Handling electrostatic potential in cube format
Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues. Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version. Thanks for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710
Hi Boaz, Regarding your later message: yes, APBS .dx is a known ESP format for Chimera and ChimeraX, along with UHBD .grd and DelPhi(academic version)/GRASP .phi: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> There isn’t any “fitting” per se with the known grid formats, the coordinates are read directly from information in the file. So it sounds like the cube file from DelPhi may be similar enough to the known format that it is read, but some difference prevents correct interpretation of the grid offset or scale. If you are OK with using APBS dx instead, never mind, but re this Delphi cube file, if you have a non-private one, you could use Help… Report a Bug (in Chimera menu) and attach an example cube file and say in the description which PDB ID it goes with. Somewhat of an aside: in Volume Viewer menu: Features… Coordinates, you can specify grid origin and spacing, but that means you would have to know what values to enter in the first place. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2019, at 2:51 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues.
Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version.
Thanks for your help. Boaz
Hi Elaine, I'm happy with the .dx format which I can easily generate via the Chimera APBS gui. Just a little question/request: in this gui there is an option to define a location for the output .dx files whereas the output log (stdout) file of the run goes to the reply.log, as far as I could tell. Is it possible to send the output log as well as the input file the run to the same location? That'll be nice. Actually the the main pdb2pqr-apbs interface lists all the files once the job is done (.dx, stdout, stdin etc.) Best regards, Boaz ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, May 5, 2019 7:19 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Handling electrostatic potential in cube format Hi Boaz, Regarding your later message: yes, APBS .dx is a known ESP format for Chimera and ChimeraX, along with UHBD .grd and DelPhi(academic version)/GRASP .phi: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> There isn’t any “fitting” per se with the known grid formats, the coordinates are read directly from information in the file. So it sounds like the cube file from DelPhi may be similar enough to the known format that it is read, but some difference prevents correct interpretation of the grid offset or scale. If you are OK with using APBS dx instead, never mind, but re this Delphi cube file, if you have a non-private one, you could use Help… Report a Bug (in Chimera menu) and attach an example cube file and say in the description which PDB ID it goes with. Somewhat of an aside: in Volume Viewer menu: Features… Coordinates, you can specify grid origin and spacing, but that means you would have to know what values to enter in the first place. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2019, at 2:51 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues.
Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version.
Thanks for your help. Boaz
Hi, Boaz. That sounds like a good idea and it doesn't sound too difficult, but I don't have time to do it right now. I've created a ticket (http://plato.cgl.ucsf.edu/trac/chimera/ticket/16820#ticket) and will try to get to it when I have some time. Sorry. Conrad On 5/5/2019 11:47 AM, Boaz Shaanan wrote:
Hi Elaine,
I'm happy with the .dx format which I can easily generate via the Chimera APBS gui. Just a little question/request: in this gui there is an option to define a location for the output .dx files whereas the output log (stdout) file of the run goes to the reply.log, as far as I could tell. Is it possible to send the output log as well as the input file the run to the same location? That'll be nice. Actually the the main pdb2pqr-apbs interface lists all the files once the job is done (.dx, stdout, stdin etc.)
Best regards,
Boaz ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, May 5, 2019 7:19 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Handling electrostatic potential in cube format
Hi Boaz, Regarding your later message: yes, APBS .dx is a known ESP format for Chimera and ChimeraX, along with UHBD .grd and DelPhi(academic version)/GRASP .phi:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
There isn’t any “fitting” per se with the known grid formats, the coordinates are read directly from information in the file. So it sounds like the cube file from DelPhi may be similar enough to the known format that it is read, but some difference prevents correct interpretation of the grid offset or scale. If you are OK with using APBS dx instead, never mind, but re this Delphi cube file, if you have a non-private one, you could use Help… Report a Bug (in Chimera menu) and attach an example cube file and say in the description which PDB ID it goes with.
Somewhat of an aside: in Volume Viewer menu: Features… Coordinates, you can specify grid origin and spacing, but that means you would have to know what values to enter in the first place. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2019, at 2:51 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues.
Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version.
Thanks for your help. Boaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Conrad, Very good. Thanks for letting me know. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Conrad Huang <conrad@cgl.ucsf.edu> Sent: Monday, May 6, 2019 10:57 PM To: בעז שאנן; Chimera User Help Subject: Re: [Chimera-users] Handling electrostatic potential in cube format Hi, Boaz. That sounds like a good idea and it doesn't sound too difficult, but I don't have time to do it right now. I've created a ticket (http://plato.cgl.ucsf.edu/trac/chimera/ticket/16820#ticket) and will try to get to it when I have some time. Sorry. Conrad On 5/5/2019 11:47 AM, Boaz Shaanan wrote:
Hi Elaine,
I'm happy with the .dx format which I can easily generate via the Chimera APBS gui. Just a little question/request: in this gui there is an option to define a location for the output .dx files whereas the output log (stdout) file of the run goes to the reply.log, as far as I could tell. Is it possible to send the output log as well as the input file the run to the same location? That'll be nice. Actually the the main pdb2pqr-apbs interface lists all the files once the job is done (.dx, stdout, stdin etc.)
Best regards,
Boaz ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, May 5, 2019 7:19 PM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Handling electrostatic potential in cube format
Hi Boaz, Regarding your later message: yes, APBS .dx is a known ESP format for Chimera and ChimeraX, along with UHBD .grd and DelPhi(academic version)/GRASP .phi:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
There isn’t any “fitting” per se with the known grid formats, the coordinates are read directly from information in the file. So it sounds like the cube file from DelPhi may be similar enough to the known format that it is read, but some difference prevents correct interpretation of the grid offset or scale. If you are OK with using APBS dx instead, never mind, but re this Delphi cube file, if you have a non-private one, you could use Help… Report a Bug (in Chimera menu) and attach an example cube file and say in the description which PDB ID it goes with.
Somewhat of an aside: in Volume Viewer menu: Features… Coordinates, you can specify grid origin and spacing, but that means you would have to know what values to enter in the first place. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 4, 2019, at 2:51 PM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:
Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues.
Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version.
Thanks for your help. Boaz
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Boaz Shaanan -
Conrad Huang -
Elaine Meng