[COOT] backup file names

[David J. Schuller]

The files in the coot-backup directory incorporate the date into their name. 
This caused a problem for one of our users, as the colon is a forbidden 
character in the file transfer application used, which is Globus. Here is the 
error message:

Error (transfer) Endpoint: Spectre (e2e2374a-5de4-11ed-8fd0-e9cb7c15c7d2) 
Server: Globus Connect File: 
/C/Users/usercl/OneDrive/Documents/Post-Doc/20221120/processing/coot-backup/coot-download_6nia.cif_Mon_Nov_21_01%3A01%3A20_2022_modification_0.cif.gz
 Command: STOR 
/C/Users/usercl/OneDrive/Documents/Post-Doc/20221120/processing/coot-backup/coot-download_6nia.cif_Mon_Nov_21_01:01:20_2022_modification_0.cif.gz
 Message: Fatal FTP response --- Details: 500 Command failed. : A filename 
cannot contain any of the following characters: \\ / : * ? " < > |\r\n

I suggest it would be preferable to substitute something else, such as an 
underscore, for the colon in naming the files.

===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu



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Re: [COOT] Pointer Atoms - Potassium

[Paul Emsley]

On 02/12/2022 15:30, John Smith wrote:

Dear all!
I am using Coot 0.9.8.5 EL (ccp4) and I want to add K/potassium ions 
during model building.
Adding Na and Cl is straightforward, but if I click on Pointer Atom 
Type other, enter K and hit OK, then a grey atom is added, but it does 
not refine.

/Warning: Failed to match the dictionary./
Similar problem occurs if I do it via /Calculate - Modelling - add 
other solvent molecules./ If I specify K as three letter code, it 
brings up potassium ion but it does not refine.


Any tips why this is not working?



Thank you John and Steven,

I have pushed a fix - the update should be available shortly. Amazing 
that this bug has lived so long.


Regards,

Paul.




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Re: [COOT] Pointer Atoms - Potassium

[Sheriff, Steven]

John:

I recently (22-Nov) pointed out to Paul Emsley that if one entered potassium 
through the popup menu, it places the "K" of potassium in the wrong column of a 
PDB file, column 13 rather than column 14. The element is right-justified, so 
single letter elements use only column 14, but two letter elements use both 
columns 13 and 14. If you manually edit your file so that the "K" is in column 
14, the potassium should then refine.

Steven

From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of John Smith
Sent: Friday, December 2, 2022 10:31 AM
To: COOT@JISCMAIL.AC.UK
Subject: Pointer Atoms - Potassium

[Use CAUTION when opening links/attachments]
Dear all!
I am using Coot 0.9.8.5 EL (ccp4) and I want to add K/potassium ions during 
model building.
Adding Na and Cl is straightforward, but if I click on Pointer Atom Type other, 
enter K and hit OK, then a grey atom is added, but it does not refine.
Warning: Failed to match the dictionary.
Similar problem occurs if I do it via Calculate - Modelling - add other solvent 
molecules. If I specify K as three letter code, it brings up potassium ion but 
it does not refine.

Any tips why this is not working?
Thank you!

Best regards
John



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[COOT] Pointer Atoms - Potassium

[John Smith]

Dear all!
I am using Coot 0.9.8.5 EL (ccp4) and I want to add K/potassium ions during
model building.
Adding Na and Cl is straightforward, but if I click on Pointer Atom Type
other, enter K and hit OK, then a grey atom is added, but it does not
refine.
*Warning: Failed to match the dictionary.*
Similar problem occurs if I do it via *Calculate - Modelling - add other
solvent molecules.* If I specify K as three letter code, it brings up
potassium ion but it does not refine.

Any tips why this is not working?
Thank you!

Best regards
John



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