Use the search tab at the RCSB web site, type in a 3 letter code, and if it has been used for a ligand then it will appear as a Chemical Component.
Thanks to Phil, I am on vacation in Mexico and cut and pasting URLs is a pain on an iPhone. Diana Sent from my iPhone On Apr 26, 2024, at 9:07 AM, 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 LIG is obsolete and definitely not in use.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. 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