When you try to use LIG in Phenix it gives you an error message as it doesn’t know that LIG is obsoleted.
Diana Sent from my iPhone > On Apr 26, 2024, at 10:08 AM, Yong Wang > <00003c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk> wrote: > > EXTERNAL MAIL > > Dear all, > > Perhaps the issue is that the refinement program should be able to handle the > priority of ligand dictionary, i.e. your custom ligand ID and dictionary > overrides any existing in the default collection. I have not had any trouble > with LIG or SX1, both existing in PDB ligands. I also never had any trouble > depositing structures containing such ligand ID's, albeit a few years ago. > The capable staff at RCSB will always assign a new ligand ID based on its > structure, regardless of what ID you have in your pdb file. > > Best, > > Yong > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Gerard Bricogne > Sent: Friday, April 26, 2024 11:47 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG > > EXTERNAL EMAIL: Use caution before replying, clicking links, and opening > attachments. > > > > > Dear Oliver and CCP4BB readers, > > This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel > Rondeau working at Novartis. He must simply have been the first person to > deposit a structure in which the ligand was called LIG ... . That molecule is > now called 89E, but as Phil showed, there are still remnants of its old > identity. > > Best wishes, > > Gerard. > > -- >> On Fri, Apr 26, 2024 at 04:31:13PM +0100, Oliver Smart wrote: >> Hi Stefanie, >> >> If you want to try Grade2 (for a non-confidential ligand) then this is >> easy to do using the Grade Web Server >> >> https://urldefense.com/v3/__https://grad/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxaesA9ZFs$ >> e.globalphasing.org%2F&data=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6 >> fed4844df87c9e08dc66082939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0% >> 7C638497432436392044%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI >> joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=mvPPcWbmv >> N%2FCuXXB%2BacAmaHf%2BqZr0O9lCoFxc9p5plk%3D&reserved=0 >> >> We have altered our default "3-letter code" (aka PDB chemical component ID) >> to "LIG". >> The reserved PDB two letter codes 01 to 99 are also fine (as are INH and >> DRG). >> We understand from users that Grade2 restraint dictionaries work well >> with REFMAC (as to AceDG) Checking my installation of CCP4 8.0 there are no >> distributed dictionaries for LIG, DRG or 01 to 99. >> >> There was a PDB component LIG that was obsoleted in 2021 >> https://urldefense.com/v3/__https://www/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxaEuNjNL0$ >> . >> ebi.ac.uk%2Fpdbe%2Fstatic%2Ffiles%2Fpdbechem_v2%2FLIG.cif&data=05%7C02 >> %7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc66082939%7C18a59a >> 81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436399432%7CUnknown%7CTW >> FpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6 >> Mn0%3D%7C0%7C%7C%7C&sdata=mFCw%2BNkuhOvtx4ozk9IeaBryFaqU6dt0CLQcneSzpm >> g%3D&reserved=0 And there was a restraint dictionary for this >> distributed with CCP4 7.0. >> >> Perhaps you are picking up things from an old CCP4 installation >> >> Hope this helps, >> >> Oliver >> >> >> >> >>>> On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE >>>> <stefanie.freitag-p...@durham.ac.uk> wrote: >>> >>> Dear all, >>> >>> thank you so much for all your suggestions. >>> >>> Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is >>> complaining that there is a clash with an already existing ligand (even >>> DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters. >>> >>> I am not quite sure how to bypass this issue as I think Refmac is >>> also insisting on 3-letters for ligands (???) >>> >>> I have not tried Grade yet. >>> >>> Any advise much appreciated. >>> >>> 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> >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK >>> <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE >>> <stefanie.freitag-p...@durham.ac.uk >>> <mailto:stefanie.freitag-p...@durham.ac.uk>> >>> Sent: 25 April 2024 13:01 >>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >>> <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> >>> Subject: [ccp4bb] add ligand with AceDRG >>> >>> [EXTERNAL EMAIL] >>> 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://urldefense.com/v3/__https://ww/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxahrK1ig4$ >>> w.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&d >>> ata=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc6608 >>> 2939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436403543 >>> %7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI >>> 6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ao19TjbOKH8X1oFJmplmTf5T8 >>> ZA8C63KRoy%2Bvnf18aw%3D&reserved=0 >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://urldefense.com/v3/__https://ww/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxahrK1ig4$ >>> w.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&d >>> ata=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc6608 >>> 2939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436407653 >>> %7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI >>> 6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=GK6lK0k%2FrUScD5qQLRiOvXU >>> IIlIqKnbNwynz8ekpzDA%3D&reserved=0 >> >> >> ###################################################################### >> ## 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