Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png]
Hi Thiru, (I added a subject line to the message so others may be able to find it later.)
(A) There are a couple ways to add a dashed or dotted line, but one easy way if you only need to add a few is to first just make distance measurements, and then hide the distance values. For example, show Distances tool (menu: Tools… Structure Analysis… Distances). Then for each line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second atom to select it …. now there are two atoms selected and you can add the line between them by clicking the “Create” button on the Distances tool.
With the Distances tool you can set “Labels” to “None” and change the distance color, line width, and line style. http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
You should do this when only one copy of the structure is open, and shown as sticks. Part (B) below describes opening a second copy to show the spheres, and if you do that first, you will have to use Model Panel to hide the spheres model temporarily (uncheck the “S” box) so that you can add the distance measurements to the sticks.
(B) To show transparent spheres and sticks at the same time, open the same structure twice. Then show one copy as spheres and make it partially transparent. For example, commands:
open pubchem:448537 open pubchem:448537 repr sphere #1 trans 50 #1 set bg_color white
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/represent.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html
The 50 means 50% transparent. You could use some other value. Also you could change the colors of the spheres (model #1 in this example) and sticks (model #0 in this example) as you like.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam tp42@nyu.edu wrote:
Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru <image.png>
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you soo much for your update and support. I will try. Thanks Thiru
On Monday, February 24, 2020, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Thiru, (I added a subject line to the message so others may be able to find it
later.)
(A) There are a couple ways to add a dashed or dotted line, but one easy
way if you only need to add a few is to first just make distance measurements, and then hide the distance values. For example, show Distances tool (menu: Tools… Structure Analysis… Distances). Then for each line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second atom to select it …. now there are two atoms selected and you can add the line between them by clicking the “Create” button on the Distances tool.
With the Distances tool you can set “Labels” to “None” and change the
distance color, line width, and line style.
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
You should do this when only one copy of the structure is open, and shown
as sticks. Part (B) below describes opening a second copy to show the spheres, and if you do that first, you will have to use Model Panel to hide the spheres model temporarily (uncheck the “S” box) so that you can add the distance measurements to the sticks.
(B) To show transparent spheres and sticks at the same time, open the
same structure twice. Then show one copy as spheres and make it partially transparent. For example, commands:
open pubchem:448537 open pubchem:448537 repr sphere #1 trans 50 #1 set bg_color white
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
The 50 means 50% transparent. You could use some other value. Also you
could change the colors of the spheres (model #1 in this example) and sticks (model #0 in this example) as you like.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam tp42@nyu.edu wrote:
Hi, I am trying to make metal coordination bond as a dotted line and also I
need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues.
Looking forward to hearing from you, Many thanks, Thiru <image.png>
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...
Hi, I need help to stack the crystal structures stack on top of each other. For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera? [image: image.png]
Thanks, Thiru
On Mon, Feb 24, 2020 at 10:31 PM Thirumurugan Prakasam tp42@nyu.edu wrote:
Thank you soo much for your update and support. I will try. Thanks Thiru
On Monday, February 24, 2020, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Thiru, (I added a subject line to the message so others may be able to find it
later.)
(A) There are a couple ways to add a dashed or dotted line, but one easy
way if you only need to add a few is to first just make distance measurements, and then hide the distance values. For example, show Distances tool (menu: Tools… Structure Analysis… Distances). Then for each line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second atom to select it …. now there are two atoms selected and you can add the line between them by clicking the “Create” button on the Distances tool.
With the Distances tool you can set “Labels” to “None” and change the
distance color, line width, and line style.
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
You should do this when only one copy of the structure is open, and
shown as sticks. Part (B) below describes opening a second copy to show the spheres, and if you do that first, you will have to use Model Panel to hide the spheres model temporarily (uncheck the “S” box) so that you can add the distance measurements to the sticks.
(B) To show transparent spheres and sticks at the same time, open the
same structure twice. Then show one copy as spheres and make it partially transparent. For example, commands:
open pubchem:448537 open pubchem:448537 repr sphere #1 trans 50 #1 set bg_color white
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
<
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer...
The 50 means 50% transparent. You could use some other value. Also you
could change the colors of the spheres (model #1 in this example) and sticks (model #0 in this example) as you like.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam tp42@nyu.edu
wrote:
Hi, I am trying to make metal coordination bond as a dotted line and also I
need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues.
Looking forward to hearing from you, Many thanks, Thiru <image.png>
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...
-- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358
Hi Thiru, If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.
E.g. if the starting structure is oriented exactly so that you can stack them in Z (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:
open myfile.pdb open myfile.pdb open myfile.pdb
... then you would have models #0,1,2. To stack (REMEMBER don't rotate the view by hand yet!):
move z 35 model #1 move z 70 model #2
If it were X or Y axis instead of Z, then you would use x or y in the command instead of z. If you mess up you can use command "reset" and then start over with the move commands.
See "move" help: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html
After you are done opening/stacking, then you can rotate the view by hand. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I need help to stack the crystal structures stack on top of each other. For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera? <image.png>
Thanks, Thiru
Thank you so much Elaine for your quick response and help. Many Thanks, Thiru
On Fri, Oct 29, 2021 at 8:40 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Thiru, If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.
E.g. if the starting structure is oriented exactly so that you can stack them in Z (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:
open myfile.pdb open myfile.pdb open myfile.pdb
... then you would have models #0,1,2. To stack (REMEMBER don't rotate the view by hand yet!):
move z 35 model #1 move z 70 model #2
If it were X or Y axis instead of Z, then you would use x or y in the command instead of z. If you mess up you can use command "reset" and then start over with the move commands.
See "move" help: < https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chime...
After you are done opening/stacking, then you can rotate the view by hand. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hi, I need help to stack the crystal structures stack on top of each other.
For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera?
<image.png>
Thanks, Thiru
Another way to make the copies is to use the Chimera sym command. For example,
sym #0 group shift,5,14 axis z
copies model #0 five times at 14 Angstrom spacing along the z axis of the model #0 coordinate system (not the view direction coordinate system).
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
Tom
On Oct 29, 2021, at 10:16 AM, Thirumurugan Prakasam via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thank you so much Elaine for your quick response and help. Many Thanks, Thiru
On Fri, Oct 29, 2021 at 8:40 PM Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote: Hi Thiru, If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.
E.g. if the starting structure is oriented exactly so that you can stack them in Z (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:
open myfile.pdb open myfile.pdb open myfile.pdb
... then you would have models #0,1,2. To stack (REMEMBER don't rotate the view by hand yet!):
move z 35 model #1 move z 70 model #2
If it were X or Y axis instead of Z, then you would use x or y in the command instead of z. If you mess up you can use command "reset" and then start over with the move commands.
See "move" help: <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chime... https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_move.html&d=DwIFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=W_iTL8zm-aasz2PWuQlh91HFZlluzIuOYNUkSse6VCg&s=hPTcvB8jZ7V052xezzJt_VpKl3mWKQVui_IsjGjRA_g&e= >
After you are done opening/stacking, then you can rotate the view by hand. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu> wrote:
Hi, I need help to stack the crystal structures stack on top of each other. For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera? <image.png>
Thanks, Thiru
-- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Tom for your suggestions. Thanks, Thiru
On Fri, Oct 29, 2021 at 10:06 PM Tom Goddard goddard@sonic.net wrote:
Another way to make the copies is to use the Chimera sym command. For example,
sym #0 group shift,5,14 axis z
copies model #0 five times at 14 Angstrom spacing along the z axis of the model #0 coordinate system (not the view direction coordinate system).
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chimera_docs_UsersGuide_midas_sym.html&d=DwMFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=I7qtfA8N7Q5sp4JqE2oPCZchG4tZN6Z7nJw71FRlb-o&s=EcVad0ZZtSpjfQ7zIJAUgEf2-0-pYw1_07oRMovpmWE&e=
Tom
On Oct 29, 2021, at 10:16 AM, Thirumurugan Prakasam via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Thank you so much Elaine for your quick response and help. Many Thanks, Thiru
On Fri, Oct 29, 2021 at 8:40 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Thiru, If the single structure is already oriented exactly with the stack direction in Z (or X or Y) then just open multiple copies of the structure and (**without rotating the view by hand** important!!) use the "move" command to place the copies along the axis.
E.g. if the starting structure is oriented exactly so that you can stack them in Z (in/out of screen direction), and you know they are supposed to be 35 angstroms apart, then:
open myfile.pdb open myfile.pdb open myfile.pdb
... then you would have models #0,1,2. To stack (REMEMBER don't rotate the view by hand yet!):
move z 35 model #1 move z 70 model #2
If it were X or Y axis instead of Z, then you would use x or y in the command instead of z. If you mess up you can use command "reset" and then start over with the move commands.
See "move" help: < https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chime...
After you are done opening/stacking, then you can rotate the view by hand. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 2:29 AM, Thirumurugan Prakasam via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hi, I need help to stack the crystal structures stack on top of each other.
For your understanding, I have just shown the image below something like that I wanted to make. Would you please help me with how to make stacked molecular structures using chimera?
<image.png>
Thanks, Thiru
-- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwMFAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=LB3Vh9WKySIt-j9ybcMrrw&m=I7qtfA8N7Q5sp4JqE2oPCZchG4tZN6Z7nJw71FRlb-o&s=q4PBxPGDg83xCyV3ZWNc5I0yR7DbjLRGf38bD3ThkAs&e=
participants (3)
-
Elaine Meng -
Thirumurugan Prakasam -
Tom Goddard