Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

-Original Message- > From: CCP4 bulletin board 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 open

Re: [ccp4bb] add ligand with AceDRG

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 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

board 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

Re: [ccp4bb] add ligand with AceDRG

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,

Re: [ccp4bb] add ligand with AceDRG

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://grade.globalphasing.org/ 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

Re: [ccp4bb] add ligand with AceDRG

Thanks for the feedback, I will let PDBe developers know that this is causing confusion and that LIG should not return results. Kind regards, Deborah On 26/04/2024 16:11, Garib Murshudov wrote: On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a

Re: [ccp4bb] add ligand with AceDRG

Indeed, as Diana points out: PDB's own components.cif defines LIG as: _chem_comp.id LIG _chem_comp.name "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H11 N3" So they probably should fix that. Also that

Re: [ccp4bb] add ligand with AceDRG

On this website: 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

Re: [ccp4bb] add ligand with AceDRG

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.

Re: [ccp4bb] add ligand with AceDRG

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 wrote:  Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See

Re: [ccp4bb] add ligand with AceDRG

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 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands:

Re: [ccp4bb] add ligand with AceDRG

Thank you Paul. I did not think about it. Stefanie, could you please send the log file to me? Regards Garib > On 26 Apr 2024, at 14:17, Paul Emsley wrote: > > > On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: >> >> >> >> I have trouble adding a ligand with AceDRG in CCP4i2 into my

Re: [ccp4bb] add ligand with AceDRG

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: 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

Re: [ccp4bb] add ligand with AceDRG

to make sure that it is not related to your ccp4 installation. Best regards Cyprian Cyprian Cukier, Ph.D. Head of Structural Biology Selvita S.A. From: CCP4 bulletin board On Behalf Of Garib Murshudov Sent: Friday, April 26, 2024 1:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] add

Re: [ccp4bb] add ligand with AceDRG

Refmac by itself should not care about duplicated residue names in the monomer library. It takes the last monomer. There should be something on the interface preventing this. Longer than three letters should be available from the next release of ccp4. New acedrg and Refmacat should be able to

Re: [ccp4bb] add ligand with AceDRG

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

Re: [ccp4bb] add ligand with AceDRG

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

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you could run from command-lines, it will be easy to solve this problem. try from command-line, type acedrg -i "your_smiles_string" -r your_3_letter_code -o your_out_file_name For example, acedrg -i "C[C@@H](C(=O)O)N" -r UNL -o UNL You will get a file called UNL.cif, which

Re: [ccp4bb] add ligand with AceDRG

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.

Re: [ccp4bb] add ligand with AceDRG

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 >

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, In CCP4Cloud, the equivalent task will generate the files using a 'free', unused code, if nothing is entered in the relevant box. However, not sure if CCP4I2's task will do the same, but worth trying. Hope this helps, Andy From: CCP4 bulletin