Good afternoon, My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue. Thank you very much,Dan
Hi Dan,
I wasn’t able to reproduce this problem. I just tested in Chimera 1.10.2 on 3 related proteins, with commands:
open 2mnr
open 1muc
open 4enl
delete :.b
mm #0 #1
mm #0 #2
tile
surf
… then invoking Coulombic Surface Coloring, just clicking Apply because all three surfaces were already chosen in the dialog. Image of the result attached (after applying publication preset 1).
I can’t think of any reason your system would behave differently, and all I can say is to make sure all the surfaces are chosen in the dialog. However, if that still doesn’t work you can always try submitting a bug report (menu: Help… Report a Bug) and attach the session so we could try to reproduce it.
Best,
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 May 13, 2016, at 11:10 AM, zona cat
Good afternoon,
My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue.
Thank you very much, Dan
Hi Elaine,
Thank you for the quick response. I was doing my work via windows, not the command line. Is there something I need to do to keep all of the surfaces/sequences open??-Danny
On Friday, May 13, 2016 3:57 PM, Elaine Meng
Hi Danny,
It should not make any difference whether you are using the graphical interfaces (dialog windows) or commands. I only put commands in my example because it is much less typing to describe.
As I mentioned before, just make sure that in the Coulombic coloring dialog, you have chosen all of the surfaces…. the most obvious reason it might only color one surface is if you only chose (highlighted) one surface in the list.
Best,
Elaine
On May 13, 2016, at 1:13 PM, zona cat
Hi Elaine,
Thank you for the quick response. I was doing my work via windows, not the command line. Is there something I need to do to keep all of the surfaces/sequences open?? -Danny
On Friday, May 13, 2016 3:57 PM, Elaine Meng
wrote: Hi Dan, I wasn’t able to reproduce this problem. I just tested in Chimera 1.10.2 on 3 related proteins, with commands:
open 2mnr open 1muc open 4enl delete :.b mm #0 #1 mm #0 #2 tile surf
… then invoking Coulombic Surface Coloring, just clicking Apply because all three surfaces were already chosen in the dialog. Image of the result attached (after applying publication preset 1).
I can’t think of any reason your system would behave differently, and all I can say is to make sure all the surfaces are chosen in the dialog. However, if that still doesn’t work you can always try submitting a bug report (menu: Help… Report a Bug) and attach the session so we could try to reproduce it.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
<3surfs.png> On May 13, 2016, at 11:10 AM, zona cat
wrote: Good afternoon,
My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue.
Thank you very much, Dan
Hi Danny,
It should not make any difference whether you are using the graphical interfaces (dialog windows) or commands. I only put commands in my example because it is much less typing to describe.
As I mentioned before, just make sure that in the Coulombic coloring dialog, you have chosen all of the surfaces…. the most obvious reason it might only color one surface is if you only chose (highlighted) one surface in the list.
Best,
Elaine
On May 13, 2016, at 1:13 PM, zona cat
Hi Elaine,
Thank you for the quick response. I was doing my work via windows, not the command line. Is there something I need to do to keep all of the surfaces/sequences open?? -Danny
On Friday, May 13, 2016 3:57 PM, Elaine Meng
wrote: Hi Dan, I wasn’t able to reproduce this problem. I just tested in Chimera 1.10.2 on 3 related proteins, with commands:
open 2mnr open 1muc open 4enl delete :.b mm #0 #1 mm #0 #2 tile surf
… then invoking Coulombic Surface Coloring, just clicking Apply because all three surfaces were already chosen in the dialog. Image of the result attached (after applying publication preset 1).
I can’t think of any reason your system would behave differently, and all I can say is to make sure all the surfaces are chosen in the dialog. However, if that still doesn’t work you can always try submitting a bug report (menu: Help… Report a Bug) and attach the session so we could try to reproduce it.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
<3surfs.png> On May 13, 2016, at 11:10 AM, zona cat
wrote: Good afternoon,
My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue.
Thank you very much, Dan
Sorry folks, I have no idea why sometimes my messages send twice!
Danny, I don’t know what you mean by keeping surfaces/sequences open. There is no need to keep windows open other than the main Chimera window and the dialog for the tool (for example, Coulombic coloring) that you are actually using. The structures and their surfaces in the main Chimera window won’t be closed or deleted unless you closed or deleted them yourself.
Elaine
On May 14, 2016, at 10:52 AM, Elaine Meng
Hi Danny, It should not make any difference whether you are using the graphical interfaces (dialog windows) or commands. I only put commands in my example because it is much less typing to describe.
As I mentioned before, just make sure that in the Coulombic coloring dialog, you have chosen all of the surfaces…. the most obvious reason it might only color one surface is if you only chose (highlighted) one surface in the list. Best, Elaine
On May 13, 2016, at 1:13 PM, zona cat
wrote: Hi Elaine,
Thank you for the quick response. I was doing my work via windows, not the command line. Is there something I need to do to keep all of the surfaces/sequences open?? -Danny
On Friday, May 13, 2016 3:57 PM, Elaine Meng
wrote: Hi Dan, I wasn’t able to reproduce this problem. I just tested in Chimera 1.10.2 on 3 related proteins, with commands:
open 2mnr open 1muc open 4enl delete :.b mm #0 #1 mm #0 #2 tile surf
… then invoking Coulombic Surface Coloring, just clicking Apply because all three surfaces were already chosen in the dialog. Image of the result attached (after applying publication preset 1).
I can’t think of any reason your system would behave differently, and all I can say is to make sure all the surfaces are chosen in the dialog. However, if that still doesn’t work you can always try submitting a bug report (menu: Help… Report a Bug) and attach the session so we could try to reproduce it.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
<3surfs.png> On May 13, 2016, at 11:10 AM, zona cat
wrote: Good afternoon,
My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue.
Thank you very much, Dan
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participants (2)
-
Elaine Meng
-
zona cat