Re: [ccp4bb] How to get a CIF configure for a designed ligand
Hi Robert, This is very easy with the CCP4 program JLigand. Just start a new ligand with the sulfur atom, add the phenyl groups, the extra bond and the hydrogens. Then regularise and save the restraint file. HTH, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert Sent: Friday, May 02, 2014 06:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to get a CIF configure for a designed ligand Dear all, How can I get a cif configure for a new ligand. Right now, I want to use the phenix to refine a complex structure. But I found that I cannot get the ligand cif file from the CCP4 search. The ligand is dibenzothiophene. So do you have any idea to help me. Thanks very much for your help. Best wishes. Robert.
Re: [ccp4bb] How to get a CIF configure for a designed ligand
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Robert, this is what I just did: 1) went to en.wikipedia.org and entered your ligands name Dibenzothiophene 2) copied the SMILES string provided for many small molecules in Wikipedia 3) went to http://http://grade.globalphasing.org and paste the SMILES string 4) downloaded the CIF-file Altogether it took longer to write this email than to get the cif-file, which is why I find the grade server so useful :-) Best regards, Tim On 05/02/2014 06:46 AM, Robert wrote: Dear all, How can I get a cif configure for a new ligand. Right now, I want to use the phenix to refine a complex structure. But I found that I cannot get the ligand cif file from the CCP4 search. The ligand is dibenzothiophene. So do you have any idea to help me. Thanks very much for your help. Best wishes. Robert. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTY1QJUxlJ7aRr7hoRAhFgAJ48OpjUBTUDjkPo1rbg74CtXFjSIwCgg3Y9 Nvrx5xUF0yrCRZkTKrrKNgI= =JD49 -END PGP SIGNATURE-
Re: [ccp4bb] How to get a CIF configure for a designed ligand
prodrg should work Robert ccp4a...@163.com wrote: Dear all, How can I get a cif configure for a new ligand. Right now, I want to use the phenix to refine a complex structure. But I found that I cannot get the ligand cif file from the CCP4 search. The ligand is dibenzothiophene. So do you have any idea to help me. Thanks very much for your help. Best wishes. Robert. -- Sent from Kaiten Mail. Please excuse my brevity.
[ccp4bb] How to get a CIF configure for a designed ligand
Dear all, Thank all of you for helping me. And my problem is solved. Robert.
[ccp4bb] How to get a CIF configure for a designed ligand
Dear all, How can I get a cif configure for a new ligand. Right now, I want to use the phenix to refine a complex structure. But I found that I cannot get the ligand cif file from the CCP4 search. The ligand is dibenzothiophene. So do you have any idea to help me. Thanks very much for your help. Best wishes. Robert.
Re: [ccp4bb] How to get a CIF configure for a designed ligand
Hello Robert, since you are going to use Phenix tools for refinement (phenix.refine, to be precise), then 1) why don't you use Phenix utilities http://phenix-online.org/version_docs/1.9-1688/ to obtain a suitable ligand dictionary (CIF file) assuming that it is going to be more compatible with the program of your choice? 2) why don't you post your question on a more specific mailing list (in this case phenixbb - Phenix mailing list)? Just wondering... Pavel On Thu, May 1, 2014 at 9:46 PM, Robert ccp4a...@163.com wrote: Dear all, How can I get a cif configure for a new ligand. Right now, I want to use the phenix to refine a complex structure. But I found that I cannot get the ligand cif file from the CCP4 search. The ligand is dibenzothiophene. So do you have any idea to help me. Thanks very much for your help. Best wishes. Robert.
