Delphi electrostatic potential visualization
Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera.
Thanks so much, you guys are great!
Sincerely, Joshua Broyde
Hi Joshua,
There is no limit to how many surfaces Chimera can color using electrostatic potential. The trouble is probably that your Delphi map is not covering the molecular surface, in fact your surface probably lies entirely outside the box containing the Delphi map and in this case the Surface Color dialog colors the surface gray. You can check this theory using the Options button on the Surface Color dialog and changing the “Color outside volume” color, then press “Color” and see if your surface becomes that new color. To see where the Delphi map is located relative to your protein you can display an outline around it, for example if the map is model #5 then use "vol #5 showoutline true”.
Tom
On Jul 31, 2014, at 1:40 PM, Joshua Broyde wrote:
Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera.
Thanks so much, you guys are great!
Sincerely, Joshua Broyde _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Josh,
If you molecule and electrostatic potential map align when they are the only two data sets you open in Chimera, but they don’t align when you have other opened data sets, I suspect you’ve run into the falling pitfall. When you open a molecule or map in Chimera it positions it using the coordinate system of the currently opened data with lowest model id number. This won’t matter if all the currently open models have the same coordinate system. But if you have moved one of those currently opened models relative to the others then they have different coordinate systems. To get your molecule and map misaligned you might open a few molecules, move the one with lowest id number relative to the others, then open your potential map which lets say is supposed to align with molecule #2. The map won’t align with that molecule, instead it will align with the lowest id model that you moved. To fix this if your opened map has model id number 3 you could use the Chimera command “matrixcopy #2 #3” to set the coordinate system of the map to match the coordinate system of molecule with id #2.
Tom
From: Joshua Broyde Subject: Re: [Chimera-users] Delphi electrostatic potential visualization Date: August 4, 2014 at 9:41:19 AM PDT To: Tom Goddard
Tom, This theory was correct. Thanks for the help. However, I notice that chimera only recognizes the surface as lying outside of the Delphi map if the model is not the only one in the Chimera session. So if I take the exact same model and open a new session with just that PDB and I map the electrostatics onto the surface, the electrostatics displays correctly. Any ideas why this could be?
Thanks!
Josh
On Jul 31, 2014, at 3:38 PM, Tom Goddard goddard@sonic.net wrote:
Hi Joshua,
There is no limit to how many surfaces Chimera can color using electrostatic potential. The trouble is probably that your Delphi map is not covering the molecular surface, in fact your surface probably lies entirely outside the box containing the Delphi map and in this case the Surface Color dialog colors the surface gray. You can check this theory using the Options button on the Surface Color dialog and changing the “Color outside volume” color, then press “Color” and see if your surface becomes that new color. To see where the Delphi map is located relative to your protein you can display an outline around it, for example if the map is model #5 then use "vol #5 showoutline true”.
Tom
On Jul 31, 2014, at 1:40 PM, Joshua Broyde wrote:
Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera.
Thanks so much, you guys are great!
Sincerely, Joshua Broyde _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Joshua, Thanks for your kind words!
I can't think of any reason why you couldn't have several different structures colored by several different maps. My only idea in your first session is that perhaps the structure was rotated/translated separately from the map so that they were no longer correctly aligned with one another. One must be careful not to change the spatial relationship between the structure and its corresponding map.
Maybe you were running DelPhi outside of Chimera because you couldn't get it to run via DelPhiController? The link you sent is rather old advice and in more current versions of Chimera, the process may work. However, if you find the separate process reasonably convenient, no reason to switch.
FYI, more recent versions of Chimera can also run APBS via web service (as well as PDB2PQR for prepping structures for APBS).
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 31, 2014, at 1:40 PM, Joshua Broyde jb3401@c2b2.columbia.edu wrote:
Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera.
Thanks so much, you guys are great!
Sincerely, Joshua Broyde
participants (3)
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Elaine Meng -
Joshua Broyde -
Tom Goddard