coot -> fetch pdb & map using EDS - phenixbb - phenix-online.org

newer
special positions

coot -> fetch pdb & map using EDS

older
strange increase of R/Rfree in the...

Murpholino Peligro

17 Jun 2014 17 Jun '14

3:53 p.m.

Hi all How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

Attachments:

attachment.html (text/html — 161 bytes)

Reply

Sign in to reply online Use email software

Show replies by date

George Devaniranjan

17 Jun 17 Jun

4:02 p.m.

You could try using PDB_REDO ? Failing which you might have to generate the map from SF? (though if its not obtainable through COOT, does it mean no SF exist? I am not sure of the answer to this) On Tue, Jun 17, 2014 at 9:53 AM, Murpholino Peligro wrote:

Hi all How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Reply

Sign in to reply online Use email software

Nathaniel Echols

5:04 p.m.

On Tue, Jun 17, 2014 at 6:53 AM, Murpholino Peligro wrote:

How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

phenix.fetch_pdb --maps ID then load the file "ID_maps.mtz" using the auto-open function in Coot.

Reply

Sign in to reply online Use email software

Murpholino Peligro

5:31 p.m.

fmp@eva02:~$ phenix.fetch_pdb --maps 1JWR Model saved to /home/fmp/1JWR.pdb Sequence saved to /home/fmp/1JWR.fa Sorry: Couldn't download structure factors for 1jwr. It is because the structure factors are not available in the PDB. So this means that there is no way to get them...right? (well...maybe I could contact the authors...but the structure is more than ten years old...) 2014-06-17 10:04 GMT-05:00 Nathaniel Echols :

On Tue, Jun 17, 2014 at 6:53 AM, Murpholino Peligro
...
wrote:

...
How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

phenix.fetch_pdb --maps ID

then load the file "ID_maps.mtz" using the auto-open function in Coot.

Reply

Sign in to reply online Use email software

Nathaniel Echols

5:36 p.m.

On Tue, Jun 17, 2014 at 8:31 AM, Murpholino Peligro wrote:

fmp@eva02:~$ phenix.fetch_pdb --maps 1JWR Model saved to /home/fmp/1JWR.pdb Sequence saved to /home/fmp/1JWR.fa Sorry: Couldn't download structure factors for 1jwr.

It is because the structure factors are not available in the PDB. So this means that there is no way to get them...right? (well...maybe I could contact the authors...but the structure is more than ten years old...)

You could try, but honestly I think it would be easier to find another human lysozyme structure that does have structure factors - there does not appear to be a shortage in the PDB. -Nat

Reply

Sign in to reply online Use email software

Murpholino Peligro

5:47 p.m.

Is just that a paper used this pdb to do a comparison between this human lysozyme vs a double mutant human lysozyme, and I just wanted to see structures and maps for both of them.....just checking.. 2014-06-17 10:36 GMT-05:00 Nathaniel Echols :

On Tue, Jun 17, 2014 at 8:31 AM, Murpholino Peligro
...
wrote:

...
fmp@eva02:~$ phenix.fetch_pdb --maps 1JWR Model saved to /home/fmp/1JWR.pdb Sequence saved to /home/fmp/1JWR.fa Sorry: Couldn't download structure factors for 1jwr.

It is because the structure factors are not available in the PDB. So this means that there is no way to get them...right? (well...maybe I could contact the authors...but the structure is more than ten years old...)

You could try, but honestly I think it would be easier to find another human lysozyme structure that does have structure factors - there does not appear to be a shortage in the PDB.

-Nat

Reply

Sign in to reply online Use email software

Dale Tronrud

5:44 p.m.

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I have found that contacting the authors often works, and sometimes you can get them to deposit the structure factors and help everyone out. The PDB is quite happy to accept structure factors for models deposited years ago. Dale Tronrud On 6/17/2014 8:31 AM, Murpholino Peligro wrote:

fmp@eva02:~$ phenix.fetch_pdb --maps 1JWR Model saved to /home/fmp/1JWR.pdb Sequence saved to /home/fmp/1JWR.fa Sorry: Couldn't download structure factors for 1jwr.

It is because the structure factors are not available in the PDB. So this means that there is no way to get them...right? (well...maybe I could contact the authors...but the structure is more than ten years old...)

2014-06-17 10:04 GMT-05:00 Nathaniel Echols mailto:[email protected]>:

On Tue, Jun 17, 2014 at 6:53 AM, Murpholino Peligro mailto:[email protected]> wrote:

How to proceed when Coot -> File -> Fetch PDB and Map using EDS does not work?

phenix.fetch_pdb --maps ID

then load the file "ID_maps.mtz" using the auto-open function in Coot.

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlOgYl0ACgkQU5C0gGfAG12MmQCeLiOiIRTgQp3a/huGrKc54Rsz BCoAnR4ZAL/k++0AJic3odSXlq39aRpn =IvfY -----END PGP SIGNATURE-----

Reply

Sign in to reply online Use email software

4029

Age (days ago)

4029

Last active (days ago)

Download

6 comments

4 participants

tags

participants (4)

Dale Tronrud
George Devaniranjan
Murpholino Peligro
Nathaniel Echols