Hi Arthur, There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I’ll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
But now I have another question that is related to the one I managed to figure out.
When I highlight an amino acid residue on a structure I know how to visualize the amino acid as a ball and stick structure. I also know how to have the residue shown as spheres. Except the Spheres are way too large.
Is there a way in which I can reduce the size of the spheres?
I couldn't find anything obvious in the Tools menu.
Thank you
Arthur G. Szabo
Elaine Thanks will try it. art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-18-15 5:57 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] helices Hi Arthur, There isn't anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I'll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The "m" is because this setting is for the whole molecule model; you can't have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
But now I have another question that is related to the one I managed to figure out.
When I highlight an amino acid residue on a structure I know how to visualize the amino acid as a ball and stick structure. I also know how to have the residue shown as spheres. Except the Spheres are way too large.
Is there a way in which I can reduce the size of the spheres?
I couldn't find anything obvious in the Tools menu.
Thank you
Arthur G. Szabo
Elaine So I tried to enlarge the size of the balls in the ball and stick image of an amino acid What you see below is the command line The command was highlighted in blue after I hit return. Nothing happened. So don't know if I have it correct or not. A part of the image is also shown below. I am trying to change the size of the balls in the tryptophan amino acid. The molecule in the large spheres is a maltose. The Trp residue shows it has been selected. Your assistance will be appreciated Thank you Arthur G. Szabo -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-18-15 5:57 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] helices Hi Arthur, There isn't anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I'll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The "m" is because this setting is for the whole molecule model; you can't have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 Nov 18, 2015, at 2:25 PM, A G Szabo < <mailto:agszabo@bell.net> agszabo@bell.net> wrote:
Elaine
But now I have another question that is related to the one I managed
to figure out.
When I highlight an amino acid residue on a structure I know how to
visualize the amino acid as a ball and stick structure. I also know
how to have the residue shown as spheres. Except the Spheres are way too large.
Is there a way in which I can reduce the size of the spheres?
I couldn't find anything obvious in the Tools menu.
Thank you
Arthur G. Szabo
Hi Arthur, Looks like you just need a space between the “ballScale” and the number. The selection is not necessary. The command will change the size of all balls. 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 Dec 4, 2015, at 9:32 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
So I tried to enlarge the size of the balls in the ball and stick image of an amino acid
What you see below is the command line The command was highlighted in blue after I hit return. Nothing happened. So don’t know if I have it correct or not.
A part of the image is also shown below. I am trying to change the size of the balls in the tryptophan amino acid. The molecule in the large spheres is a maltose. The Trp residue shows it has been selected.
Your assistance will be appreciated
Thank you
Arthur G. Szabo <image001.png>
<image002.png>
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-18-15 5:57 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] helices
Hi Arthur, There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I’ll describe one way.
When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like:
setattr m ballScale 0.5
That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model.
You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0).
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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
But now I have another question that is related to the one I managed to figure out.
When I highlight an amino acid residue on a structure I know how to visualize the amino acid as a ball and stick structure. I also know how to have the residue shown as spheres. Except the Spheres are way too large.
Is there a way in which I can reduce the size of the spheres?
I couldn't find anything obvious in the Tools menu.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine Thank you that worked. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: December-04-15 5:25 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: changing ball size Hi Arthur, Looks like you just need a space between the "ballScale" and the number. The selection is not necessary. The command will change the size of all balls. 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 Dec 4, 2015, at 9:32 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
So I tried to enlarge the size of the balls in the ball and stick image of an amino acid
What you see below is the command line The command was highlighted in blue after I hit return. Nothing happened. So don't know if I have it correct or not.
A part of the image is also shown below. I am trying to change the size of the balls in the tryptophan amino acid. The molecule in the large spheres is a maltose. The Trp residue shows it has been selected.
Your assistance will be appreciated
Thank you
Arthur G. Szabo <image001.png>
<image002.png>
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-18-15 5:57 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] helices
Hi Arthur, There isn't anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I'll describe one way.
When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like:
setattr m ballScale 0.5
That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The "m" is because this setting is for the whole molecule model; you can't have different values for different atoms in the same model.
You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0).
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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo@bell.net> wrote:
Elaine
But now I have another question that is related to the one I managed to figure out.
When I highlight an amino acid residue on a structure I know how to visualize the amino acid as a ball and stick structure. I also know how to have the residue shown as spheres. Except the Spheres are way too large.
Is there a way in which I can reduce the size of the spheres?
I couldn't find anything obvious in the Tools menu.
Thank you
Arthur G. Szabo
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng