ligand cif file

ChenTiantian

28 May 2011 28 May '11

1:12 a.m.

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ? Best Regards, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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Thomas C. Terwilliger

28 May 28 May

2:13 a.m.

Hi Tiantian, I think that if you use the GUI you can click on "Reel" and you should be able to edit the cif file very conveniently there! All the best, Tom T

...

...
Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ?

Best Regards,

Tiantian

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nigel Moriarty

31 May 31 May

6:09 p.m.

Tiantian You can also improve the results by giving eLBOW all the information you have in the best possible format. There is a hierarchy of chemical inputs that provide information about your ligand. One of the best ways to remove ambiguity about a ligand is to include the hydrogens in the input. A rough guide to inputs from lowest common denominator to highest is 1. PDB without hydrogens 2. PDB with hydrogens 3. Mol2D, Mol3D, SDF, SMILES, Tripos, Chemical Components code I'd be happy to take a long at your input to assist you. Please send files directly to me. NB. Any files sent to me will be held in strictest confidence. Nigel On Fri, May 27, 2011 at 6:12 PM, ChenTiantian wrote:

...

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ?

Best Regards,

Tiantian

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

ChenTiantian

1 Jun 1 Jun

1:29 a.m.

Hi,Nigel Thank you very much, the problem is already solved. Next time I will let you know if I meet new problems. Best, Tiantian On Wed, Jun 1, 2011 at 2:09 AM, Nigel Moriarty wrote:

...

Tiantian

You can also improve the results by giving eLBOW all the information you have in the best possible format. There is a hierarchy of chemical inputs that provide information about your ligand. One of the best ways to remove ambiguity about a ligand is to include the hydrogens in the input. A rough guide to inputs from lowest common denominator to highest is

1. PDB without hydrogens 2. PDB with hydrogens 3. Mol2D, Mol3D, SDF, SMILES, Tripos, Chemical Components code

I'd be happy to take a long at your input to assist you. Please send files directly to me.

NB. Any files sent to me will be held in strictest confidence.

Nigel

On Fri, May 27, 2011 at 6:12 PM, ChenTiantian wrote:

...
Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ?

Best Regards,

Tiantian

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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