[ccp4bb] i2run ProvideAsuContents Problem

2024-01-10 Thread zx2...@connect.hku.hk 
To whom it may concern,

I am currently working with CCP4 version 8.0.016 on an Ubuntu 22.04 system. In 
my efforts to follow the guidelines provided in the documentation 
(https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html), I have encountered an 
issue. Specifically, I have encountered a problem while trying to run 
"buccaneer_build_refine_mr." It appears that I need to provide the "--ASUIN" 
parameter. When attempting to run the "i2run ProvideAsuContents" command to get 
the asymmetric unit content files, I encountered an error.

Here are the commands I used:

/home/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/bin/i2run 
ProvideAsuContents \
--ASU_CONTENT \
sequence=MAHMFRIVVGLGKSGMSLVRYLARRGLPFAVVDTRENPPELATLRAQYPQVEV \
nCopies=1 \
polymerType=PROTEIN \
name=8T1A_1_Chains \
--noDb

The result I received is as follows:

CCP4 /home/xin/programs/ccp4-8.0
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
Starting   0.0005092620849609375
Processing command  ProvideAsuContents 
['/home/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/core/CCP4I2Runner.py',
 'ProvideAsuContents']
Processing command  noDb True
Processing command  taskName ProvideAsuContents
Processing command  jobDirectory /home/xin/0109
Processing command  ASU_CONTENT 
[['sequence=MAHMFRIVVGLGKSGMSLVRYLARRGLPFAVVDTRENPPELATLRAQYPQVEV', 
'nCopies=1', 'polymerType=PROTEIN', 'name=8T1A_1_Chains']]
Failed adding program version to parent job None None
Error in wrapper ProvideAsuContents: -ERROR- ProvideAsuContents:48 Error in 
wrapper ProvideAsuContents:: Error in the plugin script startProcess

I would appreciate your guidance on how to address this issue.

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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Structural Biology activities at the ESRF User meeting 2024

2024-01-10 Thread Montse Soler Lopez 

Dear CCP4ers,

The ESRF User Meeting for 2024 is scheduled to be held onsite from 5th 
to 7th February.

https://www.esrf.fr/home/events/conferences/2024/user-meeting-2024.html

This edition includes three Tutorials related to Structural Biology:

-    Monday 5th, 9:00 - 12:30 (hybrid event): The Structural Biology BAG 
meeting. Presentation of information and updates concerning the 
Structural Biology beamlines, exchange between the beamline scientists 
and the User Community.


-    Monday 5th, 14:00 - 16:00 or 16:00 - 18:00: Meet the Structural 
Biologist Group scientists on the beamlines. Discussions and demos on 
ID29-EBSL8, icOS, ID23-1, ID23-2, ID30A-1, ID30A-3 and ID30B.


-    Monday 5th, 14:00 - 16:00 (hybrid event): Demystifying the 
Structure-to-Solution (SOS) pipeline: a comprehensive tutorial on its 
current components. A tutorial to harness the power of high-resolution 
cryo-EM.


And a User-Dedicated Microsymposium on Serial Crystallography:

-    Wednesday 7th, 8:30 – 18:00: Towards filming macromolecular movies 
at the ESRF-EBS. This symposium aims to present the new science being 
tackled with serial and classic crystallography at 4th generation 
synchrotron, and take the opportunity to bring together both expert and 
non-expert users to discuss and promote the different methods to 
highlight structural dynamics. The event combines keynote presentations 
and invited contributions from submitted abstracts.


Keynote speakers:
Gisela Brändén, University of Gothenburg, Sweden
Gerhard Hofer, Stockholm University, Sweden
José Manuel Martin Garcia, IQF-BC CSIC Madrid, Spain
Henrike Müller-Werkmeister, University of Potsdam, Germany
Kara Zielinski, Cornell University, USA

Full programme can be found here: 
https://www.esrf.fr/files/live/sites/www/files/events/conferences/2024/User%20Meeting/UDMS/UDM1/UDM1-2024_Programme.pdf


The registration for the ESRF User meeting and satellite microsymposia 
is open until 15th January.


We look forward to seeing you at the meeting!

Best wishes,

montse

--

MontseSOLER LOPEZ

Head of the Structural Biology Group

European Synchrotron Radiation Facility

71 Avenue des Martyrs – CS 40220

F-38043 Grenoble Cedex 09




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/

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

2024-01-10 Thread Reza Khayat 
The clash score is also impressively high. Your map may have the incorrect 
hand. Have you tried flipping it?

Best wishes
Reza

From: CCP4 bulletin board  on behalf of Martyn Winn - 
STFC UKRI <7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk>
Sent: 10 January 2024 4:51 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [EXTERNAL] Re: [ccp4bb] Poor correlation coefficient of model to 
cryo-EM map.


You can also try the CCPEM list for more cryoEM-orientated advice 
https://www.jiscmail.ac.uk/CCPEM
 and look in CCP-EM for more fitting, refinement, validation tools.



Certainly, the map doesn’t look 3A, unless you have filtered it for these 
pictures. The CC for the middle and C-terminal domains is not just low, but 
essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So 
I think you need to look again at the initial fitting.



HTH

Martyn





From: CCP4 bulletin board  On Behalf Of Basil Greber
Sent: 10 January 2024 08:12
To: ccp4bb 
Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.



Are you confident that your 3 Å resolution is correct? The map in the picture 
you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is 
apparently 20 Å (?).



Basil


Gesendet mit der mobilen Mail App

Am 10.01.24 um 05:57 schrieb Ketul Saharan

Von: "Ketul Saharan" 
Datum: 10. Januar 2024
An: CCP4BB@JISCMAIL.AC.UK
Cc:
Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Dear CCP4 community,

I am building a structure model from ~3.0 Å resolution cryo-EM map. The 
structure consists of seven chains, with each chain containing an N-, middle, 
and C-terminal domain. Although I attempted to directly fit the Alfa-fold 
model, it became evident that the protein exhibited some movement, leading to 
poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold 
model into two parts: i) the N-terminal and ii) the middle and C-terminal 
domain. These fragments were then fitted into the map. After a few rounds of 
refinement using coot and phenix, the model effectively fitted all seven chains.

The refinement resulted in a model to map correlation (CC mask) of over 60% for 
the N-terminus. However, even though the model appeared to fit well inside the 
map, particularly in the middle and C-terminus regions, the refining 
consistently resulted in a map to model correlation of 0%.

For your perusal, I have included the snapshot of the phenix refinement 
results, the correlation graph, and the fitted model within the map (displaying 
one chain out of seven).

I am not able to figure out why the correlation is so poor even after fine 
fitting of model to map.

Any support in resolving this issue would be much appreciated.



Thank,

Ketul Saharan


--

Ketul Saharan

Senior Research Fellow (Ph.D. Scholar)

Laboratory of Macromolecular Crystallography (Lab-8)

Institute of Life Sciences

Nalco Square, Chandrasekharpur

Bhubaneswar – 751023

Odisha State, INDIA



Phone: +91 8708290889

[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
124.png[Image
 removed by sender.]

[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
correlation.tif[Image
 removed by sender.]

[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] map to 
model.tif[Image
 removed by sender.]





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

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

2024-01-10 Thread Eleanor Dodson 
THere must be  some error in the calculation of the CC - or you are over
optimistic about what constitutes a fit!
What does the COOT density fit show?
Eleanor

On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI <
7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You can also try the CCPEM list for more cryoEM-orientated advice
> https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting,
> refinement, validation tools.
>
>
>
> Certainly, the map doesn’t look 3A, unless you have filtered it for these
> pictures. The CC for the middle and C-terminal domains is not just low, but
> essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5.
> So I think you need to look again at the initial fitting.
>
>
>
> HTH
>
> Martyn
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Basil
> Greber
> *Sent:* 10 January 2024 08:12
> *To:* ccp4bb 
> *Subject:* Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM
> map.
>
>
>
> Are you confident that your 3 Å resolution is correct? The map in the
> picture you supplied looks more like 5 Å, and the model vs. map FSC at 0.5
> is apparently 20 Å (?).
>
>
>
> Basil
>
>
>
> Gesendet mit der mobilen Mail App
>
> Am 10.01.24 um 05:57 schrieb Ketul Saharan
>
> Von: "Ketul Saharan" 
> Datum: 10. Januar 2024
> An: CCP4BB@JISCMAIL.AC.UK
> Cc:
> Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
>
> Dear CCP4 community,
>
> I am building a structure model from ~3.0 Å resolution cryo-EM map. The
> structure consists of seven chains, with each chain containing an N-,
> middle, and C-terminal domain. Although I attempted to directly fit the
> Alfa-fold model, it became evident that the protein exhibited some
> movement, leading to poor fitting of N-terminal. To improve the fitting, I
> segmented the alfa-fold model into two parts: i) the N-terminal and ii) the
> middle and C-terminal domain. These fragments were then fitted into the
> map. After a few rounds of refinement using coot and phenix, the model
> effectively fitted all seven chains.
>
> The refinement resulted in a model to map correlation (CC mask) of over
> 60% for the N-terminus. *However, even though the model appeared to fit
> well inside the map, particularly in the middle and C-terminus regions, the
> refining consistently resulted in a map to model correlation of 0%.*
>
> For your perusal, I have included the snapshot of the phenix refinement
> results, the correlation graph, and the fitted model within the map
> (displaying one chain out of seven).
>
> I am not able to figure out why the correlation is so poor even after fine
> fitting of model to map.
>
> Any support in resolving this issue would be much appreciated.
>
>
>
> Thank,
>
> Ketul Saharan
>
>
>
> --
>
> Ketul Saharan
>
> Senior Research Fellow (Ph.D. Scholar)
>
> Laboratory of Macromolecular Crystallography (Lab-8)
>
> Institute of Life Sciences
>
> Nalco Square, Chandrasekharpur
>
> Bhubaneswar – 751023
>
> Odisha State, INDIA
>
>
>
> Phone: +91 8708290889
>
> * 124.png
> [image:
> Image removed by sender.] *
>
> * correlation.tif
> [image:
> Image removed by sender.] *
>
> * map to model.tif
> [image:
> Image removed by sender.] *
>
>
> --
>
> 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
>
> --
>
> 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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

2024-01-10 Thread Deborah Harrus 

Dear all,

wwPDB anticipates that all the four character PDB accession codes (PDB 
ID) will be consumed by 2029.


With the continuous growth of PDB archive, wwPDB has revised the PDB 
accession code format by extending its length and prepending “PDB” 
(e.g., "1abc" will become "pdb_1abc"). This process will enable text 
mining detection of PDB entries in the published literature and allow 
for more informative and transparent delivery of revised data files.


Entries with extended PDB IDs (12 characters) will not be compatible 
with the legacy PDB file format once four-character PDB IDs are 
consumed. wwPDB encourages scientific journals, PDB community and users 
to transition to using the PDBx/mmCIF format and the extended PDB ID 
format as soon as possible.


Resources are available to help PDB users with this transition through 
thewwPDB resource portal page (Extended PDB ID With 12 Characters) 
. This page 
links to useful resources for handling this change, including anFAQ on 
PDB ID extension 
, materials to 
learn more about PDBx/mmCIF format, and links to other PDBx/mmCIF 
resources and software tools. As the transition phase progresses, more 
training resources will be added to this page.


Additionally, a PDB “beta” archive will be provided during the 
transition phase in 2026. The directory structure of this “beta” archive 
will mirror the data organization of thePDB Versioned Archive 
in the form of 
https://files-beta.org/pub/pdb/data/entries//two-letter-hash///pdb_accession_code///entry_data_File_names/. 
The two-letter hash will be based on the n-2 and n-3 characters. For 
example, PDB entry PDB_12345678 will be under /67/. This will maintain 
consistency with the current PDB archive, where e.g. PDB entry 1abc is 
under /ab.


Once all the four character PDB accession codes are consumed, this PDB 
“beta” archive will become the PDB main archive and the current PDB 
archive will be removed.


Download example files containing extended PDB IDs for software 
adoptionfrom GitHub 
.


wwPDB recently announced that PDB three-character Chemical Component IDs 
have been consumed. 
Five-character 
alphanumeric accession codes for CCD IDs are now issued by the OneDep 
system.


For any further information please contact us ati...@wwpdb.org.

Kind regards,

Deborah Harrus, on behalf of the wwPDB

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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/

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

2024-01-10 Thread Martyn Winn - STFC UKRI 
You can also try the CCPEM list for more cryoEM-orientated advice 
https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, 
refinement, validation tools.

Certainly, the map doesn’t look 3A, unless you have filtered it for these 
pictures. The CC for the middle and C-terminal domains is not just low, but 
essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So 
I think you need to look again at the initial fitting.

HTH
Martyn


From: CCP4 bulletin board  On Behalf Of Basil Greber
Sent: 10 January 2024 08:12
To: ccp4bb 
Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Are you confident that your 3 Å resolution is correct? The map in the picture 
you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is 
apparently 20 Å (?).

Basil


Gesendet mit der mobilen Mail App

Am 10.01.24 um 05:57 schrieb Ketul Saharan
Von: "Ketul Saharan" 
Datum: 10. Januar 2024
An: CCP4BB@JISCMAIL.AC.UK
Cc:
Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
Dear CCP4 community,
I am building a structure model from ~3.0 Å resolution cryo-EM map. The 
structure consists of seven chains, with each chain containing an N-, middle, 
and C-terminal domain. Although I attempted to directly fit the Alfa-fold 
model, it became evident that the protein exhibited some movement, leading to 
poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold 
model into two parts: i) the N-terminal and ii) the middle and C-terminal 
domain. These fragments were then fitted into the map. After a few rounds of 
refinement using coot and phenix, the model effectively fitted all seven chains.
The refinement resulted in a model to map correlation (CC mask) of over 60% for 
the N-terminus. However, even though the model appeared to fit well inside the 
map, particularly in the middle and C-terminus regions, the refining 
consistently resulted in a map to model correlation of 0%.
For your perusal, I have included the snapshot of the phenix refinement 
results, the correlation graph, and the fitted model within the map (displaying 
one chain out of seven).
I am not able to figure out why the correlation is so poor even after fine 
fitting of model to map.
Any support in resolving this issue would be much appreciated.

Thank,
Ketul Saharan


--
Ketul Saharan
Senior Research Fellow (Ph.D. Scholar)
Laboratory of Macromolecular Crystallography (Lab-8)
Institute of Life Sciences
Nalco Square, Chandrasekharpur
Bhubaneswar – 751023
Odisha State, INDIA

Phone: +91 8708290889
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
124.png[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
correlation.tif[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] map to 
model.tif[Image
 removed by sender.]



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



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/

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

2024-01-10 Thread Martyn Winn - STFC UKRI 
You can also try the CCPEM list for more cryoEM-orientated advice 
https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, 
refinement, validation tools.

Certainly, the map doesn’t look 3A, unless you have filtered it for these 
pictures. The CC for the middle and C-terminal domains is not just low, but 
essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So 
I think you need to look again at the initial fitting.

HTH
Martyn


From: CCP4 bulletin board  On Behalf Of Basil Greber
Sent: 10 January 2024 08:12
To: ccp4bb 
Subject: Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Are you confident that your 3 Å resolution is correct? The map in the picture 
you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is 
apparently 20 Å (?).

Basil


Gesendet mit der mobilen Mail App

Am 10.01.24 um 05:57 schrieb Ketul Saharan
Von: "Ketul Saharan" 
Datum: 10. Januar 2024
An: CCP4BB@JISCMAIL.AC.UK
Cc:
Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.
Dear CCP4 community,
I am building a structure model from ~3.0 Å resolution cryo-EM map. The 
structure consists of seven chains, with each chain containing an N-, middle, 
and C-terminal domain. Although I attempted to directly fit the Alfa-fold 
model, it became evident that the protein exhibited some movement, leading to 
poor fitting of N-terminal. To improve the fitting, I segmented the alfa-fold 
model into two parts: i) the N-terminal and ii) the middle and C-terminal 
domain. These fragments were then fitted into the map. After a few rounds of 
refinement using coot and phenix, the model effectively fitted all seven chains.
The refinement resulted in a model to map correlation (CC mask) of over 60% for 
the N-terminus. However, even though the model appeared to fit well inside the 
map, particularly in the middle and C-terminus regions, the refining 
consistently resulted in a map to model correlation of 0%.
For your perusal, I have included the snapshot of the phenix refinement 
results, the correlation graph, and the fitted model within the map (displaying 
one chain out of seven).
I am not able to figure out why the correlation is so poor even after fine 
fitting of model to map.
Any support in resolving this issue would be much appreciated.

Thank,
Ketul Saharan


--
Ketul Saharan
Senior Research Fellow (Ph.D. Scholar)
Laboratory of Macromolecular Crystallography (Lab-8)
Institute of Life Sciences
Nalco Square, Chandrasekharpur
Bhubaneswar – 751023
Odisha State, INDIA

Phone: +91 8708290889
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
124.png[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] 
correlation.tif[Image
 removed by sender.]
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] map to 
model.tif[Image
 removed by sender.]



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



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/

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

2024-01-10 Thread Basil Greber 




Are you confident that your 3 Å resolution is correct? The map in the picture you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is apparently 20 Å (?).BasilGesendet mit der mobilen Mail AppAm 10.01.24 um 05:57 schrieb Ketul Saharan




Von: "Ketul Saharan" Datum: 10. Januar 2024An: CCP4BB@JISCMAIL.AC.UKCc: Betreff: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.





















Dear CCP4 community,

I am building a structure model
from ~3.0 Å resolution cryo-EM map. The structure consists of seven
chains, with each chain containing an N-, middle, and C-terminal domain.
Although I attempted to directly fit the Alfa-fold model, it became evident
that the protein exhibited some movement, leading to poor fitting of N-terminal.
To improve the fitting, I segmented the alfa-fold model into two parts: i) the
N-terminal and ii) the middle and C-terminal domain. These fragments were then fitted
into the map. After a few rounds of refinement using coot and phenix, the model
effectively fitted all seven chains.

The refinement resulted in a
model to map correlation (CC mask) of over 60% for the N-terminus. However,
even though the model appeared to fit well inside the map, particularly in the
middle and C-terminus regions, the refining consistently resulted in a map to
model correlation of 0%.

For your perusal, I have included the snapshot of the phenix
refinement results, the correlation graph,
and the fitted model within the map (displaying one chain out of seven). 
I am not able to figure out why the correlation is so poor even after fine  fitting of model to map.

Any support in resolving this issue would be much
appreciated.

Thank,
Ketul Saharan






-- 

Ketul
Saharan


Senior
Research Fellow (Ph.D. Scholar)

Laboratory
of Macromolecular Crystallography (Lab-8)

Institute
of Life Sciences

Nalco
Square, Chandrasekharpur

Bhubaneswar
– 751023

Odisha
State, INDIA

 

Phone:
+91 8708290889

 124.png


 correlation.tif


 map to model.tif






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