as out of density. Probably I should low the contour level but I
don't want to go for a trial-and-error approach, there must be a way to convert
the contour level from coot (the one that I used for modelling) in the one
required for deposition!
Any advice?
Thank you,
Anna
on and characterisation)
With kind regards,
EMBL Hamburg User Office
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Thi
s the
values are the same.
Best wishes,
Colin
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of anna anna
Sent: Thursday, September 26, 2024 11:13 AM
To: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: [ccp4bb] contour level for cryoEM deposition: coot vs chime
any viruses. UCB accepts no liability for any
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ontour level but I don't want to go for a trial-and-error
>> approach, there must be a way to convert the contour level from coot (the
>> one that I used for modelling) in the one required for deposition!
>>
>> Any advice?
>>
<mailto:bioc...@uiowa.edu>
https://medicine.uiowa.edu/biochemistry-molecular-biology/
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o for a trial-and-error
> approach, there must be a way to convert the contour level from coot (the one
> that I used for modelling) in the one required for deposition!
>
> Any advice?
>
> Thank you,
> Anna
>
> ---
&g
board On Behalf Of anna anna
Sent: Thursday, September 26, 2024 11:13 AM
To: ccp4bb
Subject: [ccp4bb] contour level for cryoEM deposition: coot vs chimera
Dear all,
I am depositing my first cryoEM structure and I am facing the following problem
concerning the contour level of the map.
Briefly
gt; should low the contour level but I don't want to go for a trial-and-error
> approach, there must be a way to convert the contour level from coot (the one
> that I used for modelling) in the one required for deposition!
>
> Any advice?
>
> Thank you,
> Anna
>
> ---
: CCP4 WG2 ; CCP4 WG1
; ccp4bb@jiscmail.ac.uk
Subject: Registration now open for CCP4 Study Weekend 2025 - Using software, AI
and other methods to advance macromolecular models
Importance: High
Dear all,
Registration is now open for the 2025 CCP4 study weekend entitled " Using
softwar
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tion!
Any advice?
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the atomic charge is for Mn2+.
Any ideas?
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ed at poissonboltzmann.org to run
pdb2pqr and apps but run into the problem of not knowing what the atomic
charge is for Mn2+.
Any ideas?
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your assistance.
Best regards,
Xin
*From:* CCP4 bulletin board on behalf of
zx2...@connect.hku.hk
*Sent:* 23 September 2024 09:13
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Phenix.autobuild command problem
*This is an
sequence file or no sequence file
I have also attached the log file for your reference.
Thank you very much for your assistance.
Best regards,
Xin
From: CCP4 bulletin board on behalf of
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Sent: 23 September 2024 09:13
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wait, pre-registration closes soon! Visit
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Hello,Please could you post on ccp4bb this information about a position for a research engineer in our laboratory?Many thanks. Sincerely,
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We would greatly appreciate any
pointers to get us started.
Thank you,
Doeke
=
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Assistant Professor of Molecular & Cellular Biology, and of Applied
Physics (SEAS),
Director of Undergraduate Studies, Chemical and Physical Biology
Center for Systems B
gt; Admin: 617-495-5651 (Lin Song)
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l.edu
From: CCP4 bulletin board on behalf of Oliver H. Weiergräber
Sent: Thursday, September 12, 2024 4:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 v9 installation issue
Dear community,
I am running into an unexpected problem while trying to install CCP4 v9
on a
t%3D1573738541933000&sa=D&ust=1573738541949000&usg=AFQjCNEVlkGKz9w6EBf_zJz7OpcQo8f-tA>
[E6CD5E50]
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==
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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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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 h
eck
@bubecklab
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I2BC, UMR 9198
Bat 532, pièce 24B, CEA Saclay
91190 Gif-sur-Yvette
Tel : (33) (0)1 69 08 31 41
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structural changes take place during the binding process.
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ance
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(FragMAX)
Thomas Ursby thomas.ur...@maxiv.lu.se (MicroMAX)
Ann Terry ann.te...@maxiv.lu.se (CoSAXS)
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-- Forwarded message -
From: Arpita Goswami
Date: Sun, Sep 8, 2024, 03:11
Subject: Re: [ccp4bb] Studying hydrogen bonding network by neutron
diffraction in sample with D2O
To: John R Helliwell
Dear Dr. John and others,
Good day! Thank you all for the clarifications
ond Light Source Limited (company no. 4375679). Registered in England and
Wales with its registered office at Diamond House, Harwell Science and
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom.
To unsubscribe
(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 hydrog
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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: CCP4 bulletin board on behalf of Qingping Xu
<292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk>
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Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US
This Message Is From an External Sender
This messag
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
). Registered in England and
Wales with its registered office at Diamond House, Harwell Science and
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom.
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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
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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tacrystal.org>
Hauptman-Woodward Medical Research Institute
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: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
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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
e 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
>
&
d, Sweden
www.cmps.lu.se
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has been scanned for viruses and malware by ProofPoint
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Roeland Boer.
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rity in selection.
>>
>> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2024/
>>
>> -- David (on behalf of the organisers)
>>
>
####
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yone!
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h
!
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anged (2HB -> HB2).
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. 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&#
>
> ... 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
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…
>
> --
>
>
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:
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eads = 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 yo
ndChildren(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 reg
ype' 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 unsubscrib
youtu.be/UKstDCFjYI8
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anks,
Thomas
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t: 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
y, 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?
ley
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 th
.1.10.
Paul.
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ulletin 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 sente
MacCHESS, Cornell University
schul...@cornell.edu
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Th
ng 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
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 li
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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ttps://rb.gy/bshuqp>
*
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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 ccp
AMBER Linkedin:
https://www.linkedin.com/company/amber-postdoctoral-programme
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This message
emical Biology, UK. AMBER is
coordinated by LINXS.
Link to the AMBER Linkedin:
https://www.linkedin.com/company/amber-postdoctoral-programme.
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