Thanks! Just to clarify, should I define the iodide as "I-" or "I1-" in the PDB file? Owen On Jul 14, 2010, at 5:19 PM, Pavel Afonine wrote:

Hi Owen,

no, it's not the case anymore: phenix.refine uses the charge, and this is available in phenix build 1.6.1-343 or higher. The charge must be defined in PDB file:

Example:

HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+

To be sure it works, in the phenix.refine output, look for:

Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 <<<<<< HERE S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0.

Pavel.

On 7/14/10 2:04 PM, Owen Pornillos wrote:

...

Hi BB,

I am refining a structure that contains iodide ions. I remember some previous posts that PHENIX does not take into account the charge state and uses scattering factors for neutral atoms only. Is this still true?

Thanks,

Owen

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Hi Owen, to be sure, try both and check the .log file - this will avoid guesswork. However, I think "I1-" should work. Pavel. On 7/14/10 2:22 PM, Owen Pornillos wrote:

Thanks! Just to clarify, should I define the iodide as "I-" or "I1-" in the PDB file?

Owen

On Jul 14, 2010, at 5:19 PM, Pavel Afonine wrote:

...

Hi Owen,

no, it's not the case anymore: phenix.refine uses the charge, and this is available in phenix build 1.6.1-343 or higher. The charge must be defined in PDB file:

Example:

HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN2+

To be sure it works, in the phenix.refine output, look for:

Number of scattering types: 6 Type Number sf(0) Zn2+ 2 28.00 <<<<<< HERE S 13 16.00 Na 2 11.00 O 240 8.00 N 113 7.00 C 442 6.00 sf(0) = scattering factor at diffraction angle 0.

Pavel.

On 7/14/10 2:04 PM, Owen Pornillos wrote:

...

Hi BB,

I am refining a structure that contains iodide ions. I remember some previous posts that PHENIX does not take into account the charge state and uses scattering factors for neutral atoms only. Is this still true?

Thanks,

Owen

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It seems that phenix.refine at some point changes the charge state of iodide, and outputs the following to the PDB.

HETATM 7801 I I F 1 18.611 -6.385 1.709 0.66 54.88 I+1

The same atom in the input file was:

HETATM 7937 I I F 1 18.600 -6.380 1.702 0.64 52.59 I-1

I cannot reproduce this problem. I tried "I1-", "I-1", and "I- ", which are all copied correctly to the output pdb. Could you send me inputs and commands to reproduce your problem? A fragment of the original structure will be fine as long as it can be used to demonstrate the problem. Ralf