Re: [ccp4bb] New ligand 3-letter code

2015-06-06 Thread Edward A. Berry 

Neat! It's true the PDB will choose a unique code for you,
but they will use what you supply if it is already unique,
and it is nice to be able to choose something that can help
you remember what it stands for.
Gone are the days when we could choose meaningfull pdb ID's
(like 1PRC, 2PRC, 3PRC etc are all photosynthetic reaction center),
but there is still some freedom in choosing the ligand ID's.
They are filling up fast, though!

locust 123% elbow.get_new_ligand_code AC
Unique ligand code : AC3

locust 129% elbow.get_new_ligand_code "A?3"
Unique ligand code : A?3

eab

On 06/06/2015 12:13 PM, Nigel Moriarty wrote:

I wrote something a while ago the finds an unused code.


% elbow.get_new_ligand_code


Unique ligand code : 7V8


% elbow.get_new_ligand_code A


Unique ligand code : A6E


Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov 

On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> wrote:


I use any 3 letter/number code that i want. If you read the corresponding 
cif file into coot it is used in preference to any in the library. The PDB 
deposition team will assign a code if it is a new ligand to the database. Could 
you relay this to original poster?

Thanks

Jim Brannigan


On 5 June 2015 at 14:58, Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> wrote:

OK - thank you.
How are things?
E


-- Forwarded message --
From: *Jim Brannigan* mailto:jim.branni...@york.ac.uk>>
Date: 5 June 2015 at 14:39
Subject: Re: New ligand 3-letter code
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>


Hi Eleanor

I use any 3 letter/number code that i want. If you read the 
corresponding cif file into coot it is used in preference to any in the 
library. The PDB deposition team will assign a code if it is a new ligand to 
the database. Could you relay this to original poster?

Thanks

Jim Brannigan

On 5 June 2015 at 11:28, Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> wrote:

I use your method - trial & error..
It would be nice if at least there was a list somewhere of 
unassigned codes!


On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) mailto:lau_sze...@immunol.a-star.edu.sg>> wrote:

Hi,

What is the proper way of generating 3-letter code for a new 
ligand? As of now, I insert my ligand in Coot using smiles string and for the 
3-letter code I picked a non-existent code by trial and error (not very 
efficient). A cif file with corresponding name which I generated using Phenix 
was imported into Coot.

I am sure there is a proper way of doing this. Appreciate your 
feedback.

Regards,
Sze Yi

Re: [ccp4bb] New ligand 3-letter code

2015-06-06 Thread Nigel Moriarty 
I wrote something a while ago the finds an unused code.

> % elbow.get_new_ligand_code

Unique ligand code : 7V8

> % elbow.get_new_ligand_code A

Unique ligand code : A6E

Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson 
wrote:

>
> I use any 3 letter/number code that i want. If you read the corresponding
> cif file into coot it is used in preference to any in the library. The PDB
> deposition team will assign a code if it is a new ligand to the database.
> Could you relay this to original poster?
>
> Thanks
>
> Jim Brannigan
>
>
> On 5 June 2015 at 14:58, Eleanor Dodson  wrote:
>
>> OK - thank you.
>> How are things?
>> E
>>
>>
>> -- Forwarded message --
>> From: Jim Brannigan 
>> Date: 5 June 2015 at 14:39
>> Subject: Re: New ligand 3-letter code
>> To: Eleanor Dodson 
>>
>>
>> Hi Eleanor
>>
>> I use any 3 letter/number code that i want. If you read the corresponding
>> cif file into coot it is used in preference to any in the library. The PDB
>> deposition team will assign a code if it is a new ligand to the database.
>> Could you relay this to original poster?
>>
>> Thanks
>>
>> Jim Brannigan
>>
>> On 5 June 2015 at 11:28, Eleanor Dodson 
>> wrote:
>>
>>> I use your method - trial & error..
>>> It would be nice if at least there was a list somewhere of unassigned
>>> codes!
>>>
>>>
>>> On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) <
>>> lau_sze...@immunol.a-star.edu.sg> wrote:
>>>
 Hi,

 What is the proper way of generating 3-letter code for a new ligand? As
 of now, I insert my ligand in Coot using smiles string and for the 3-letter
 code I picked a non-existent code by trial and error (not very efficient).
 A cif file with corresponding name which I generated using Phenix was
 imported into Coot.

 I am sure there is a proper way of doing this. Appreciate your feedback.

 Regards,
 Sze Yi

>>>
>>>
>>
>>
>