Re: [ccp4bb] CIF file problem

[Ning Li]

Thank you for the information.

On Thu, Apr 20, 2023 at 5:14 PM Tim Gruene  wrote:

> Dear Ning,
> their is some confusion. When a small molecule crystal structure is
> determined, the coordinates and data are usually submitted to the CCDC
> or the COD (crystallographic open database).  The structure receives a
> checkcif report which, as Phil has pointed out, is specific to small
> molecule structures.
> As you submitted a macromolecular structure to the PDB, the PDB code
> replaces the CCDC ID during the submission process.
>
> Best wishes,
> Tim
>
>
> On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li  wrote:
>
> > Hi Phil,
> >
> > Thank you for the clarification, I didn't realize the CheckCIF is for
> > small molecules. We tried to submit the manuscript to a chemical
> > magazine and found "CheckCIF reports must be submitted to the
> > Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript
> > submission". In fact I have had the validation for protein structure
> > as I submitted the structure to PDB library. I'll ask our
> > collaborator whether they really need it for protein structure.*
> >
> > *Thanks*
> >
> > *Ning*
> >
> > On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey 
> > wrote:
> >
> > > Hello Ning
> > >
> > > CheckCIF checks small molecule crystallographic cif files - the
> > > dictionaries and expectations on the contents are not the same as
> > > for mmcif, although the underlying syntax is the same.
> > >
> > > I'm unaware of anything that does the equivalent of CheckCIF for
> > > macromolecular cif files.
> > >
> > > Phil Jeffrey
> > > Princeton
> > >
> > >
> > > On 4/20/23 4:02 PM, Ning Li wrote:
> > > > Hi all,
> > > >
> > > > Does anybody know why I got this error message:
> > > >
> > > > /Checking for embedded fcf data in CIF .../
> > > > /No extractable fcf data in found in CIF/
> > > >
> > > > as I uploaded the CIF file to https://checkcif.iucr.org/
> > > > <
> > >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0
> >
> > > for structure validation? The CIF file was directly from
> > > phenix.refine during structure refinement.
> > > >
> > > > Appreciate your help
> > > >
> > > > Ning
> > > >
> > > >
> > > >
> 
> > > >
> > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > > <
> > >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0
> > >
> > > >
> > > >
> > >
> > >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
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>
>
>
> --
> --
> 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] CIF file problem

[Tim Gruene]

Dear Ning,
their is some confusion. When a small molecule crystal structure is
determined, the coordinates and data are usually submitted to the CCDC
or the COD (crystallographic open database).  The structure receives a
checkcif report which, as Phil has pointed out, is specific to small
molecule structures.
As you submitted a macromolecular structure to the PDB, the PDB code
replaces the CCDC ID during the submission process.

Best wishes,
Tim


On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li  wrote:

> Hi Phil,
> 
> Thank you for the clarification, I didn't realize the CheckCIF is for
> small molecules. We tried to submit the manuscript to a chemical
> magazine and found "CheckCIF reports must be submitted to the
> Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript
> submission". In fact I have had the validation for protein structure
> as I submitted the structure to PDB library. I'll ask our
> collaborator whether they really need it for protein structure.*
> 
> *Thanks*
> 
> *Ning*
> 
> On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey 
> wrote:
> 
> > Hello Ning
> >
> > CheckCIF checks small molecule crystallographic cif files - the
> > dictionaries and expectations on the contents are not the same as
> > for mmcif, although the underlying syntax is the same.
> >
> > I'm unaware of anything that does the equivalent of CheckCIF for
> > macromolecular cif files.
> >
> > Phil Jeffrey
> > Princeton
> >
> >
> > On 4/20/23 4:02 PM, Ning Li wrote:  
> > > Hi all,
> > >
> > > Does anybody know why I got this error message:
> > >
> > > /Checking for embedded fcf data in CIF .../
> > > /No extractable fcf data in found in CIF/
> > >
> > > as I uploaded the CIF file to https://checkcif.iucr.org/
> > > <
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0>
> > for structure validation? The CIF file was directly from
> > phenix.refine during structure refinement.  
> > >
> > > Appreciate your help
> > >
> > > Ning
> > >
> > >
> > > 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > <  
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0
> >  
> > >
> > >  
> >
> >  
> 
> 
> 
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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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Description: OpenPGP digital signature

Re: [ccp4bb] CIF file problem

[Ning Li]

Hi Phil,

Thank you for the clarification, I didn't realize the CheckCIF is for small
molecules. We tried to submit the manuscript to a chemical magazine and
found "CheckCIF reports must be submitted to the Cambridge Crystallographic
Data Centre (CCDC) *prior to manuscript submission". In fact I have had the
validation for protein structure as I submitted the structure to PDB
library. I'll ask our collaborator whether they really need it for protein
structure.*

*Thanks*

*Ning*

On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey  wrote:

> Hello Ning
>
> CheckCIF checks small molecule crystallographic cif files - the
> dictionaries and expectations on the contents are not the same as for
> mmcif, although the underlying syntax is the same.
>
> I'm unaware of anything that does the equivalent of CheckCIF for
> macromolecular cif files.
>
> Phil Jeffrey
> Princeton
>
>
> On 4/20/23 4:02 PM, Ning Li wrote:
> > Hi all,
> >
> > Does anybody know why I got this error message:
> >
> > /Checking for embedded fcf data in CIF .../
> > /No extractable fcf data in found in CIF/
> >
> > as I uploaded the CIF file to https://checkcif.iucr.org/
> > <
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0>
>  for
> structure validation? The CIF file was directly from phenix.refine during
> structure refinement.
> >
> > Appreciate your help
> >
> > Ning
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > <
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> >
> >
>
>



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Re: [ccp4bb] CIF file problem

[Phil Jeffrey]

Hello Ning

CheckCIF checks small molecule crystallographic cif files - the 
dictionaries and expectations on the contents are not the same as for 
mmcif, although the underlying syntax is the same.


I'm unaware of anything that does the equivalent of CheckCIF for 
macromolecular cif files.


Phil Jeffrey
Princeton


On 4/20/23 4:02 PM, Ning Li wrote:

Hi all,

Does anybody know why I got this error message:

/Checking for embedded fcf data in CIF .../
/No extractable fcf data in found in CIF/

as I uploaded the CIF file to https://checkcif.iucr.org/ 
 for structure validation? The CIF file was directly from phenix.refine during structure refinement.


Appreciate your help

Ning




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[ccp4bb] CIF file problem

[Ning Li]

Hi all,



Does anybody know why I got this error message:

*Checking for embedded fcf data in CIF ...*
*No extractable fcf data in found in CIF*

as I uploaded the CIF file to https://checkcif.iucr.org/ for structure
validation? The CIF file was directly from phenix.refine during structure
refinement.



Appreciate your help



Ning



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[ccp4bb] CBMS workbench: Structural Biology

[Stojanoff, Vivian]

Dear All,

We'd like to bring to your attention that the registration is open for the CBMS 
Structural Biology Workbench, scheduled May 15 through May 18.  Participants 
can choose between SAXS and MX or attend both. The event will be held 
virtually.  Registration is free:

https://www.bnl.gov/cbmsworkbench/

Kind regards,

Vivian

--
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e nsls.lifescien...@gmail.com
w https://www.bnl.gov/ps/lifesciences/

Address:
Center for Biomolecular Structure
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973

Supporting Grants: CBMS is supported by NIH-NIGMS #P30GM133893, and by the 
DOE-BER #KP1605010. Any work performed at NSLS-II is supported by DOE-BES  
under contract # DE-SC0012704.





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[ccp4bb] CBMS Workbench: Structural Biology

[Stojanoff, Vivian]

Dear All,

We'd like to bring to your attention that the registration is open for the CBMS 
Structural Biology Workbench, scheduled May 15 through May 18.  Participants 
can choose between SAXS and MX or attend both. The event will be held 
virtually.  Registration is free:

https://www.bnl.gov/cbmsworkbench/

Kind regards,

Vivian

--
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e nsls.lifescien...@gmail.com
w https://www.bnl.gov/ps/lifesciences/

Address:
Center for Biomolecular Structure
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973

Supporting Grants: CBMS is supported by NIH-NIGMS #P30GM133893, and by the 
DOE-BER #KP1605010. Any work performed at NSLS-II is supported by DOE-BES  
under contract # DE-SC0012704.





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[ccp4bb] UK/Japan "dynamic crystallography" meeting Leicester UK Sept 14 & 15

[Peter Moody]

We are delighted to announce #time_resolved_23
Find out more and register through https://timeresolved23.le.ac.uk/

*Dynamic Crystallography - XFELs and Synchrotrons to study enzyme reactions
 13-15 September, Leicester, UK*



The  meeting is sponsored by the UK’s BBSRC Japan Partnering Award Scheme,
the meeting aims to bring researchers from Japan who are developing and
using techniques to exploit XFELs and synchrotrons for time-resolved
studies of enzyme mechanisms together with researchers from the UK and our
partners with similar interests to present and discuss prospects, progress
and, of course, results. All with a view to establishing and furthering
collaborations.







The current planned outline of the meeting/workshop is:  (see the meeting
website timeresolved23.le.ac.uk for updates)



*Thursday 14 September *

*Preparation* – How to make suitable samples to enable the study of
transient or short-lived enzyme reaction stats

*Validation* – How to monitor reactions in crystals

*Data Collection* – Strategies and protocols for the collection of
diffraction and spectroscopic data



*Friday 15 September *

*Data Processing* – Strategies, and protocols for the optimal recovery of
high-quality data

*Analysis and interpretation* – How to overcome temporal uncertainty with
respect to reaction coordinates and how to interpret mixed populations.

*Results *– Examples of the application of dynamic investigation of protein
mechanisms using structural and spectroscopic techniques.



At the time of writing  we have the following colleagues from Japan who
will participate (with titles of contributions where we have them):

   -
  - * Hiroshi Sugimoto* (SACLA Spring-8/RIKEN) “Dynamics of hydrogen
  atom revealed by ultra-high resolution structure of the heme acquisition
  protein”
  - *Takehiko Tosha* (University of Hyogo) “Characterization of the
  short-lived reaction intermediate of NO reductase with caged substrate”
  - *Yoshitsugu Shiro* (University of Hyogo)
  - *Hitomi Sawai* (University of Nakasaki)
  - *Michihiro Suga* (Okayama University)
  - *Minoru Kubo* (University of Hyogo) “Time resolved spectroscopy for
  monitoring the protein dynamics in microcrystals”
  - *Tetsuo Katayama (Japan Synchrotron Radiation Research
Institute) *"Instrumental
  development and data analysis of X-ray emission spectroscopy
supporting SFX
  at SACLA"
  - * Tetsunari Kimura* (Kobe University) “Development of the
  microfluidic mixer for time-resolved SFX and spectroscopy”

   Speakers from Europe we currently have confirmed:
   - * Allen Orville* (XFEL Hub at Diamond Light Source)
  - * Ivo Tews* (University of Southampton)
  - * Mike Hough* (Diamond Light Source)*Dr Briony Yorke* (University
  of Leeds)  "Developing multiplexing methods for time-resolved
  crystallographic experiments"
  - *Robin Owen* (Diamond Light Source) “Efficient sample delivery for
  time resolved SSX and SFX” (TBC)
  - *Thomas Ursby *(MAX IV Laboratory) "Serial Crystallography at
  MicroMAX - Flexibility offering new possibilities"
  - *Emily Freeman* (University of Oxford) “Time-resolved
  macromolecular crystallography studies of AmpC from *Escherichia
coli* using
  synchrotron and XFEL radiation”.
  - *Jack Stubbs* (University of Southampton and Diamond Light Source)
  "Size matters: Microfluidics for defining protein crystal dimensions and
  rapid micromixing for time-resolved serial crystallography"
  - *Patrick Shaw Stewart *(Douglas Instruments) "Preparing crystal
  samples for serial data collection and microED: using microseeding and
  phase diagrams with microbatch-under-oil"
  - *James Beilsten- Edmands* (Diamond Light Source) “Processing serial
  diffraction data with DIALS & xia2”.
  - *Marcus Gallagher-Jones* (Rosalind Franklin Institute)
  - *Thomas Barends* (MPI-IMF Heidelberg)


Please don't use "reply to" with this email, if you want to get in touch
with me use my university email address  peter.moody at le.ac.uk



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Re: [ccp4bb] Unknown electron density

[Alastair MC EWEN]

Hi Betty,


I've seen very similar looking similar looking density from trifluoroacetic 
acid that was present with a synthetic peptide. Could be something to check if 
you have a peptide bound.


Best,

Alastair


~
Alastair McEwen, PhD
Integrated Structural Biology Platform
IGBMC
1 rue Laurent Fries
67404 ILLKIRCH - FRANCE
tel: +33 (0)3 69 48 52 82

From: CCP4 bulletin board  on behalf of Betty Chu 

Sent: 19 April 2023 18:58:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density that 
looks like an anvil (see link). Has anyone seen this before and have an idea of 
what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the 
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



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Re: [ccp4bb] Unknown electron density

[Anat Bashan]

Hi Betty,

You may use the two following applications from the minor lab :
CheckMyMetal - https://cmm.minorlab.org/
CheckMyBlob -  https://cmm.minorlab.org/

Best, Anat.

From: CCP4 bulletin board  On Behalf Of Betty Chu
Sent: Wednesday, 19 April 2023 19:59
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4bb] Unknown electron density

Dear CCP4BB,

I am working on a structure refinement and came across a blob of density that 
looks like an anvil (see link). Has anyone seen this before and have an idea of 
what it is?


https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing

The protein is in potassium phosphate and the components in the 
crystallization/cryo condition are zinc acetate, PEG, and glycerol.

Thank you in advance for your time and help!

Betty



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