Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL

[Dale Tronrud]

Hi,

   I copied the file Paul recommended into 
lib/python2.7/site-packages/coot and I'm now able to download 
coordinates and maps from EBI from within 0.9.8.1 again.  Thanks.


   This file doesn't work in 1.0.01 because that program uses python 3.8.

Dale Tronrud

On 6/8/2023 3:55 AM, Paul Emsley wrote:


Hi Dale,

Without testing, I guess that you can replace get_ebi.py with this one

https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py

(use Raw of course)

Paul.


On 08/06/2023 08:35, Sameer Velankar wrote:


CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender 
and know the content is safe.

*.-owner-c...@jiscmail.ac.uk-.*

Hi Dale

The correct url for accessing files are as follows -
1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif

Kind regards
Sameer


On 8 Jun 2023, at 07:25, Dale Tronrud  wrote:

Hi,

  When I click on "Fetch PDB entry using Accession Code..." or "Fetch 
PDB & Map using EDS..." I get


PDB Accession Code: 3eoj
DEBUG:: extracted accession code handle mode n 1
BL WARNING:: retrieve of url 
https://www.ebi.ac.uk/pdbe-srv/view/files/3eoj.ent failed

handle_read_draw_molecule_with_recentre ("coot-download/3eoj.pdb.ent".1)
WARNING:: Error reading coot-download/3eoj.pdb.ent

  That web site, indeed, does not exist and I presume the PDBe has 
moved the data.


  To the best of my knowledge this is the most recent version of 
WinCoot.  I've downloaded the "unstable" version 1.0.01 and it fails 
in the same way (but does show a very pretty display when downloading 
from PDB Redo).


  I've done my best to search the "coot" and "ccp4bb" archives and 
don't see mention of this problem, but my search skills are limited.


  What do I do to download PDB's and maps again?

Dale Tronrud



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Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL

[Bernhard Lohkamp]

Hi Dale,

The file link Paul sent should be the same WinCoot has. I believe the issue is 
with a relocation of the EDS files. I believe these are the ones you are after 
(fetch from EBI as such should work). No idea where/if EDS files are still 
available at the EBI. Maybe Sameer knows...

B

***

Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent

Teaching Unit/Biomedicum D9
Dept. of Medical Biochemistry and Biophysics (MBB) |
Karolinska Institutet
SE-171 77 Stockholm
Sweden
+46 8 52487055
bernhard.lohk...@ki.se | ki.se

> -Original Message-
> From: Mailing list for users of COOT Crystallographic Software
>  On Behalf Of Paul Emsley
> Sent: Thursday, June 8, 2023 12:55 PM
> To: COOT@JISCMAIL.AC.UK
> Subject: Re: Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL
>
>
>
>
> Hi Dale,
>
> Without testing, I guess that you can replace get_ebi.py with this one
>
> https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py
>  b.com%2Fpemsley%2Fcoot%2Fblob%2Frefinement%2Fpython%2Fget_ebi.py
> =05%7C01%7CBernhard.Lohkamp%40KI.SE%7C7781e97a5001413dac9e
> 08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C63821
> 8185468716853%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLC
> JQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
> ta=UWnV1KWvMH62eMRSVIyte8BVugqgRX3AS%2FHW4yDsDHI%3D
> d=0>
>
> (use Raw of course)
>
> Paul.
>
>
>
>
> On 08/06/2023 08:35, Sameer Velankar wrote:
>
>
>
>   CAUTION: This email originated from outside of the LMB.
>   Do not click links or open attachments unless you recognize the
> sender and know the content is safe.
>   .-owner-c...@jiscmail.ac.uk-.
>
>
>
>   Hi Dale
>
>   The correct url for accessing files are as follows -
>   1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
>  w.ebi.ac.uk%2Fpdbe%2Fentry-
> files%2Fpdb1cbs.ent=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C77
> 81e97a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d
> %7C0%7C0%7C638218185468873076%7CUnknown%7CTWFpbGZsb3d8eyJWI
> joiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3
> 000%7C%7C%7C=fOmGfhmQSp0fXKr%2BmCLzO7ZGEx3fE1gSZVHKax6
> 5f%2FA%3D=0>
>   2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif
>  w.ebi.ac.uk%2Fpdbe%2Fentry-
> files%2F1cbs.cif=05%7C01%7CBernhard.Lohkamp%40KI.SE%7C7781e97
> a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0
> %7C0%7C638218185468873076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC
> 4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%
> 7C%7C%7C=6IA6JacL3iZw04wWFlKZv6xXa0bEbzpN5mjRjEf02tg%3D
> eserved=0>
>
>   Kind regards
>   Sameer
>
>
>
>   On 8 Jun 2023, at 07:25, Dale Tronrud
>  
> wrote:
>
>   Hi,
>
> When I click on "Fetch PDB entry using Accession Code..." or
> "Fetch PDB & Map using EDS..." I get
>
>   PDB Accession Code: 3eoj
>   DEBUG:: extracted accession code handle mode n 1
>   BL WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe-
> srv/view/files/3eoj.ent
>  w.ebi.ac.uk%2Fpdbe-
> srv%2Fview%2Ffiles%2F3eoj.ent=05%7C01%7CBernhard.Lohkamp%40
> KI.SE%7C7781e97a5001413dac9e08db680edfe3%7Cbff7eef1cf4b4f32be3da1
> dda043c05d%7C0%7C0%7C638218185468873076%7CUnknown%7CTWFpbGZ
> sb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6M
> n0%3D%7C3000%7C%7C%7C=%2FJJGmg36m7HvIVLfW%2FT5L3qiYrm
> PWUgcnNt7OMgxp5s%3D=0>  failed
>   handle_read_draw_molecule_with_recentre ("coot-
> download/3eoj.pdb.ent".1)
>   WARNING:: Error reading coot-download/3eoj.pdb.ent
>
> That web site, indeed, does not exist and I presume the
> PDBe has moved the data.
>
> To the best of my knowledge this is the most recent version
> of WinCoot.  I've downloaded the "unstable" version 1.0.01 and it fails in the
> same way (but does show a very pretty display when downloading from PDB
> Redo).
>
> I've done my best to search the "coot" and "ccp4bb"
> archives and don't see mention of this problem, but my search skills are
> limited.
>
> What do I do to download PDB's and maps again?
>
>   Dale Tronrud
>
>
>   #
> ###
>
>   To unsubscribe from the COOT list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-
> JISC.exe?SUBED1=COOT=1
>  w.jiscmail.ac.uk%2Fcgi-bin%2FWA-
> JISC.exe%3FSUBED1%3DCOOT%26A%3D1=05%7C01%7CBernhard.Lohk
> 

Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL

[Paul Emsley]

Hi Dale,

Without testing, I guess that you can replace get_ebi.py with this one

https://github.com/pemsley/coot/blob/refinement/python/get_ebi.py

(use Raw of course)

Paul.


On 08/06/2023 08:35, Sameer Velankar wrote:


CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender 
and know the content is safe.

*.-owner-c...@jiscmail.ac.uk-.*

Hi Dale

The correct url for accessing files are as follows -
1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif

Kind regards
Sameer


On 8 Jun 2023, at 07:25, Dale Tronrud  wrote:

Hi,

  When I click on "Fetch PDB entry using Accession Code..." or "Fetch 
PDB & Map using EDS..." I get


PDB Accession Code: 3eoj
DEBUG:: extracted accession code handle mode n 1
BL WARNING:: retrieve of url 
https://www.ebi.ac.uk/pdbe-srv/view/files/3eoj.ent failed

handle_read_draw_molecule_with_recentre ("coot-download/3eoj.pdb.ent".1)
WARNING:: Error reading coot-download/3eoj.pdb.ent

  That web site, indeed, does not exist and I presume the PDBe has 
moved the data.


  To the best of my knowledge this is the most recent version of 
WinCoot.  I've downloaded the "unstable" version 1.0.01 and it fails 
in the same way (but does show a very pretty display when downloading 
from PDB Redo).


  I've done my best to search the "coot" and "ccp4bb" archives and 
don't see mention of this problem, but my search skills are limited.


  What do I do to download PDB's and maps again?

Dale Tronrud



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

This message was issued to members of www.jiscmail.ac.uk/COOT, a 
mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
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To unsubscribe from the COOT list, click the following link:
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Re: [COOT] Can't download pdb files nor density maps in WinCoot 0.9.8.1 EL

[Sameer Velankar]

Hi Dale

The correct url for accessing files are as follows -
1. PDB file - https://www.ebi.ac.uk/pdbe/entry-files/pdb1cbs.ent
2. mmCIF file - https://www.ebi.ac.uk/pdbe/entry-files/1cbs.cif

Kind regards
Sameer

> On 8 Jun 2023, at 07:25, Dale Tronrud  wrote:
> 
> Hi,
> 
>   When I click on "Fetch PDB entry using Accession Code..." or "Fetch PDB & 
> Map using EDS..." I get
> 
> PDB Accession Code: 3eoj
> DEBUG:: extracted accession code handle mode n 1
> BL WARNING:: retrieve of url 
> https://www.ebi.ac.uk/pdbe-srv/view/files/3eoj.ent failed
> handle_read_draw_molecule_with_recentre ("coot-download/3eoj.pdb.ent".1)
> WARNING:: Error reading coot-download/3eoj.pdb.ent
> 
>   That web site, indeed, does not exist and I presume the PDBe has moved the 
> data.
> 
>   To the best of my knowledge this is the most recent version of WinCoot.  
> I've downloaded the "unstable" version 1.0.01 and it fails in the same way 
> (but does show a very pretty display when downloading from PDB Redo).
> 
>   I've done my best to search the "coot" and "ccp4bb" archives and don't see 
> mention of this problem, but my search skills are limited.
> 
>   What do I do to download PDB's and maps again?
> 
> Dale Tronrud
> 
> 
> 
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> 
> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
> hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/




To unsubscribe from the COOT list, click the following link:
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This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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