RE: [Ifeffit] graphics and fit
Hi Stefano, Another free program that can read the output from atoms is ghemical. http://www.uku.fi/~thassine/ghemical/ I have written a rather specialized code that allows you to rotate a group of atoms until one of those atoms is at a determined distance from the original atom. Here let me explain for the specific example that I used it for. Say you have a Uranium atom and attached to it through an oxygen atom you have a PO4 group. One of the oxygen atoms of the PO4 group is shared with the uranium atom. Now from your exafs data you know that the U-P distance should be some number call it Rp. This program will leave the shared oxygen atom at the same spot, but move the PO3 atoms until the distance for U-P matches Rp. There are lots of ways that you can move the PO3 atom. The program is written to try to bend the PO3 group first and then translate the PO3 group to make the distance match. Then the program writes out the coordinates for all the atoms. This code is written in perl and doesn't have a gui interface, but I would be happy to share. Shelly
-----Original Message----- From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] Sent: Thursday, May 13, 2004 5:31 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] graphics and fit
Hello,
just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite?
Stefano -- ____________________________________________
Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit
rasmol and xmakemol also can read "*.xyz" files as well as many other formats. These programs are more suited to macromolecular structures. Carlo On Thu, 13 May 2004, Kelly, Shelly D. wrote:
Hi Stefano,
Another free program that can read the output from atoms is ghemical. http://www.uku.fi/~thassine/ghemical/
I have written a rather specialized code that allows you to rotate a group of atoms until one of those atoms is at a determined distance from the original atom. Here let me explain for the specific example that I used it for. Say you have a Uranium atom and attached to it through an oxygen atom you have a PO4 group. One of the oxygen atoms of the PO4 group is shared with the uranium atom. Now from your exafs data you know that the U-P distance should be some number call it Rp. This program will leave the shared oxygen atom at the same spot, but move the PO3 atoms until the distance for U-P matches Rp. There are lots of ways that you can move the PO3 atom. The program is written to try to bend the PO3 group first and then translate the PO3 group to make the distance match. Then the program writes out the coordinates for all the atoms. This code is written in perl and doesn't have a gui interface, but I would be happy to share.
Shelly
-----Original Message----- From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] Sent: Thursday, May 13, 2004 5:31 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] graphics and fit
Hello,
just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite?
Stefano -- ____________________________________________
Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@agni.phys.iit.edu http://www.iit.edu/~segre
Hi Shelly, That would be a great program to have. I often have to do this. I hope that you make the program available. Jeff On May 13, 2004, at 10:13 AM, Kelly, Shelly D. wrote:
I have written a rather specialized code that allows you to rotate a group of atoms until one of those atoms is at a determined distance from the original atom. Here let me explain for the specific example that I used it for. Say you have a Uranium atom and attached to it through an oxygen atom you have a PO4 group. One of the oxygen atoms of the PO4 group is shared with the uranium atom. Now from your exafs data you know that the U-P distance should be some number call it Rp. This program will leave the shared oxygen atom at the same spot, but move the PO3 atoms until the distance for U-P matches Rp. There are lots of ways that you can move the PO3 atom. The program is written to try to bend the PO3 group first and then translate the PO3 group to make the distance match. Then the program writes out the coordinates for all the atoms. This code is written in perl and doesn't have a gui interface, but I would be happy to share.
Shelly
-----Original Message----- From: Stefano Ciurli [mailto:stefano.ciurli@unibo.it] Sent: Thursday, May 13, 2004 5:31 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] graphics and fit
Hello,
just a thought: wouldn't it be nice to be able to read the feff.inp file directly into a simple molecular graphics program in order to see if the used coordinates contain any error? Maybe it is possible already and I am not aware of it. I understand that the program is mainly used by material scientists, but for us working with biological samples of metalloproteins it would be nice. Another suggestion: I know that Excurve is able to treat the histidine rings as a unity, and when performing the fit that program is able to maintain the ring rigid while fitting the distance between the metal and the imidazole ring of the histidine. How can I do that simply using your suite?
Stefano -- ____________________________________________
Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listi> nfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (3)
-
Carlo U. Segre -
Jeff Terry -
Kelly, Shelly D.