Iodide scattering factor
![](https://secure.gravatar.com/avatar/bd81c2c6f178dbd9ce5ea3d0e482d153.jpg?s=120&d=mm&r=g)
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
![](https://secure.gravatar.com/avatar/7984547b53fca6ae837ba286f9c92e29.jpg?s=120&d=mm&r=g)
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
![](https://secure.gravatar.com/avatar/bd81c2c6f178dbd9ce5ea3d0e482d153.jpg?s=120&d=mm&r=g)
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
![](https://secure.gravatar.com/avatar/7984547b53fca6ae837ba286f9c92e29.jpg?s=120&d=mm&r=g)
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
![](https://secure.gravatar.com/avatar/bd81c2c6f178dbd9ce5ea3d0e482d153.jpg?s=120&d=mm&r=g)
Hi - I've noticed a bug. 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 Refinement appeared to occur normally, and correct scattering factors were declared in the log file: Number of scattering types: 5 Type Number sf(0) I1- 7 53.91 S 65 16.00 O 1503 8.00 N 1372 7.00 C 5005 6.00 Owen ________________________________________ From: [email protected] [[email protected] ] On Behalf Of Pavel Afonine [[email protected]] Sent: Wednesday, July 14, 2010 2:25 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Iodide scattering factor 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
![](https://secure.gravatar.com/avatar/c59c83b372c7116eff6b73580ab053ed.jpg?s=120&d=mm&r=g)
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
participants (3)
-
Owen Pornillos
-
Pavel Afonine
-
Ralf W. Grosse-Kunstleve