Drawing a set of spheres describing a pocket in a protein
Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busin.....
Hi Saverio, There are several different ways you could draw spheres of specified radius in Chimera. However, note that transparency may not be rendered correctly when there are multiple transparent objects. With regard to transparency, see also command "set singleLayer" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer> Here are some different ways to draw spheres in Chimera: (1) make a BILD format file (filename.bld) which is a simple text format for making geometric shapes, described here <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> then open the file in Chimera. Lines in a BILD file for describing a sphere shape include x,y,z coordinates of the center and the radius. You can also include lines for defining color and transparency, but note that transparency of BILD objects may not be rendered correctly. (2) use command "shape sphere" several times, once for each sphere, for example: shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3 <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere> (3) make a PDB file where the spheres are fake atoms (If this is to show spheres for docking with the DOCK program, if I remember correctly, DOCK includes another program "showsphere" to do this so you don't have to do it manually, if I remember correctly.) Since you aren't showing real atoms, the first 6 characters of the lines should be "HETATM" instead of "ATOM " to prevent drawing bonds. Open the PDB file in Chimera, and then make sure to display the resulting model in the sphere representation to show the full VDW radii. For example, if opened as model 0: display #0 rep sphere #0 transparency 50 #0 However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> ...or see (3a) below. (3a) instead make a PQR file, which is similar to a PDB file except that it includes an "R" column for the radius. This format is described at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQR> If you use this PQR approach, you could just put zeroes in the "Q" (charge) column of the PQR file. For method 3 or 3a (fake atoms), an alternative to transparency is showing VDW dot surfaces instead. You can display a dot surface with "vdw" and adjust the dot density with "vdwdensity": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdw.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdensity.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2022, at 1:09 AM, svle--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio
On May 26, 2022, at 12:48 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
[...] make a PDB file where the spheres are fake atoms [...]
However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
Correction: a better/easier way than "setattr" to change atomic VDW radii in Chimera is with the "vdwdefine" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> Best, Elaine
If Elaine did not give you enough options, here is one more. You can write an XML Chimera marker file (suffix .cmm) that specifies sphere positions, radii and colors as described in the Chimera documentation that can be read in directly. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/v... <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles> Tom <marker_set name="my spheres"> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217" r="0" g="1" b="1"/> ... </marker_set>
On May 26, 2022, at 2:16 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
On May 26, 2022, at 12:48 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
[...] make a PDB file where the spheres are fake atoms [...]
However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
Correction: a better/easier way than "setattr" to change atomic VDW radii in Chimera is with the "vdwdefine" command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>
Best, Elaine _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thanks for the suggestions. For the method (2) "(2) use command "shape sphere" several times, once for each sphere, for example: shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3" as I need to use it many time I obtain many models. Each set of spheres are to give an idea of the shape of a pocket and I need to to disp and ~disp these sets. Using Model Panel I can select and group a set of models into one model and many submodels and then use modeldisplay to disp and ~disp each set of spheres ( right ? ). There is a way to group some models into one model and submodels from the command line? Thanks. Saverio Il 26.05.2022 21:48 Elaine Meng ha scritto:
Hi Saverio, There are several different ways you could draw spheres of specified radius in Chimera. However, note that transparency may not be rendered correctly when there are multiple transparent objects. With regard to transparency, see also command "set singleLayer"
Here are some different ways to draw spheres in Chimera:
(1) make a BILD format file (filename.bld) which is a simple text format for making geometric shapes, described here
then open the file in Chimera. Lines in a BILD file for describing a sphere shape include x,y,z coordinates of the center and the radius. You can also include lines for defining color and transparency, but note that transparency of BILD objects may not be rendered correctly.
(2) use command "shape sphere" several times, once for each sphere, for example:
shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3
(3) make a PDB file where the spheres are fake atoms (If this is to show spheres for docking with the DOCK program, if I remember correctly, DOCK includes another program "showsphere" to do this so you don't have to do it manually, if I remember correctly.) Since you aren't showing real atoms, the first 6 characters of the lines should be "HETATM" instead of "ATOM " to prevent drawing bonds. Open the PDB file in Chimera, and then make sure to display the resulting model in the sphere representation to show the full VDW radii. For example, if opened as model 0: display #0 rep sphere #0 transparency 50 #0
However, this would not include your radius values, which would need to be set separately, e.g. with "setattr":
...or see (3a) below. (3a) instead make a PQR file, which is similar to a PDB file except that it includes an "R" column for the radius. This format is described at the bottom of this page:
If you use this PQR approach, you could just put zeroes in the "Q" (charge) column of the PQR file.
For method 3 or 3a (fake atoms), an alternative to transparency is showing VDW dot surfaces instead. You can display a dot surface with "vdw" and adjust the dot density with "vdwdensity":
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry
University of California, San Francisco
On May 26, 2022, at 1:09
AM, svle--- via Chimera-users wrote: Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busin.....
Hi Saverio, there is no need to group/ungroup the models, you can just specify multiple models in the various commands, e.g. as comma-separated lists (but no spaces) that can include ranges: ~modeldisp #3,5-25 modeldisp #6-32 Or if you would rather just give a name to the multiple models one time and then use it in other commands, something like alias myspheres1 #3,5-25 alias myspheres2 #26-32 ~modeldisp myspheres1 modeldisp myspheres2 <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2022, at 12:07 AM, saverio via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thanks for the suggestions. For the method (2) "(2) use command "shape sphere" several times, once for each sphere, for example:
shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3"
as I need to use it many time I obtain many models. Each set of spheres are to give an idea of the shape of a pocket and I need to to disp and ~disp these sets. Using Model Panel I can select and group a set of models into one model and many submodels and then use modeldisplay to disp and ~disp each set of spheres ( right ? ). There is a way to group some models into one model and submodels from the command line? Thanks. Saverio Il 26.05.2022 21:48 Elaine Meng ha scritto:
Hi Saverio, There are several different ways you could draw spheres of specified radius in Chimera. However, note that transparency may not be rendered correctly when there are multiple transparent objects. With regard to transparency, see also command "set singleLayer" < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer
Here are some different ways to draw spheres in Chimera:
(1) make a BILD format file (filename.bld) which is a simple text format for making geometric shapes, described here < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html
then open the file in Chimera. Lines in a BILD file for describing a sphere shape include x,y,z coordinates of the center and the radius. You can also include lines for defining color and transparency, but note that transparency of BILD objects may not be rendered correctly.
(2) use command "shape sphere" several times, once for each sphere, for example:
shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere
(3) make a PDB file where the spheres are fake atoms (If this is to show spheres for docking with the DOCK program, if I remember correctly, DOCK includes another program "showsphere" to do this so you don't have to do it manually, if I remember correctly.) Since you aren't showing real atoms, the first 6 characters of the lines should be "HETATM" instead of "ATOM " to prevent drawing bonds. Open the PDB file in Chimera, and then make sure to display the resulting model in the sphere representation to show the full VDW radii. For example, if opened as model 0: display #0 rep sphere #0 transparency 50 #0
However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html
...or see (3a) below. (3a) instead make a PQR file, which is similar to a PDB file except that it includes an "R" column for the radius. This format is described at the bottom of this page: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQ...
If you use this PQR approach, you could just put zeroes in the "Q" (charge) column of the PQR file.
For method 3 or 3a (fake atoms), an alternative to transparency is showing VDW dot surfaces instead. You can display a dot surface with "vdw" and adjust the dot density with "vdwdensity": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdw.html
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdensity.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2022, at 1:09 AM, svle--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio
Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busin...
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Ok. Many thanks. Saverio Il 30.05.2022 18:00 Elaine Meng ha scritto:
Hi Saverio, there is no need to group/ungroup the models, you can just specify multiple models in the various commands, e.g. as comma-separated lists (but no spaces) that can include ranges:
~modeldisp #3,5-25
modeldisp #6-32
Or if you would rather just give a name to the multiple models one time and then use it in other commands, something like
alias myspheres1 #3,5-25 alias myspheres2 #26-32 ~modeldisp myspheres1 modeldisp myspheres2
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 30, 2022, at 12:07 AM, saverio via Chimera-users wrote: Thanks for the suggestions. For the method (2) "(2) use command "shape sphere" several times, once for each sphere, for example: shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3" as I need to use it many time I obtain many models. Each set of spheres are to give an idea of the shape of a pocket and I need to to disp and ~disp these sets. Using Model Panel I can select and group a set of models into one model and many submodels and then use modeldisplay to disp and ~disp each set of spheres ( right ? ). There is a way to group some models into one model and submodels from the command line? Thanks. Saverio Il 26.05.2022 21:48 Elaine Meng ha scritto:
Hi Saverio, There are several different ways you could draw spheres of specified radius in Chimera. However, note that transparency may not be rendered correctly when there are multiple transparent objects. With regard to transparency, see also command "set singleLayer" < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#singlelayer [2] Here are some different ways to draw spheres in Chimera: (1) make a BILD format file (filename.bld) which is a simple text format for making geometric shapes, described here < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html [3]then open the file in Chimera. Lines in a BILD file for describing a sphere shape include x,y,z coordinates of the center and the radius. You can also include lines for defining color and transparency, but note that transparency of BILD objects may not be rendered correctly. (2) use command "shape sphere" several times, once for each sphere, for example: shape sphere radius 1.4 center 0,5,5 color 1,0.25,0.8,0.3 < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere [4] (3) make a PDB file where the spheres are fake atoms (If this is to show spheres for docking with the DOCK program, if I remember correctly, DOCK includes another program "showsphere" to do this so you don't have to do it manually, if I remember correctly.) Since you aren't showing real atoms, the first 6 characters of the lines should be "HETATM" instead of "ATOM " to prevent drawing bonds. Open the PDB file in Chimera, and then make sure to display the resulting model in the sphere representation to show the full VDW radii. For example, if opened as model 0: display #0 rep sphere #0 transparency 50 #0 However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html [5] ...or see (3a) below. (3a) instead make a PQR file, which is similar to a PDB file except that it includes an "R" column for the radius. This format is described at the bottom of this page: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#PQ... [6] If you use this PQR approach, you could just put zeroes in the "Q" (charge) column of the PQR file. For method 3 or 3a (fake atoms), an alternative to transparency is showing VDW dot surfaces instead. You can display a dot surface with "vdw" and adjust the dot density with "vdwdensity": < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdw.html [7]< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdensity.html [8]I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2022, at 1:09 AM, svle--- via Chimera-users wrote: Hi all, I would like to draw a set of colored and transparent spheres that describes a pocket knowing the coordinates of the center and the radius for each of these shapes. For example: radius: 0.7777, y: 18.333, x: -23.99, z: -64.765 and so on. Can you suggest me a way to do this. Thanks. Saverio Voucher MISE per P.IVA e PMI: fino a 2500EUR per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busin... [10] _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu [11] Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users [12]
Voucher MISE per P.IVA e PMI: fino a 2500€ per la Banda Ultralarga. https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busin.....
participants (3)
-
Elaine Meng -
svle＠tiscali.it -
Tom Goddard