Dear ChimeraX users, I just subscribed so apologies if this has been asked before. When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue. I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain. I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally. Is it possible to assign a specific color per chain using this command? Thank you for your help. best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Hi Vincent, Check that your map is model #2 and your atomic structure is model #1 by looking at the id numbers in the Models panel. Also if you hover the mouse over an atom you can check that your atomic structure as chain A. I see that If you get the model numbers wrong the command does not warn you that nothing was colored. I will fix that so it gives a warning. Tom
On Sep 20, 2021, at 2:45 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users,
I just subscribed so apologies if this has been asked before.
When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue
I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue.
I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain.
I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally.
Is it possible to assign a specific color per chain using this command?
Thank you for your help. best Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr <http://www.appicom.cnrs.fr/> http://mmsb.cnrs.fr/en/ <http://mmsb.cnrs.fr/en/>
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Hi Tom, I figured it out. My chain and volume were correctly defined, it is the original coloring of the model when first opened in ChimeraX that was different. For some reason, "open 7lup" opens the pdb in ball and stick with one color per chain. When I open my PDB, it opens it in sticks with one color per atom type. Using the color zone command colors according to the color of the PDB, thus by atom type. Cf the 2 attached pictures for clarity. If I say: color #1/A yellow color zone #2 near #1 then I can change the colors as I want and color chain A in yellow. I'm using version 1.2 (2021-04-27) Best Vincent Le 20/09/2021 à 19:58, Tom Goddard a écrit :
Hi Vincent,
Check that your map is model #2 and your atomic structure is model #1 by looking at the id numbers in the Models panel. Also if you hover the mouse over an atom you can check that your atomic structure as chain A.
I see that If you get the model numbers wrong the command does not warn you that nothing was colored. I will fix that so it gives a warning.
Tom
On Sep 20, 2021, at 2:45 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX users,
I just subscribed so apologies if this has been asked before.
When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue
I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue.
I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain.
I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally.
Is it possible to assign a specific color per chain using this command?
Thank you for your help. best Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Hi Vincent, ChimeraX chooses the initial coloring and styles (atoms or ribbon) to show when an atomic structure is just opened based on the size of the structure (number of atoms and chains). This is called "smart initial display" https://www.cgl.ucsf.edu/chimerax/docs/user/autostyle.html You can give each chain a single color with command color bychain You might want to use ambient lighting so your maps look more 3 dimensional in images using command "light soft" or the soft lighting toolbar icon. Tom
On Sep 21, 2021, at 12:40 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
I figured it out. My chain and volume were correctly defined, it is the original coloring of the model when first opened in ChimeraX that was different. For some reason, "open 7lup" opens the pdb in ball and stick with one color per chain. When I open my PDB, it opens it in sticks with one color per atom type.
Using the color zone command colors according to the color of the PDB, thus by atom type. Cf the 2 attached pictures for clarity.
If I say: color #1/A yellow color zone #2 near #1
then I can change the colors as I want and color chain A in yellow.
I'm using version 1.2 (2021-04-27)
Best Vincent
Le 20/09/2021 à 19:58, Tom Goddard a écrit :
Hi Vincent,
Check that your map is model #2 and your atomic structure is model #1 by looking at the id numbers in the Models panel. Also if you hover the mouse over an atom you can check that your atomic structure as chain A.
I see that If you get the model numbers wrong the command does not warn you that nothing was colored. I will fix that so it gives a warning.
Tom
On Sep 20, 2021, at 2:45 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX users,
I just subscribed so apologies if this has been asked before.
When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue
I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue.
I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain.
I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally.
Is it possible to assign a specific color per chain using this command?
Thank you for your help. best Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr <http://www.appicom.cnrs.fr/> http://mmsb.cnrs.fr/en/ <http://mmsb.cnrs.fr/en/>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr <http://www.appicom.cnrs.fr/> http://mmsb.cnrs.fr/en/ <http://mmsb.cnrs.fr/en/>
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participants (2)
-
Tom Goddard -
vincent Chaptal