On this website:
https://www.ebi.ac.uk/pdbe-srv/pdbechem/
<https://www.ebi.ac.uk/pdbe-srv/pdbechem/>
If you search for LIG it returns a ligand. With small letters it says:
The chemical component you are trying to view (LIG) has been obsoleted.
You have been redirected to the component which superceded it.
On RCSB website it does not return anything. Perhaps, on the PDBe website it
could also not return anything.
Regards
Garib
> On 26 Apr 2024, at 16:07, Deborah Harrus <dhar...@ebi.ac.uk> wrote:
>
> Hi Diana,
>
> Could you please clarify where you are searching?
>
> LIG is obsolete and definitely not in use.
>
> Cheers,
>
> Deborah
>
> On 26/04/2024 15:40, Diana Tomchick wrote:
>> But I think that is a mistake, if you search for LIG in the PDB, it brings
>> up a definite ligand that has that 3-letter code.
>>
>> Diana
>>
>> Sent from my iPhone
>>
>>> On Apr 26, 2024, at 8:04 AM, Deborah Harrus <dhar...@ebi.ac.uk>
>>> <mailto:dhar...@ebi.ac.uk> wrote:
>>>
>>>
>>> Dear all,
>>>
>>> Just to clarify, "LIG" is also a reserved code, so it's safe to use.
>>>
>>> See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6
>>> <https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2023*656f4404d78e004e766a96c6__;Iw!!MznTZTSvDXGV0Co!AfUYvlrA8vP5MVBYtrpLM9ngnPKUQR90_5Jw6YGFmeUccyiJEyYjJIBepH4mugozZQSzLqpZiP0rVKHw73KmyZ_ryOpJ8Pw$>
>>> Kind regards,
>>>
>>> Deborah Harrus
>>>
>>> PDBe
>>>
>>> On 25/04/2024 16:04, Diana Tomchick wrote:
>>>> The PDB has reserved the following codes for unknown ligands:
>>>>
>>>> DRG
>>>> INH
>>>> 01 - 99
>>>>
>>>> Using one of these should not cause you the described problems. I
>>>> successfully used
>>>>
>>>> 99
>>>>
>>>> just last week. If you try to use
>>>>
>>>> 999 or LIG
>>>>
>>>> these will not work, there are ligands assigned to those codes.
>>>>
>>>>
>>>> Diana
>>>>
>>>> Sent from my iPhone
>>>>
>>>>> On Apr 25, 2024, at 8:03 AM, Nicholas Clark
>>>>> <0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk>
>>>>> <mailto:0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>>>
>>>>>
>>>>> EXTERNAL MAIL
>>>>>
>>>>>
>>>>> Hi Stefanie,
>>>>>
>>>>> Why can you only use "taken" three letter codes? In the "output monomer"
>>>>> box, you should be able to enter whatever you'd like for the "Three
>>>>> letter code for output monomer". In the attached image, this is shown as
>>>>> "DRG" but can be changed to any 3 letter code of your choice. Obviously,
>>>>> just make sure your existing selection does not exist in the PDB.
>>>>>
>>>>> Best,
>>>>>
>>>>> Nick Clark
>>>>> <AdeDRG_jobwindow.png>
>>>>>
>>>>>
>>>>> On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson
>>>>> <maria.hakans...@saromics.com <mailto:maria.hakans...@saromics.com>>
>>>>> wrote:
>>>>> Hi Stefanie,
>>>>> Can you manually edit the restraints file using TextEdit and find and
>>>>> replace and the pdb
>>>>> file of course?
>>>>> Other option is to use Grade or Grade2 and the smiles string if you have
>>>>> this software installed.
>>>>> I often find this easier than ccp4i2.
>>>>>
>>>>> Best regards and good luck!
>>>>> Maria
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE
>>>>>> <stefanie.freitag-p...@durham.ac.uk
>>>>>> <mailto:stefanie.freitag-p...@durham.ac.uk>> wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
>>>>>>
>>>>>> I put in a smilesstring and the ligand is written ok, but since I can
>>>>>> only chose already 'taken' 3-letter-codes the refinement always crashes
>>>>>> as there is a clash with existing library entries.
>>>>>> Is there any way around this? How do I add a novel ligand?
>>>>>>
>>>>>> Thanks so much for your help.
>>>>>>
>>>>>> Best wishes,
>>>>>> Stefanie
>>>>>>
>>>>>>
>>>>>>
>>>>>> Dr. Stefanie Freitag-Pohl (she/her)
>>>>>> Durham University
>>>>>> Department of Chemistry
>>>>>> South Road, Durham
>>>>>> DH1 3LE
>>>>>> United Kingdom
>>>>>> 0191 334 2596
>>>>>> stefanie.freitag-p...@durham.ac.uk
>>>>>> <mailto:stefanie.freitag-p...@durham.ac.uk>
>>>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1&data=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C&sdata=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$>
>>>>> Maria Håkansson, PhD,
>>>>> Principal Scientist
>>>>>
>>>>> SARomics Biostructures AB
>>>>> Medicon Village
>>>>> SE-223 81 Lund, Sweden
>>>>>
>>>>> Mobile: +46 (0)76 8585706
>>>>> Web: www.saromics.com
>>>>> <https://urldefense.com/v3/__http://www.saromics.com__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6Sf4INmI8$>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.jiscmail.ac.uk*2Fcgi-bin*2FWA-JISC.exe*3FSUBED1*3DCCP4BB*26A*3D1&data=05*7C02*7Cndclark2*40g-mail.buffalo.edu*7C24412f35c13142fe49dc08dc65265a9f*7C96464a8af8ed40b199e25f6b50a20250*7C0*7C0*7C638496462720640727*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C0*7C*7C*7C&sdata=jcPNODLx5BJRvJt5UAQ99sMjWsY*2Bx7lil*2F6jF4rKxY8*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6S7EPRktY$>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>>> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!CQY9Ex2w1tfRofs9ZzM1ost58GieUu-kuX4wZBJLmNpAxJ3y96S4g-3tG25Bp4dKhWslwfnWyCiVOtFpZij1ydt_5BqeNO54IDAL6k6SdhSxg4M$>
>>>>> CAUTION: This email originated from outside UTSW. Please be cautious of
>>>>> links or attachments, and validate the sender's email address before
>>>>> replying.
>>>>>
>>>>
>>>> UT Southwestern
>>>>
>>>> Medical Center
>>>>
>>>>
>>>> The future of medicine, today.
>>>>
>>>>
>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!AfUYvlrA8vP5MVBYtrpLM9ngnPKUQR90_5Jw6YGFmeUccyiJEyYjJIBepH4mugozZQSzLqpZiP0rVKHw73KmyZ_rqrjtRCY$>--
>>>>
>>> -------------------------------------------------------------------
>>> 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
>>> <https://urldefense.com/v3/__http://www.PDBe.org__;!!MznTZTSvDXGV0Co!AfUYvlrA8vP5MVBYtrpLM9ngnPKUQR90_5Jw6YGFmeUccyiJEyYjJIBepH4mugozZQSzLqpZiP0rVKHw73KmyZ_rZI6C8CA$>
>>> -------------------------------------------------------------------
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
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>>>
> -------------------------------------------------------------------
> 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 <http://www.pdbe.org/>
> -------------------------------------------------------------------
>
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