Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list.
Hi George, As mentioned in this recent post, <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006379.html> you can do this with the Axes/Planes/Centroids tool (not PipesAndPlanks). If you define axes, one of the choices is to show an axis (cylinder) for each helix. You can specify cylinder radii or have them determined automatically, and after the axes (cylinders) are created, you can use the square color wells in the Axes/Planes/Centroids table to change their colors. Documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> 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 May 22, 2011, at 5:39 AM, George Tzotzos wrote:
Hi everybody, I'm dealing with a dimeric hexahelical bundle. I've been trying to name the individual helices (e.g. a1, a2, etc) and colour them differently to no avail. Obviously, I'm missing something. Your guidance will be greatly appreciated. Have a good weekend George
PS. Sorry if you receive this message for a second time. It was sent from a different address earlier and I'm not sure if it reached the list.
Hello all, is there any possibility how to select all atoms which belongs to the given molecule ? I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures. Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together. Thanks a lot in advance for advices ! Best wishes, Marek Maly
Hello Marek Maly, If you already have the one atom selected, you can press the up arrow key (on the keyboard) to expand the selection to whole residue, then again for the whole chain, then whole molecule model. Depending on the structure, there may be fewer layers; for example, the whole chain may be the same as the whole molecule model. To go back down, you could use the down arrow key. Also, the commands "select up" and "select down" do the same thing. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer> If you didn't have any atom selected but you know you want to select all the atoms in a particular model, you can use the select command with the model number (example: select #0), or you could open the Model Panel from the Favorites menu, and in that panel choose the model on the left side and click the "select" button on the right side. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> 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 May 23, 2011, at 7:39 AM, Marek Maly wrote:
Hello all, is there any possibility how to select all atoms which belongs to the given molecule ?
I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures.
Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together.
Thanks a lot in advance for advices ! Best wishes, Marek Maly
Dear Elaine, first of all thank you very much for your prompt response ! Unfortunately your suggestions do not cover cases when one has molecular system composed of two or more molecules loaded as one "Chimera molecular model" without possibility to recognize individual molecules using chain ID (e.g. visualization of frames from MD trajectory). For such cases only solution (in my opinion) is, some general routine which can quickly find all the atoms which could be accessed from the previously selected one through several (1,2 ....N) covalent bonds. Is something like this implemented in actual version of Chimera ? Do you see any solution for above described case ? Thank you very much in advance for this additional info, Best wishes, Marek Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hello Marek Maly, If you already have the one atom selected, you can press the up arrow key (on the keyboard) to expand the selection to whole residue, then again for the whole chain, then whole molecule model. Depending on the structure, there may be fewer layers; for example, the whole chain may be the same as the whole molecule model. To go back down, you could use the down arrow key. Also, the commands "select up" and "select down" do the same thing.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
If you didn't have any atom selected but you know you want to select all the atoms in a particular model, you can use the select command with the model number (example: select #0), or you could open the Model Panel from the Favorites menu, and in that panel choose the model on the left side and click the "select" button on the right side.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
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 May 23, 2011, at 7:39 AM, Marek Maly wrote:
Hello all, is there any possibility how to select all atoms which belongs to the given molecule ?
I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures.
Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together.
Thanks a lot in advance for advices ! Best wishes, Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 6145 (20110523) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, There is nothing exactly like that in Chimera, but here are a couple more ideas: - the "select chain(s)" function in the Model Panel has a "by connectivity" option that could allow you to get the whole bonded molecule even if the chain ID or the whole model would include more atoms than that. - you could use the "select" command with specific chain ID, residue numbers, and atom names. However, figuring out what they are is more work for you. I remember someone else on the chimera-users list asking about selection through a specified number of covalent connections, but I don't remember the details -- that person may have written some python code to do it. 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 23, 2011, at 9:43 AM, Marek Maly wrote:
Dear Elaine,
first of all thank you very much for your prompt response !
Unfortunately your suggestions do not cover cases when one has molecular system composed of two or more molecules loaded as one "Chimera molecular model" without possibility to recognize individual molecules using chain ID (e.g. visualization of frames from MD trajectory).
For such cases only solution (in my opinion) is, some general routine which can quickly find all the atoms which could be accessed from the previously selected one through several (1,2 ....N) covalent bonds. Is something like this implemented in actual version of Chimera ?
Do you see any solution for above described case ?
Thank you very much in advance for this additional info, Best wishes, Marek
Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hello Marek Maly, If you already have the one atom selected, you can press the up arrow key (on the keyboard) to expand the selection to whole residue, then again for the whole chain, then whole molecule model. Depending on the structure, there may be fewer layers; for example, the whole chain may be the same as the whole molecule model. To go back down, you could use the down arrow key. Also, the commands "select up" and "select down" do the same thing.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
If you didn't have any atom selected but you know you want to select all the atoms in a particular model, you can use the select command with the model number (example: select #0), or you could open the Model Panel from the Favorites menu, and in that panel choose the model on the left side and click the "select" button on the right side.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
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 May 23, 2011, at 7:39 AM, Marek Maly wrote:
Hello all, is there any possibility how to select all atoms which belongs to the given molecule ?
I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures.
Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together.
Thanks a lot in advance for advices ! Best wishes, Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 6145 (20110523) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elanie, thanks again very much ! Your suggestion ( the "select chain(s)" function in the Model Panel has a "by connectivity" ) was exactly what I was looking for ! Best wishes, Marek Dne Mon, 23 May 2011 19:04:56 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, There is nothing exactly like that in Chimera, but here are a couple more ideas:
- the "select chain(s)" function in the Model Panel has a "by connectivity" option that could allow you to get the whole bonded molecule even if the chain ID or the whole model would include more atoms than that.
- you could use the "select" command with specific chain ID, residue numbers, and atom names. However, figuring out what they are is more work for you.
I remember someone else on the chimera-users list asking about selection through a specified number of covalent connections, but I don't remember the details -- that person may have written some python code to do it. 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 23, 2011, at 9:43 AM, Marek Maly wrote:
Dear Elaine,
first of all thank you very much for your prompt response !
Unfortunately your suggestions do not cover cases when one has molecular system composed of two or more molecules loaded as one "Chimera molecular model" without possibility to recognize individual molecules using chain ID (e.g. visualization of frames from MD trajectory).
For such cases only solution (in my opinion) is, some general routine which can quickly find all the atoms which could be accessed from the previously selected one through several (1,2 ....N) covalent bonds. Is something like this implemented in actual version of Chimera ?
Do you see any solution for above described case ?
Thank you very much in advance for this additional info, Best wishes, Marek
Dne Mon, 23 May 2011 18:32:53 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hello Marek Maly, If you already have the one atom selected, you can press the up arrow key (on the keyboard) to expand the selection to whole residue, then again for the whole chain, then whole molecule model. Depending on the structure, there may be fewer layers; for example, the whole chain may be the same as the whole molecule model. To go back down, you could use the down arrow key. Also, the commands "select up" and "select down" do the same thing.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/select.html#newer>
If you didn't have any atom selected but you know you want to select all the atoms in a particular model, you can use the select command with the model number (example: select #0), or you could open the Model Panel from the Favorites menu, and in that panel choose the model on the left side and click the "select" button on the right side.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
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 May 23, 2011, at 7:39 AM, Marek Maly wrote:
Hello all, is there any possibility how to select all atoms which belongs to the given molecule ?
I mean something which allow me to select whole molecule to which belongs previously selected atom. Unfortunately ZONE selection is not useful here as it allow to select only atoms or residues, not whole molecular structures.
Selection by hand/mouse is not possible to use in cases when two or more molecules are very close together.
Thanks a lot in advance for advices ! Best wishes, Marek Maly
__________ Informace od ESET NOD32 Antivirus, verze databaze 6145 (20110523) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
__________ Informace od ESET NOD32 Antivirus, verze databaze 6145 (20110523) __________
Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
participants (3)
-
Elaine Meng -
George Tzotzos -
Marek Maly