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://grad/ > 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://www/. > 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://ww/ > > 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://ww/ > > 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 > > > ###################################################################### > ## > > To unsubscribe from the CCP4BB list, click the following link: > https://www/. > jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data= > 05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc66082939%7 > C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436411693%7CUnkno > wn%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiL > CJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=aicCCOR81EZ%2BGCJ7g%2FBGy5vRoi5O0iOK5 > NKZduDEV5U%3D&reserved=0 > > This message was issued to members of > http://www.j/ > iscmail.ac.uk%2FCCP4BB&data=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6 > fed4844df87c9e08dc66082939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0% > 7C638497432436415770%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI > joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EBBfVqjJo > dwbFwJ1QU2bbCLGTZrSNQNOmJ39c4aIrAA%3D&reserved=0, a mailing list > hosted by > http://www.j/ > iscmail.ac.uk%2F&data=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed484 > 4df87c9e08dc66082939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%7C6384 > 97432436419761%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2l > uMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=FWU2KZlJHRDrODy > WnWE6QNaTUKCl5h89UbrhqBd%2FLro%3D&reserved=0, terms & conditions are > available at > https://www/. > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7CWANG_YONG_Y%40LIL > LY.COM%7C00daf6fed4844df87c9e08dc66082939%7C18a59a81eea84c30948ad8824c > dc2580%7C0%7C0%7C638497432436423739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC > 4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C& > sdata=C9NBMZ%2BfTWKv0U32fJxHa24k93DJjXPNFnUcw%2FJ4FvA%3D&reserved=0 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
