Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-02-05 Thread Deborah Harrus 

Dear Maria,

Apologies for late reply. I'm not sure which version of 
"adding_stats_to_mmcif" is in CCP4 at the moment, but if you're facing 
the issue again in the future please could you try using the latest 
version at https://github.com/wwPDB/py-adding_stats_to_mmcif ? If it 
doesn't work, please feel free to send me your file and I will troubleshoot.


Kind regards,

Deborah Harrus

PDBe

On 30/01/2024 17:36, mdimarog wrote:

Dear all,

I am trying to deposit 2 structures to the PDBe, solved and refined in 
CCP4 (version 7), and checked in PRIVATEER as they have a lot of 
sugars in. To this end, I used "Prepare and validate files for 
deposition" task, as I had previously (and succesfully) done. However, 
and in spite of switching to the latest CCP4 version (8.0.017), I keep 
getting this error message "adding_stats_to_mmcif_i2_gui:Error in 
wrapper Failed to add 204". I am using macOS Monterey, version 12.6.5.


Does anybody have an idea what is going wrong? If not, does anybody 
know a different way to submit the reflection data to the PDBe? For 
example, would this be somehow possible just using the output from 
Refmac and AIMLESS? I wouldn't want to repeat the 
scaling/MR/refinement procedure because there are a lot of sugars 
there, quite difficult to built.


Many thanks in advance for your help!

Kind regards,

Maria





--
---
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
---



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Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-01-31 Thread mdimarog 

Στις 2024-01-31 22:48, Nicholas Clark έγραψε:

Maria,

Apologies for the second email. I forgot that "Prepare files for
deposition" also merges the CCP4 formatted files into an MTZ. If I
recall correctly, I used "CONVERT2MTZ" in the command line to complete
the merging of the CCP4 files to generate the necessary MTZ for
deposition. Instructions can be found here:
https://www.ccp4.ac.uk/html/convert2mtz.html.

Best regards,

Nick Clark

On Tue, Jan 30, 2024 at 12:47 PM mdimarog 
wrote:


Dear all,

I am trying to deposit 2 structures to the PDBe, solved and refined
in
CCP4 (version 7), and checked in PRIVATEER as they have a lot of
sugars
in. To this end, I used "Prepare and validate files for deposition"
task, as I had previously (and succesfully) done. However, and in
spite
of switching to the latest CCP4 version (8.0.017), I keep getting
this
error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed
to
add 204". I am using macOS Monterey, version 12.6.5.

Does anybody have an idea what is going wrong? If not, does anybody
know
a different way to submit the reflection data to the PDBe? For
example,
would this be somehow possible just using the output from Refmac and

AIMLESS? I wouldn't want to repeat the scaling/MR/refinement
procedure
because there are a lot of sugars there, quite difficult to built.

Many thanks in advance for your help!

Kind regards,

Maria

--
Maria Dimarogona
Assistant Professor
Department of Chemical Engineering
University of Patras
Greece






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--

Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences

955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908

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Dear Nick,

Thank you very much for your input.
I finally ran aimless in the old CCP4 version, and uploaded the output 
to the PDBe.

But I will keep your advice for future "troubles".

Kind regards,

Maria

--
Maria Dimarogona
Assistant Professor
Department of Chemical Engineering
University of Patras
Greece



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Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-01-31 Thread Oganesyan, Vaheh 
Nick,

What files do you mean when call them CCP4 formatted? Coordinates are accepted 
only in mmCIF. Experimental data in mtz. What else?

Thank you.

Vaheh

From: CCP4 bulletin board  On Behalf Of Nicholas Clark
Sent: Wednesday, January 31, 2024 3:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

Maria,

Apologies for the second email. I forgot that "Prepare files for deposition" 
also merges the CCP4 formatted files into an MTZ. If I recall correctly, I used 
"CONVERT2MTZ" in the command line to complete the merging of the CCP4 files to 
generate the necessary MTZ for deposition. Instructions can be found here: 
https://www.ccp4.ac.uk/html/convert2mtz.html.

Best regards,

Nick Clark

On Tue, Jan 30, 2024 at 12:47 PM mdimarog 
mailto:mdima...@central.ntua.gr>> wrote:
Dear all,

I am trying to deposit 2 structures to the PDBe, solved and refined in
CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars
in. To this end, I used "Prepare and validate files for deposition"
task, as I had previously (and succesfully) done. However, and in spite
of switching to the latest CCP4 version (8.0.017), I keep getting this
error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to
add 204". I am using macOS Monterey, version 12.6.5.

Does anybody have an idea what is going wrong? If not, does anybody know
a different way to submit the reflection data to the PDBe? For example,
would this be somehow possible just using the output from Refmac and
AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure
because there are a lot of sugars there, quite difficult to built.

Many thanks in advance for your help!

Kind regards,

Maria




--
Maria Dimarogona
Assistant Professor
Department of Chemical Engineering
University of Patras
Greece



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Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-01-31 Thread Nicholas Clark 
Maria,

Apologies for the second email. I forgot that "Prepare files for
deposition" also merges the CCP4 formatted files into an MTZ. If I recall
correctly, I used "CONVERT2MTZ" in the command line to complete the merging
of the CCP4 files to generate the necessary MTZ for deposition.
Instructions can be found here: https://www.ccp4.ac.uk/html/convert2mtz.html
.

Best regards,

Nick Clark

On Tue, Jan 30, 2024 at 12:47 PM mdimarog  wrote:

> Dear all,
>
> I am trying to deposit 2 structures to the PDBe, solved and refined in
> CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars
> in. To this end, I used "Prepare and validate files for deposition"
> task, as I had previously (and succesfully) done. However, and in spite
> of switching to the latest CCP4 version (8.0.017), I keep getting this
> error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to
> add 204". I am using macOS Monterey, version 12.6.5.
>
> Does anybody have an idea what is going wrong? If not, does anybody know
> a different way to submit the reflection data to the PDBe? For example,
> would this be somehow possible just using the output from Refmac and
> AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure
> because there are a lot of sugars there, quite difficult to built.
>
> Many thanks in advance for your help!
>
> Kind regards,
>
> Maria
>
>
>
>
> --
> Maria Dimarogona
> Assistant Professor
> Department of Chemical Engineering
> University of Patras
> Greece
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=YKfa3h9sRJj6cbgJFBxpBi5EVoqQzgQ2WhR3emet%2FpA%3D=0
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-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-01-31 Thread Nicholas Clark 
Hi Maria,

I'm not sure if anyone has replied to this chain. However, I had a similar
issue when I was trying to prepare files for deposition in the past. You
can use the PDB file and upload it to https://pdb-extract.wwpdb.org/ to
generate the CIF file for deposition.

Best,

Nick Clark

On Tue, Jan 30, 2024 at 12:47 PM mdimarog  wrote:

> Dear all,
>
> I am trying to deposit 2 structures to the PDBe, solved and refined in
> CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars
> in. To this end, I used "Prepare and validate files for deposition"
> task, as I had previously (and succesfully) done. However, and in spite
> of switching to the latest CCP4 version (8.0.017), I keep getting this
> error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to
> add 204". I am using macOS Monterey, version 12.6.5.
>
> Does anybody have an idea what is going wrong? If not, does anybody know
> a different way to submit the reflection data to the PDBe? For example,
> would this be somehow possible just using the output from Refmac and
> AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure
> because there are a lot of sugars there, quite difficult to built.
>
> Many thanks in advance for your help!
>
> Kind regards,
>
> Maria
>
>
>
>
> --
> Maria Dimarogona
> Assistant Professor
> Department of Chemical Engineering
> University of Patras
> Greece
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C545ac7ba998f4ce2969808dc21bb8142%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638422336438814400%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=YKfa3h9sRJj6cbgJFBxpBi5EVoqQzgQ2WhR3emet%2FpA%3D=0
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-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Error in "Prepare and validate files for deposition" task"

2024-01-30 Thread mdimarog 

Dear all,

I am trying to deposit 2 structures to the PDBe, solved and refined in 
CCP4 (version 7), and checked in PRIVATEER as they have a lot of sugars 
in. To this end, I used "Prepare and validate files for deposition" 
task, as I had previously (and succesfully) done. However, and in spite 
of switching to the latest CCP4 version (8.0.017), I keep getting this 
error message "adding_stats_to_mmcif_i2_gui:Error in wrapper Failed to 
add 204". I am using macOS Monterey, version 12.6.5.


Does anybody have an idea what is going wrong? If not, does anybody know 
a different way to submit the reflection data to the PDBe? For example, 
would this be somehow possible just using the output from Refmac and 
AIMLESS? I wouldn't want to repeat the scaling/MR/refinement procedure 
because there are a lot of sugars there, quite difficult to built.


Many thanks in advance for your help!

Kind regards,

Maria




--
Maria Dimarogona
Assistant Professor
Department of Chemical Engineering
University of Patras
Greece



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