-like AF models, I was considering depositing a combined
> model in the PDB.
> Once R/Rfree reach a minimum for the model truncated in poorly resolved
> loops, I would calculate an augmented model with AF calculated missing
> regions (provided they have an acceptable pLDDT value), assign them zero
> occupancy, and run only one cycle of refinement to calculate the formal
> refinement statistics.
> Would that be acceptable? Has anyone tried a similar approach?
> I'd rather do that instead of depositing a counterintuitive model with
> truncated regions that few people would find useful!!
>
> Thank you for your comments,
>
> Javier
>
> --
> Dr. Javier M. González
> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
> Universidad Nacional de Santiago del Estero (UNSE)
> RN9, Km 1125. Villa El Zanjón. (G4206XCP)
> Santiago del Estero. Argentina
> Tel: +54-(0385)-4238352
> Email  Twitter 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

[Artem Evdokimov]

Dear Markus,

I've had to solve this exact issue in the past. Putting a 'simple' (nothing
is simple these days, everything has some kind of AI or other evil gnomes
in it) spectrofluorimeter into the cold room *should* be OK.

Caveat #1: I don't know if this will work with your specific device
Caveat #2: I've done this with a Bio-tek device and a FeraStar. Both
survived.

Condensation is indeed the enemy. Placing the spectrofluorimeter in the
cold room isn't much of an issue, because the instrument is warm, going
into the cold. Please note that many instruments these days have a
thermostated environment inside, meaning you may have to actually switch
off or adjust the thermal control otherwise the instrument will maintain
its preset temperature.

Taking the instrument out is where issues may occur. In the past, some of
the filters and other delicate elements were coated in
condensation-sensitive materials that would degrade upon exposure to
moisture. I am fairly certain that this is not the current practice.
Instruments get shipped in winter all the time, and the manufacturer
normally would recommend 24-48 hours in a thermally conditioned environment
(i.e. your lab) before turning the instrument on, so that condensation can
safely evaporate in an off state.

If you're very concerned, and have the energy to do this, you could load
the instrument into a nice large airtight bag in the cold room, and shove a
large dessicant pack into the bag - or perhaps into one of the compartments
of the instrument itself, wait a day, then take the whole thing out of the
cold room, let it warm up, and then remove the bag - that will very likely
avoid condensation entirely.

Probably best to avoid P2O5 or anything aggressive, but a pound of
pre-baked silica gel beads in a clean sock should do the trick.

With warmest regards,

Artem

On Fri, Jul 26, 2024 at 11:09 AM Markus Seeliger 
wrote:

> Dear All,
> apologies for the off-topic question. I am facing the problem of running
> enzyme activity assays at low temperature (close to 4C would be ideal) in a
> fluorescence plate reader. Before I get labeled in our department as "the
> one who voids warranties" and destroys our beloved plate reader, I wanted
> to pick your communal brains for any experience on this matter.
> It is odd - we have had FPLCs, drop setting robots, PCs etc in the cold
> room for years without much problem, but I have scruples about putting a
> plate reader in frigid environments. I assume that humidity and
> condensation would be the number 1 threat to the plate reader (aside from
> yours truly and his merry coworkers), and if you have any advice on how to
> minimize humidity in the cold environment, I would appreciate any
> suggestions.
> Am I wrong to think that most condensation should occur on the heat
> exchangers of the cold box/cold room which are the coldest spot in the
> system and therefore humidity should be reasonably low within the chilled
> volume (unless we frequently open and close the doors to the jungle-like
> atmosphere of the lab)?
>
> Thank you for your advice
>
> Markus
>
> ***
> Markus Seeliger
>
> Professor
> Department of Pharmacological Sciences
> Stony Brook University Medical School, BST 7-170
> Stony Brook, NY 11794-8651
> office: (631) 444-3558
> lab: (631) 638-1299
> fax: (631) 444-9749
>
> https://www.pharm.stonybrook.edu/markus-seeliger-lab-welcome
>
> markus.seeli...@stonybrook.edu
> ***
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Presence of negative density in Sim Omit map

[John Bacik]

 Happy to do it! 

All the best,JP

On Friday, July 26, 2024 at 12:28:22 PM CDT, Renuka Kadirvelraj 
<de831e80596f-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 Hi John,Thanks again for helping us! Regarding the map after placing missing 
residues and refinement: you are correct, both the negative and positive 
densities have gone away from the loop.Thanks,Renu
-Renu Kadirvelraj, Ph.D.Research 
Scientist
A428, Biochemistry and Molecular Biology120, East Green StreetUniversity of 
GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 bulletin board 
 on behalf of John Bacik 
<b45abf420e1f-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, July 26, 2024 11:18 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map 
|  | You don't often get email from 
b45abf420e1f-dmarc-requ...@jiscmail.ac.uk.Learn why this is important |  |

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Renu, how do the maps look (2Fo-Fc and Fo-Fc) after you run a standard 
refinement in Phenix with the missing residues in place? If the negative 
density disappears in the Fo-Fc then there is not necessarily a problem. Of 
course the positive density should also go away in the Fo-Fc map since it is 
now accounted for by the model.

All the best,JP

On Friday, July 26, 2024 at 10:03:10 AM CDT, Renuka Kadirvelraj 
<de831e80596f-dmarc-requ...@jiscmail.ac.uk> wrote:

Follow up to OP: Presence of negative density in Sim Omit map Hi CCP4bb,Thank 
you very much for the help and apologies for some missing info from the earlier 
post, it is here below. Also, thanks to Oleg, John, Edward, Eleanor, Dave and 
Andrea for their advice, suggestions and things to try.The updated pic (left) 
shows the misbehaving lysine, the contour level of this Sim Omit map is 3 
sigma. The residue is not disordered per se, we had no trouble modelling it; 
the Sim Omit was to make sure it is a true outlier.We used Wilson scaling while 
converting the I’s to F’s to approximate the F000. The negative density showed 
up in the Sim Omit map and only around the loop that was deleted. We did not 
see a complementary negative density near that loop nor elsewhere in the 
regular, non-omitted difference map (at 3 sigma or at a lower contour level of 
2.7 sigma).We ran a bog-standard difference map like Eleanor suggested; set the 
loop occupancy to zero and then run cycles of refinement. The positive density 
for the Lys shows up; unfortunately, the flanking red density shows up as well. 
Difference density map pic on the right, contour level 3 sigma.Perhaps this is 
just the complementary sagging around the peak, like Edward suggested with his 
child-standing-on-water-bed’ analogy. Also, we’re looking into the incorrectly 
modelled bulk solvent issue that Dave and Andrea mentioned.Thanks again,Renu
-Renu Kadirvelraj, Ph.D.Research 
ScientistA428, Biochemistry and Molecular Biology120, East Green 
StreetUniversity of GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 
bulletin board  on behalf of John Bacik 
<b45abf420e1f-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 25, 2024 12:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map 
|  | You don't often get email from 
b45abf420e1f-dmarc-requ...@jiscmail.ac.uk. Learn why this is important |  |

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


I also noticed one residue looks like a Phe and there is another that may be a 
Lys but not a very good view of it. When doing simulated annealing its not 
outside the realm of possibility that it will introduce errors in other parts 
of the model that could in theory explain the additional red density. The 
density does look a bit unusual though and it would be interesting to see if 
this simply disappears with another round of refinement. I believe you may in 
certain cases see some red density in for example hydrophobic pockets where in 
reality there is little or no bulk solvent and it is not properly accounted for 
in the refinement.
JPOn Thursday, July 25, 2024 at 01:11:05 AM CDT, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?As Edward 
suggests - if you omit a well ordered feature the resultant difference maps 
often show high positive density and a surrounding complementary "sag" of 
negative density - not really something to worry about..But I wonder why you 
don't just do a bog standard difference map? Set the occupancies of the loop 
you want to omit to 0.00 - do a few cycles of refinement and see what comes 
back? A prediction - the well ordered features will show up loud and clear and 
your surface LYS wont! High resolution structures show they often are in 
multiple conformat

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

[Edward Berry]

I think you are right, in the final equilibrium all the moisture would condense 
on the (evaporator?) coils, and there should be provision for them to drip into 
a reservoir outside. However each time the door opens and humid air is 
admitted, there will be condensation everywhere. If you leave the plate reader 
powered on, it will be slightly warmer (some parts more so than others) than 
the walls, floor, and bench, so will not be able to compete effectively for 
collecting moisture, and will be the first to dry off as the humidity goes 
down. The real chance for condensation is when you finish and take it out of 
the cold.  Laptops I enclose in a plastic bag when removing from the cold, 
don't know how practical that would be for your plate reader.
eab

Markus Seeliger wrote on 7/26/2024 11:09 AM:

Dear All,
apologies for the off-topic question. I am facing the problem of running enzyme activity 
assays at low temperature (close to 4C would be ideal) in a fluorescence plate reader. 
Before I get labeled in our department as "the one who voids warranties" and 
destroys our beloved plate reader, I wanted to pick your communal brains for any 
experience on this matter.
It is odd - we have had FPLCs, drop setting robots, PCs etc in the cold room 
for years without much problem, but I have scruples about putting a plate 
reader in frigid environments. I assume that humidity and condensation would be 
the number 1 threat to the plate reader (aside from yours truly and his merry 
coworkers), and if you have any advice on how to minimize humidity in the cold 
environment, I would appreciate any suggestions.
Am I wrong to think that most condensation should occur on the heat exchangers 
of the cold box/cold room which are the coldest spot in the system and 
therefore humidity should be reasonably low within the chilled volume (unless 
we frequently open and close the doors to the jungle-like atmosphere of the 
lab)?

Thank you for your advice

Markus

***
Markus Seeliger

Professor
Department of Pharmacological Sciences
Stony Brook University Medical School, BST 7-170
Stony Brook, NY 11794-8651
office: (631) 444-3558
lab: (631) 638-1299
fax: (631) 444-9749

https://www.pharm.stonybrook.edu/markus-seeliger-lab-welcome

markus.seeli...@stonybrook.edu 
***

--

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Re: [ccp4bb] Presence of negative density in Sim Omit map

[Renuka Kadirvelraj]

Hi John,
Thanks again for helping us! Regarding the map after placing missing residues 
and refinement: you are correct, both the negative and positive densities have 
gone away from the loop.
Thanks,
Renu

-
Renu Kadirvelraj, Ph.D.
Research Scientist
A428, Biochemistry and Molecular Biology
120, East Green Street
University of Georgia
Athens, GA 30602
Tel: (706) 583 0303

From: CCP4 bulletin board  on behalf of John Bacik 
<b45abf420e1f-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, July 26, 2024 11:18 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map

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Hi Renu, how do the maps look (2Fo-Fc and Fo-Fc) after you run a standard 
refinement in Phenix with the missing residues in place? If the negative 
density disappears in the Fo-Fc then there is not necessarily a problem. Of 
course the positive density should also go away in the Fo-Fc map since it is 
now accounted for by the model.

All the best,
JP

On Friday, July 26, 2024 at 10:03:10 AM CDT, Renuka Kadirvelraj 
<de831e80596f-dmarc-requ...@jiscmail.ac.uk> wrote:


Follow up to OP: Presence of negative density in Sim Omit map

Hi CCP4bb,
Thank you very much for the help and apologies for some missing info from the 
earlier post, it is here below. Also, thanks to Oleg, John, Edward, Eleanor, 
Dave and Andrea for their advice, suggestions and things to try.
The updated pic (left) shows the misbehaving lysine, the contour level of this 
Sim Omit map is 3 sigma. The residue is not disordered per se, we had no 
trouble modelling it; the Sim Omit was to make sure it is a true outlier.
We used Wilson scaling while converting the I’s to F’s to approximate the F000. 
The negative density showed up in the Sim Omit map and only around the loop 
that was deleted. We did not see a complementary negative density near that 
loop nor elsewhere in the regular, non-omitted difference map (at 3 sigma or at 
a lower contour level of 2.7 sigma).
We ran a bog-standard difference map like Eleanor suggested; set the loop 
occupancy to zero and then run cycles of refinement. The positive density for 
the Lys shows up; unfortunately, the flanking red density shows up as well. 
Difference density map pic on the right, contour level 3 sigma.
Perhaps this is just the complementary sagging around the peak, like Edward 
suggested with his child-standing-on-water-bed’ analogy. Also, we’re looking 
into the incorrectly modelled bulk solvent issue that Dave and Andrea mentioned.
Thanks again,
Renu

-
Renu Kadirvelraj, Ph.D.
Research Scientist
A428, Biochemistry and Molecular Biology
120, East Green Street
University of Georgia
Athens, GA 30602
Tel: (706) 583 0303

From: CCP4 bulletin board  on behalf of John Bacik 
<b45abf420e1f-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 25, 2024 12:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map

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I also noticed one residue looks like a Phe and there is another that may be a 
Lys but not a very good view of it. When doing simulated annealing its not 
outside the realm of possibility that it will introduce errors in other parts 
of the model that could in theory explain the additional red density. The 
density does look a bit unusual though and it would be interesting to see if 
this simply disappears with another round of refinement. I believe you may in 
certain cases see some red density in for example hydrophobic pockets where in 
reality there is little or no bulk solvent and it is not properly accounted for 
in the refinement.

JP
On Thursday, July 25, 2024 at 01:11:05 AM CDT, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:


Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?
As Edward suggests - if you omit a well ordered feature the resultant 
difference maps often show high positive density and a surrounding 
complementary "sag" of negative density - not really something to worry about..
But I wonder why you don't just do a bog standard difference map? Set the 
occupancies of the loop you want to omit to 0.00 - do a few cycles of 
refinement and see what comes back? A prediction - the well ordered features 
will show up loud and clear and your surface LYS wont! High resolution 
structures show they often are in multiple conf

Re: [ccp4bb] Presence of negative density in Sim Omit map

[John Bacik]

 Hi Renu, how do the maps look (2Fo-Fc and Fo-Fc) after you run a standard 
refinement in Phenix with the missing residues in place? If the negative 
density disappears in the Fo-Fc then there is not necessarily a problem. Of 
course the positive density should also go away in the Fo-Fc map since it is 
now accounted for by the model.

All the best,JP

On Friday, July 26, 2024 at 10:03:10 AM CDT, Renuka Kadirvelraj 
<de831e80596f-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 #yiv4749023127 P {margin-top:0;margin-bottom:0;}Follow up to OP: Presence of 
negative density in Sim Omit map Hi CCP4bb,Thank you very much for the help and 
apologies for some missing info from the earlier post, it is here below. Also, 
thanks to Oleg, John, Edward, Eleanor, Dave and Andrea for their advice, 
suggestions and things to try.The updated pic (left) shows the misbehaving 
lysine, the contour level of this Sim Omit map is 3 sigma. The residue is not 
disordered per se, we had no trouble modelling it; the Sim Omit was to make 
sure it is a true outlier.We used Wilson scaling while converting the I’s to 
F’s to approximate the F000. The negative density showed up in the Sim Omit map 
and only around the loop that was deleted. We did not see a complementary 
negative density near that loop nor elsewhere in the regular, non-omitted 
difference map (at 3 sigma or at a lower contour level of 2.7 sigma).We ran a 
bog-standard difference map like Eleanor suggested; set the loop occupancy to 
zero and then run cycles of refinement. The positive density for the Lys shows 
up; unfortunately, the flanking red density shows up as well. Difference 
density map pic on the right, contour level 3 sigma.Perhaps this is just the 
complementary sagging around the peak, like Edward suggested with his 
child-standing-on-water-bed’ analogy. Also, we’re looking into the incorrectly 
modelled bulk solvent issue that Dave and Andrea mentioned.Thanks again,Renu
-Renu Kadirvelraj, Ph.D.Research 
ScientistA428, Biochemistry and Molecular Biology120, East Green 
StreetUniversity of GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 
bulletin board  on behalf of John Bacik 
<b45abf420e1f-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 25, 2024 12:21 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map 
|  | You don't often get email from 
b45abf420e1f-dmarc-requ...@jiscmail.ac.uk. Learn why this is important |  |

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


I also noticed one residue looks like a Phe and there is another that may be a 
Lys but not a very good view of it. When doing simulated annealing its not 
outside the realm of possibility that it will introduce errors in other parts 
of the model that could in theory explain the additional red density. The 
density does look a bit unusual though and it would be interesting to see if 
this simply disappears with another round of refinement. I believe you may in 
certain cases see some red density in for example hydrophobic pockets where in 
reality there is little or no bulk solvent and it is not properly accounted for 
in the refinement.
JPOn Thursday, July 25, 2024 at 01:11:05 AM CDT, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?As Edward 
suggests - if you omit a well ordered feature the resultant difference maps 
often show high positive density and a surrounding complementary "sag" of 
negative density - not really something to worry about..But I wonder why you 
don't just do a bog standard difference map? Set the occupancies of the loop 
you want to omit to 0.00 - do a few cycles of refinement and see what comes 
back? A prediction - the well ordered features will show up loud and clear and 
your surface LYS wont! High resolution structures show they often are in 
multiple conformations, which would be hard to model at 2.1A. 
And just a thought about negative features in difference maps. I often see 
random "holes" which don't seem to have any logical explanation.. I sloppily 
put them down to "data defects - missing data? poorly measured data? etc - but 
does anyone have a more satisfactory explanation?Or dont other people see 
them??Eleanor
On Thu, 25 Jul 2024 at 01:48, Edward A. Berry  wrote:
Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps 
are constructed by
Fourier transform without the 0 0 0 reflection, they have mean of zero (because 
the mean of a
sinusoid over one period is zero).  That means that any time you add positive 
(difference) density,
which raises the mean value of the absolute map, the Fourier map has to sink 
down a little to bring
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflect

Re: [ccp4bb] Presence of negative density in Sim Omit map

[Andrea Smith]

Hi Eleanor,
 
I had basically the same question that I asked in phenixbb recently, the answer 
was also that the reason for red blobs is the solvent mask. In phenix there is 
mosaic modelling available that deals with the red blobs:
https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4909

Best,
Andrea



On Friday, July 26, 2024 09:27 CEST, David Briggs  
wrote:

 Hi Eleanor,
 My understanding about negative holes in difference maps is that it is down to 
incorrectly modelled bulk solvent. I have seen this in structures where there 
are voids inside a protein that are perhaps in reality empty, but get modelled 
as bulk solvent, and so you get a negative difference peak filling the void.
 I am more than happy to be corrected, though.
 Best,
 Dave
 
--
Dr David C. Briggs CSci MRSB (he/him)
Principal Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
Working hours: Mon-Fri 0900-1700
==
about.me/david_briggs | OrcID | Google Scholar  
__

From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: 25 July 2024 07:10
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map External 
Sender: Use caution.
Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?As Edward 
suggests - if you omit a well ordered feature the resultant difference maps 
often show high positive density and a surrounding complementary "sag" of 
negative density - not really something to worry about..But I wonder why you 
don't just do a bog standard difference map? Set the occupancies of the loop 
you want to omit to 0.00 - do a few cycles of refinement and see what comes 
back? A prediction - the well ordered features will show up loud and clear and 
your surface LYS wont! High resolution structures show they often are in 
multiple conformations, which would be hard to model at 2.1A. 
 And just a thought about negative features in difference maps. I often see 
random "holes" which don't seem to have any logical explanation.. I sloppily 
put them down to "data defects - missing data? poorly measured data? etc - but 
does anyone have a more satisfactory explanation?Or dont other people see 
them??Eleanor

 On Thu, 25 Jul 2024 at 01:48, Edward A. Berry  wrote:
 
Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps 
are constructed by 
Fourier transform without the 0 0 0 reflection, they have mean of zero (because 
the mean of a 
sinusoid over one period is zero).  That means that any time you add positive 
(difference) density, 
which raises the mean value of the absolute map, the Fourier map has to sink 
down a little to bring 
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflection, this would move 
the floor down 
everywhere by a small amount to balance the large increase at the local peak, 
and it would not go 
below the negative contour limit. But without the ultra-low resolution 
amplitudes the FT cannot make 
a constant offset, and instead you get sagging around the peak, like a 
water-bed sagging around the 
spot where a child (the peak) is standing. This could lead to the sagging part 
going below the 
negative contour and giving you the red density.
However I would not have expected the negative density to be quite so localized 
around the peak - 
depending on your low-res cutoff. As John Bacik suggested you should check for 
a mis-modeled part of 
a symm-related molecule, but if that were the case, you should see the red 
density even before 
omitting the loop, and you should see the red density somewhere else on your 
model. If it just 
appeared after omitting the loop, it could be due to the map sagging under the 
weight of the peak, 
and should go away as soon as the residue is replaced.
eab

Renuka Kadirvelraj wrote:
> Hi CCP4bb,
> We would greatly appreciate your advice regarding an odd problem that has 
> cropped up with one of our 
> crystal structures. We have a protein structure in space group P6(3)22 at 2.1 
> A resolution and in 
> the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran 
> simulated annealing to 
> rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit map 
> showed the positive 
> density expected from the omission of the loop (colored green in attached 
> pics). However, flanking 
> the positive density, there is a complimentary negative density (in red). We 
> are puzzled as to the 
> cause of the appearance of the negative density. Can you help us?
> Many thanks,
> Renu
> 
> -
> Renu Kadirvelraj, Ph.D.
> Research Scientist
> A428, Biochemistry an

Re: [ccp4bb] Presence of negative density in Sim Omit map

[David Briggs]

Hi Eleanor,

My understanding about negative holes in difference maps is that it is down to 
incorrectly modelled bulk solvent. I have seen this in structures where there 
are voids inside a protein that are perhaps in reality empty, but get modelled 
as bulk solvent, and so you get a negative difference peak filling the void.

I am more than happy to be corrected, though.

Best,

Dave


--

Dr David C. Briggs CSci MRSB (he/him)

Principal Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

Working hours: Mon-Fri 0900-1700

==

about.me/david_briggs<https://about.me/david_briggs> | 
OrcID<https://orcid.org/-0002-9793-7339> | Google Scholar 
<https://scholar.google.co.uk/citations?user=DRKG5KwJ>


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: 25 July 2024 07:10
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map


External Sender: Use caution.

Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?
As Edward suggests - if you omit a well ordered feature the resultant 
difference maps often show high positive density and a surrounding 
complementary "sag" of negative density - not really something to worry about..
But I wonder why you don't just do a bog standard difference map? Set the 
occupancies of the loop you want to omit to 0.00 - do a few cycles of 
refinement and see what comes back? A prediction - the well ordered features 
will show up loud and clear and your surface LYS wont! High resolution 
structures show they often are in multiple conformations, which would be hard 
to model at 2.1A.

And just a thought about negative features in difference maps. I often see 
random "holes" which don't seem to have any logical explanation.. I sloppily 
put them down to "data defects - missing data? poorly measured data? etc - but 
does anyone have a more satisfactory explanation?
Or dont other people see them??
Eleanor

On Thu, 25 Jul 2024 at 01:48, Edward A. Berry 
mailto:eaber...@gmail.com>> wrote:
Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps 
are constructed by
Fourier transform without the 0 0 0 reflection, they have mean of zero (because 
the mean of a
sinusoid over one period is zero).  That means that any time you add positive 
(difference) density,
which raises the mean value of the absolute map, the Fourier map has to sink 
down a little to bring
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflection, this would move 
the floor down
everywhere by a small amount to balance the large increase at the local peak, 
and it would not go
below the negative contour limit. But without the ultra-low resolution 
amplitudes the FT cannot make
a constant offset, and instead you get sagging around the peak, like a 
water-bed sagging around the
spot where a child (the peak) is standing. This could lead to the sagging part 
going below the
negative contour and giving you the red density.
However I would not have expected the negative density to be quite so localized 
around the peak -
depending on your low-res cutoff. As John Bacik suggested you should check for 
a mis-modeled part of
a symm-related molecule, but if that were the case, you should see the red 
density even before
omitting the loop, and you should see the red density somewhere else on your 
model. If it just
appeared after omitting the loop, it could be due to the map sagging under the 
weight of the peak,
and should go away as soon as the residue is replaced.
eab

Renuka Kadirvelraj wrote:
> Hi CCP4bb,
> We would greatly appreciate your advice regarding an odd problem that has 
> cropped up with one of our
> crystal structures. We have a protein structure in space group P6(3)22 at 2.1 
> A resolution and in
> the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran 
> simulated annealing to
> rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit map 
> showed the positive
> density expected from the omission of the loop (colored green in attached 
> pics). However, flanking
> the positive density, there is a complimentary negative density (in red). We 
> are puzzled as to the
> cause of the appearance of the negative density. Can you help us?
> Many thanks,
> Renu
>
> -
> Renu Kadirvelraj, Ph.D.
> Research Scientist
> A428, Biochemistry and Molecular Biology
> 120, East Green Street
> University of Georgia
> Athens, GA 30602
> Tel: (706) 583 0303
>
> 

Re: [ccp4bb] High clash score in refinement of cryoEM structure

[Edward Berry]

To improve the clashscore you could try increasing the value of the 
nonbonded_weight parameter, starting at 1000 (which I understand at one time 
was the default in phenix.refine, but recently for me already gives a huge 
decrease in clashscore). Since this will be avoiding clashes at the expense of 
(a) not fitting the map as well, and (b) potentially not fitting standard 
geometry as well, you need to watch that it doesn't increase real-space R or 
RMSD bonds/angles significantly. (My experience is with reciprocal space 
phenix.refine, but I expect there is a similar parameter in real-space_refine)
First look for errors in the model that may cause classhes- more the .geo file and search 
to "Nonbonded". The interactions are listed under this, starting with the worst 
offenders. Examine those residues and see if thay are right. But if you say you have 
fixed these and the refinement reverts to bad values because map quality is poor, I think 
nonbonded_weight is the key.
eab


Srivastava, Dhiraj wrote on 7/25/2024 10:08 AM:

Hi
        We solved several structures of a protein (in different ligand bound 
form) using cryoEM. While I was able to get reasonable fewer clash score and 
rotamer outlier in my best data set, in other data set with poor map quality, I 
am getting  lots of clashes and rotamers outlier. I am fixing these issues and 
after refining the structure using phenix real space refinement (global 
minimization, local grid search and adp), it's getting back to same old 
structure with clashes. The reason is poor quality map. does anyone know a way 
to fix this issue?

Thank you
Dhiraj

--

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Re: [ccp4bb] Presence of negative density in Sim Omit map

[John Bacik]

 
I also noticed one residue looks like a Phe and there is another that may be a 
Lys but not a very good view of it. When doing simulated annealing its not 
outside the realm of possibility that it will introduce errors in other parts 
of the model that could in theory explain the additional red density. The 
density does look a bit unusual though and it would be interesting to see if 
this simply disappears with another round of refinement. I believe you may in 
certain cases see some red density in for example hydrophobic pockets where in 
reality there is little or no bulk solvent and it is not properly accounted for 
in the refinement.
JP
On Thursday, July 25, 2024 at 01:11:05 AM CDT, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:  
 
 Hmm - I cant quite understand your map - that density is not for the lysine ? 
It looks like a well ordered PHE contoured at quite a high level?As Edward 
suggests - if you omit a well ordered feature the resultant difference maps 
often show high positive density and a surrounding complementary "sag" of 
negative density - not really something to worry about..But I wonder why you 
don't just do a bog standard difference map? Set the occupancies of the loop 
you want to omit to 0.00 - do a few cycles of refinement and see what comes 
back? A prediction - the well ordered features will show up loud and clear and 
your surface LYS wont! High resolution structures show they often are in 
multiple conformations, which would be hard to model at 2.1A. 
And just a thought about negative features in difference maps. I often see 
random "holes" which don't seem to have any logical explanation.. I sloppily 
put them down to "data defects - missing data? poorly measured data? etc - but 
does anyone have a more satisfactory explanation?Or dont other people see 
them??Eleanor
On Thu, 25 Jul 2024 at 01:48, Edward A. Berry  wrote:

Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps 
are constructed by 
Fourier transform without the 0 0 0 reflection, they have mean of zero (because 
the mean of a 
sinusoid over one period is zero).  That means that any time you add positive 
(difference) density, 
which raises the mean value of the absolute map, the Fourier map has to sink 
down a little to bring 
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflection, this would move 
the floor down 
everywhere by a small amount to balance the large increase at the local peak, 
and it would not go 
below the negative contour limit. But without the ultra-low resolution 
amplitudes the FT cannot make 
a constant offset, and instead you get sagging around the peak, like a 
water-bed sagging around the 
spot where a child (the peak) is standing. This could lead to the sagging part 
going below the 
negative contour and giving you the red density.
However I would not have expected the negative density to be quite so localized 
around the peak - 
depending on your low-res cutoff. As John Bacik suggested you should check for 
a mis-modeled part of 
a symm-related molecule, but if that were the case, you should see the red 
density even before 
omitting the loop, and you should see the red density somewhere else on your 
model. If it just 
appeared after omitting the loop, it could be due to the map sagging under the 
weight of the peak, 
and should go away as soon as the residue is replaced.
eab

Renuka Kadirvelraj wrote:
> Hi CCP4bb,
> We would greatly appreciate your advice regarding an odd problem that has 
> cropped up with one of our 
> crystal structures. We have a protein structure in space group P6(3)22 at 2.1 
> A resolution and in 
> the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran 
> simulated annealing to 
> rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit map 
> showed the positive 
> density expected from the omission of the loop (colored green in attached 
> pics). However, flanking 
> the positive density, there is a complimentary negative density (in red). We 
> are puzzled as to the 
> cause of the appearance of the negative density. Can you help us?
> Many thanks,
> Renu
> 
> -
> Renu Kadirvelraj, Ph.D.
> Research Scientist
> A428, Biochemistry and Molecular Biology
> 120, East Green Street
> University of Georgia
> Athens, GA 30602
> Tel: (706) 583 0303
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 



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hosted by www.jiscmail.ac.uk, te

Re: [ccp4bb] Presence of negative density in Sim Omit map

[Eleanor Dodson]

Hmm - I cant quite understand your map - that density is not for the lysine
? It looks like a well ordered PHE contoured at quite a high level?
As Edward suggests - if you omit a well ordered feature the resultant
difference maps often show high positive density and a surrounding
complementary "sag" of negative density - not really something to worry
about..
But I wonder why you don't just do a bog standard difference map? Set the
occupancies of the loop you want to omit to 0.00 - do a few cycles of
refinement and see what comes back? A prediction - the well ordered
features will show up loud and clear and your surface LYS wont! High
resolution structures show they often are in multiple conformations, which
would be hard to model at 2.1A.

And just a thought about negative features in difference maps. I often see
random "holes" which don't seem to have any logical explanation.. I
sloppily put them down to "data defects - missing data? poorly measured
data? etc - but does anyone have a more satisfactory explanation?
Or dont other people see them??
Eleanor

On Thu, 25 Jul 2024 at 01:48, Edward A. Berry  wrote:

> Does your difference map have mean value ~zero (over 1 ASU or cell)? If
> maps are constructed by
> Fourier transform without the 0 0 0 reflection, they have mean of zero
> (because the mean of a
> sinusoid over one period is zero).  That means that any time you add
> positive (difference) density,
> which raises the mean value of the absolute map, the Fourier map has to
> sink down a little to bring
> that new mean value to zero.
> Now if your data were complete except for the 0 0 0 reflection, this would
> move the floor down
> everywhere by a small amount to balance the large increase at the local
> peak, and it would not go
> below the negative contour limit. But without the ultra-low resolution
> amplitudes the FT cannot make
> a constant offset, and instead you get sagging around the peak, like a
> water-bed sagging around the
> spot where a child (the peak) is standing. This could lead to the sagging
> part going below the
> negative contour and giving you the red density.
> However I would not have expected the negative density to be quite so
> localized around the peak -
> depending on your low-res cutoff. As John Bacik suggested you should check
> for a mis-modeled part of
> a symm-related molecule, but if that were the case, you should see the red
> density even before
> omitting the loop, and you should see the red density somewhere else on
> your model. If it just
> appeared after omitting the loop, it could be due to the map sagging under
> the weight of the peak,
> and should go away as soon as the residue is replaced.
> eab
>
> Renuka Kadirvelraj wrote:
> > Hi CCP4bb,
> > We would greatly appreciate your advice regarding an odd problem that
> has cropped up with one of our
> > crystal structures. We have a protein structure in space group P6(3)22
> at 2.1 A resolution and in
> > the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When
> we ran simulated annealing to
> > rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit
> map showed the positive
> > density expected from the omission of the loop (colored green in
> attached pics). However, flanking
> > the positive density, there is a complimentary negative density (in
> red). We are puzzled as to the
> > cause of the appearance of the negative density. Can you help us?
> > Many thanks,
> > Renu
> >
> > -
> > Renu Kadirvelraj, Ph.D.
> > Research Scientist
> > A428, Biochemistry and Molecular Biology
> > 120, East Green Street
> > University of Georgia
> > Athens, GA 30602
> > Tel: (706) 583 0303
> >
> >
> 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
>
> 
>
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Re: [ccp4bb] Presence of negative density in Sim Omit map

[Edward A. Berry]

Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps are constructed by 
Fourier transform without the 0 0 0 reflection, they have mean of zero (because the mean of a 
sinusoid over one period is zero).  That means that any time you add positive (difference) density, 
which raises the mean value of the absolute map, the Fourier map has to sink down a little to bring 
that new mean value to zero.
Now if your data were complete except for the 0 0 0 reflection, this would move the floor down 
everywhere by a small amount to balance the large increase at the local peak, and it would not go 
below the negative contour limit. But without the ultra-low resolution amplitudes the FT cannot make 
a constant offset, and instead you get sagging around the peak, like a water-bed sagging around the 
spot where a child (the peak) is standing. This could lead to the sagging part going below the 
negative contour and giving you the red density.
However I would not have expected the negative density to be quite so localized around the peak - 
depending on your low-res cutoff. As John Bacik suggested you should check for a mis-modeled part of 
a symm-related molecule, but if that were the case, you should see the red density even before 
omitting the loop, and you should see the red density somewhere else on your model. If it just 
appeared after omitting the loop, it could be due to the map sagging under the weight of the peak, 
and should go away as soon as the residue is replaced.

eab

Renuka Kadirvelraj wrote:

Hi CCP4bb,
We would greatly appreciate your advice regarding an odd problem that has cropped up with one of our 
crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in 
the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to 
rebuild an outlier Lysine residue in a loop (using Phenix), the Sim Omit map showed the positive 
density expected from the omission of the loop (colored green in attached pics). However, flanking 
the positive density, there is a complimentary negative density (in red). We are puzzled as to the 
cause of the appearance of the negative density. Can you help us?

Many thanks,
Renu

-
Renu Kadirvelraj, Ph.D.
Research Scientist
A428, Biochemistry and Molecular Biology
120, East Green Street
University of Georgia
Athens, GA 30602
Tel: (706) 583 0303



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Re: [ccp4bb] Presence of negative density in Sim Omit map

[John Bacik]

 Hi Renu, you may try using a Polder omit map for the region rather than a 
simulated annealing map. You may also check if the red density is due to a 
symmetry related molecule that is not modeled well. Hope it helps.
JP
On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj 
 wrote:  
 
  #yiv8512769868 P {margin-top:0;margin-bottom:0;}Hi CCP4bb, We would greatly 
appreciate your advice regarding an odd problem that has cropped up with one of 
our crystal structures. We have a protein structure in space group P6(3)22 at 
2.1 A resolution and in the final refinement stages with Rwork of 0.20 and 
Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine 
residue in a loop (using Phenix), the Sim Omit map showed the positive density 
expected from the omission of the loop (colored green in attached pics). 
However, flanking the positive density, there is a complimentary negative 
density (in red). We are puzzled as to the cause of the appearance of the 
negative density. Can you help us? Many thanks,Renu
-Renu Kadirvelraj, Ph.D.Research 
Scientist
A428, Biochemistry and Molecular Biology120, East Green StreetUniversity of 
GeorgiaAthens, GA 30602Tel: (706) 583 0303

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Re: [ccp4bb] Off topic: Nobel prize stats

[Nukri Sanishvili]

Thank you all for useful links, slides and thoughtful comments.
I completely agree with Mark's comment that it is difficult to quote a
single number. Precisely for the reasons he mentioned.
The link to PDB,
https://pdb101.rcsb.org/learn/other-resources/structural-biology-and-nobel-prizes
seems the most comprehensive, although this one too is missing Günter Blobel
.
It appears that the number to be quoted would be highly contextual.
Best wishes,
Nukri



On Mon, Jul 22, 2024 at 1:41 PM Nukri Sanishvili  wrote:

> Dear All,
> Does anyone know the number of Nobel Prizes awarded for macromolecular
> structures?
> This would be a very effective way to explain the importance of structural
> biology to the uninitiated.
> I suppose I could look at the whole list of laureates and figure out what
> was given for what, but if someone already has this number at their
> fingertips, it would save me a lot of time.
> Thank you in advance.
> Nukri
>
>



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Re: [ccp4bb] Ccp4i2 execution problem

[Stuart McNicholas]

Dear Maria,
  Could you please try deleting the file
/home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml ?

I think that this file is corrupted (empty) and that this is causing
the problems.

Best wishes,
Stuart McNicholas

On Wed, 24 Jul 2024 at 12:22, Marian Oliva  wrote:
>
> Dear all,
>
> Since yesterday I’m having some issues for running of ccp4i2. At the begging 
> I though it was a disk space memory problem but it wasn´t. I have re-install 
> ccp4 (indeed, I have tried with ccp4-8 and ccp4-9 installations) with the 
> same result. I can run all other programs (ccp4, ccp4cloud…) but ccp4i2.
>
> My machine is Ubuntu 22.04.4 and I have the error messages shown below when 
> trying to execute ccp4i2.
>
> Any help will be really appreciate
>
> Best,
> Marian
>
> Running CCP4i2 browser from: 
> /opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2
> Python 3.9.18 (main, Feb 15 2024, 15:40:47)
> [GCC 9.3.1 20200408 (Red Hat 9.3.1-2)]
> Qt version 5.15.3
>
> ccp4i2 version 1.1.0
> ccp4i2 source revision 6539
> CPrintHandler saving print output to directory: 
> /home/msa/.CCP4I2/logs/started_1721818556
> None
> None
> Starting Project Manager
> Current schema version: ('0.1.22', '23-09-2016')
> CCP4i2 opening database file /home/msa/.CCP4I2/db/database.sqlite
> updateDbSchema 0.1.22 23-09-2016
> Starting Project Manager - DONE
> Starting Job Controller
> Starting Job Controller - DONE
> Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT35C51
> exportProjectXml a25752da1bc311ee8776afbed6b8f83a 
> /home/msa/CCP4I2_PROJECTS/TRT35C51/DATABASE.db.xml
> Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT84A11B
> exportProjectXml 15ec8f74f27611eea3f08fdd9b93c48d 
> /home/msa/CCP4I2_PROJECTS/TRT84A11B/DATABASE.db.xml
> Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT84A11C
> exportProjectXml 3c81ce1af31611eea3f08fdd9b93c48d 
> /home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml
> Traceback (most recent call last):
>   File "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/bin/browser.py", 
> line 109, in 
> startBrowser(sys.argv[1:], app=app, splash=splash)
>   File 
> "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line 
> 248, in startBrowser
> createMissingDATABASEdbXML()
>   File 
> "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line 
> 177, in createMissingDATABASEdbXML
> tree = parse_from_unicode(s)
>   File 
> "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line 
> 173, in parse_from_unicode
> return etree.fromstring(s, parser=utf8_parser)
>   File "src/lxml/etree.pyx", line 3222, in lxml.etree.fromstring
>   File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument
>   File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc
>   File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc
>   File "src/lxml/parser.pxi", line 601, in 
> lxml.etree._ParserContext._handleParseResultDoc
>   File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult
>   File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError
>   File "", line 1
> lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
>
>
> 
>
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Re: [ccp4bb] Question about micro RNA structures

[Tales Rocha]

Hi Careina,

This recent publication evaluate several methods, might be a useful
resource.
https://doi.org/10.1093/nar/gkae541

And a webtool:
https://doi.org/10.1093/nar/gkae356

Best regards,
Tales

On Tue, Jul 23, 2024 at 10:02 AM careinaedgo...@yahoo.com <
02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Everyone.
> I am working with miRNA for the first time. I would like to start of doing
> some docking studies to protein. Are there any suggestions on good tools to
> use to generate the miRNA structure from it's sequence?
> Kind regards
> Careina
>
> Yahoo Mail: Search, Organize, Conquer
> 
>
> --
>
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-- 

Tales Rocha Moura



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