Re: [phenixbb] creating cif for Zn

Hi Pavel, Thanks for your mail. Sorry, It was my mistake. I fixed that. By the by, one more question. I want to create Fo(native protein)-Fo(native protein + drug) map in phenix using the phase calculated from the refined structure of native protein to see if the density for the drug can pop up. Can you tell me how I can do that? I am now using version phenix-1.4-3. Do I need to install current version? Thanks... Raja ----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 26, 2009 1:58 pm Subject: Re: [phenixbb] creating cif for Zn To: PHENIX user mailing list

Hi Raja,

this should work (the rightmost Zn is shifted one space left as required by PDB format):

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 Zn

let me know if it doesn't.

Pavel.

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Hi Pavel, I enclosed the line below:

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Z

I also tried with

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Zn

None worked.

Raja ----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 26, 2009 12:40 pm Subject: Re: [phenixbb] creating cif for Zn To: PHENIX user mailing list

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Hi Raja,

normally phenix.refine should recognize Zn atoms without any problems and you don't need run elbow for this. If it doesn't, that most likely means your PDB file is ill-formatted (for example, no element type defined in 77(?) column). Could you please send me copy of the ATOM line from your PDB file containing Zn so I can tell what is wrong?

Pavel.

On 5/26/09 12:31 PM, Raja Dey wrote:

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Dear Friends, I have Zn atoms in my pdb file. So, I

On 5/26/09 1:52 PM, Raja Dey wrote: think

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I need to run elbow to create the cif otherwise refinement stops.

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I did the following and got the error as follows:

phenix.elbow generate_easy_r4.pdb --do-all

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electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) --------------------------------------------------------------- --

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Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing

Parsing Parsing P

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No molecule read

Use --all-residues to view residues if this is a PDB file

Can anyone suggests at this point, what I should do? Thanking you in advance...

Raja

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