On the adding of the dynamics effect on the static structure
Dear Chimera Users! I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure? Thanks so much for any suggestions! James
Hi James, (A) If you have only one conformation of the structure, Chimera does not include any simple way of producing additional conformations that show its structural fluctuations. To do that, people often use some kind of “normal mode analysis," for which there are several web servers, e.g. elNemo <http://www.sciences.univ-nantes.fr/elnemo/> ANM web server <http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi> WEBnma <http://apps.cbu.uib.no/webnma/home> … and probably many others. I don’t have experience using them, I just know of their existence and that they produce various different kinds of output and show results in different ways. In Chimera, one possibility is to just color the structure and/or use “worm” fatness to show its B-factor. Of course, for that you would need to have a crystal structure that includes B-factor values. This type of coloring and showing worms is done with Render by Attribute (in menu under Tools… Structure Analysis), and for coloring ribbons and showing worms (which are special ribbons), you would need to use the residue attribute “average bfactor” (average value from the atoms in the residue). Here is an example image of PDB 2gbp with average bfactor per residue shown with ribbon colors and worms: (B) if you have two conformations of the structure, you can calculate a morph trajectory in Chimera with Morph Conformations (in menu under Tools… Structure Comparison). Essentially it interpolates and makes additional structures that are intermediates between the two input structures. Then if you save the trajectory as multiple PDB files (or a single multi-model PDB file) you can superimpose the starting structures with one or more of the intermediate structures, as I did when making the figure shown in the Morph Conformations manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> (if it is just a trajectory in the MD Movie tool, you can only see one conformation at a time, that’s why you’d have to save as PDB and reopen to see multiple conformations together) See also general discussion of how to superimpose structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> There is also a “ViewMotions” web server that will take the two structures as input, calculate intermediate structures, and show them all together as a rainbow. It creates a Chimera session, so you can open the results in Chimera and change the view etc. as you like before saving an image. <http://viewmotions.bc.edu/> (C) if you already have multiple conformations of the structure, such as from a NMR ensemble multi-model PDB file, then there are a few different possibilities: i) just superimpose them or a subset of them (see also Ensemble Cluster for identifying representatives if there are too many to show all at once) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html> The MD Movie tool also includes a similar clustering function to identify representatives from a trajectory. ii) just show one representative but (similar to the B-factor stuff above) color and/or worm it to show the structural variability from the whole set of conformations. You would do this by superimposing all of the conformations, then associating all of them with a single sequence, hiding all of the conformations except one, and then using the per-residue RMSD values along the sequence to color/worm that structure. The basic steps are outlined in the previous post linked below, except now you have the choice of other RMSDs over more atoms, not just the CA-RMSD. Note, however, that RMSDs including sidechain atoms are not automatically symmetry-corrected… even though some phenylalanine ring could look exactly superimposed, for example, if the atoms with the same names are on opposite sides of the ring, Chimera is not smart enough to calculate the lowest RMSD given the chemical equivalences (it uses the names only). <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.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 Nov 19, 2016, at 1:22 PM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure?
Thanks so much for any suggestions!
James
Hi Elaine and thank you so much for the interesting ideas! (B) should works for me, however I will also play with NMR ensemble of another protein and write here whether (C) is also works for my case. Regarding (A): I like visualisation in worm-style at least from the visual perspective, however it will be great idea to include in future Chimera realize some built-in Normal mode tool to i) calculate Hessian for specified structure ii) obtain normal modes via it diagonalisation and finally iii) deform initial structure along chosen sub-set of normal modes to obtain it alternative conformers which iv) after superimposition against reference might be interesting concept to produce perception of NMR ensemble. James 2016-11-21 21:41 GMT+04:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, (A) If you have only one conformation of the structure, Chimera does not include any simple way of producing additional conformations that show its structural fluctuations. To do that, people often use some kind of “normal mode analysis," for which there are several web servers, e.g.
elNemo <http://www.sciences.univ-nantes.fr/elnemo/> ANM web server <http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi> WEBnma <http://apps.cbu.uib.no/webnma/home>
… and probably many others. I don’t have experience using them, I just know of their existence and that they produce various different kinds of output and show results in different ways.
In Chimera, one possibility is to just color the structure and/or use “worm” fatness to show its B-factor. Of course, for that you would need to have a crystal structure that includes B-factor values. This type of coloring and showing worms is done with Render by Attribute (in menu under Tools… Structure Analysis), and for coloring ribbons and showing worms (which are special ribbons), you would need to use the residue attribute “average bfactor” (average value from the atoms in the residue). Here is an example image of PDB 2gbp with average bfactor per residue shown with ribbon colors and worms:
(B) if you have two conformations of the structure, you can calculate a morph trajectory in Chimera with Morph Conformations (in menu under Tools… Structure Comparison). Essentially it interpolates and makes additional structures that are intermediates between the two input structures. Then if you save the trajectory as multiple PDB files (or a single multi-model PDB file) you can superimpose the starting structures with one or more of the intermediate structures, as I did when making the figure shown in the Morph Conformations manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html> (if it is just a trajectory in the MD Movie tool, you can only see one conformation at a time, that’s why you’d have to save as PDB and reopen to see multiple conformations together)
See also general discussion of how to superimpose structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
There is also a “ViewMotions” web server that will take the two structures as input, calculate intermediate structures, and show them all together as a rainbow. It creates a Chimera session, so you can open the results in Chimera and change the view etc. as you like before saving an image. <http://viewmotions.bc.edu/>
(C) if you already have multiple conformations of the structure, such as from a NMR ensemble multi-model PDB file, then there are a few different possibilities: i) just superimpose them or a subset of them (see also Ensemble Cluster for identifying representatives if there are too many to show all at once) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblecluster/ensemblecluster.html> The MD Movie tool also includes a similar clustering function to identify representatives from a trajectory.
ii) just show one representative but (similar to the B-factor stuff above) color and/or worm it to show the structural variability from the whole set of conformations. You would do this by superimposing all of the conformations, then associating all of them with a single sequence, hiding all of the conformations except one, and then using the per-residue RMSD values along the sequence to color/worm that structure. The basic steps are outlined in the previous post linked below, except now you have the choice of other RMSDs over more atoms, not just the CA-RMSD. Note, however, that RMSDs including sidechain atoms are not automatically symmetry-corrected… even though some phenylalanine ring could look exactly superimposed, for example, if the atoms with the same names are on opposite sides of the ring, Chimera is not smart enough to calculate the lowest RMSD given the chemical equivalences (it uses the names only).
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.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 Nov 19, 2016, at 1:22 PM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure?
Thanks so much for any suggestions!
James
update - on screen is the result which I have composed using morphing (B): [image: Встроенное изображение 1] my question - is it possible to select one of the conformer from the ensemble (assuming that all are merged within one model) end changes its popersties regardless of others? E.g I want to select "the middle" state, making it visual state as solid (call it reference) and set transparency to others states, eventually producing impression of the deformation of the reference state (shown as solied) where rest conformers (shown as transparent) indicate the collective directions of it. James 2016-11-25 0:22 GMT+04:00 James Starlight <jmsstarlight@gmail.com>:
Hi Elaine and thank you so much for the interesting ideas! (B) should works for me, however I will also play with NMR ensemble of another protein and write here whether (C) is also works for my case.
Regarding (A): I like visualisation in worm-style at least from the visual perspective, however it will be great idea to include in future Chimera realize some built-in Normal mode tool to i) calculate Hessian for specified structure ii) obtain normal modes via it diagonalisation and finally iii) deform initial structure along chosen sub-set of normal modes to obtain it alternative conformers which iv) after superimposition against reference might be interesting concept to produce perception of NMR ensemble.
James
2016-11-21 21:41 GMT+04:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi James, (A) If you have only one conformation of the structure, Chimera does not include any simple way of producing additional conformations that show its structural fluctuations. To do that, people often use some kind of “normal mode analysis," for which there are several web servers, e.g.
elNemo <http://www.sciences.univ-nantes.fr/elnemo/> ANM web server <http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi> WEBnma <http://apps.cbu.uib.no/webnma/home>
… and probably many others. I don’t have experience using them, I just know of their existence and that they produce various different kinds of output and show results in different ways.
In Chimera, one possibility is to just color the structure and/or use “worm” fatness to show its B-factor. Of course, for that you would need to have a crystal structure that includes B-factor values. This type of coloring and showing worms is done with Render by Attribute (in menu under Tools… Structure Analysis), and for coloring ribbons and showing worms (which are special ribbons), you would need to use the residue attribute “average bfactor” (average value from the atoms in the residue). Here is an example image of PDB 2gbp with average bfactor per residue shown with ribbon colors and worms:
(B) if you have two conformations of the structure, you can calculate a morph trajectory in Chimera with Morph Conformations (in menu under Tools… Structure Comparison). Essentially it interpolates and makes additional structures that are intermediates between the two input structures. Then if you save the trajectory as multiple PDB files (or a single multi-model PDB file) you can superimpose the starting structures with one or more of the intermediate structures, as I did when making the figure shown in the Morph Conformations manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ morph/morph.html> (if it is just a trajectory in the MD Movie tool, you can only see one conformation at a time, that’s why you’d have to save as PDB and reopen to see multiple conformations together)
See also general discussion of how to superimpose structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
There is also a “ViewMotions” web server that will take the two structures as input, calculate intermediate structures, and show them all together as a rainbow. It creates a Chimera session, so you can open the results in Chimera and change the view etc. as you like before saving an image. <http://viewmotions.bc.edu/>
(C) if you already have multiple conformations of the structure, such as from a NMR ensemble multi-model PDB file, then there are a few different possibilities: i) just superimpose them or a subset of them (see also Ensemble Cluster for identifying representatives if there are too many to show all at once) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/e nsemblecluster/ensemblecluster.html> The MD Movie tool also includes a similar clustering function to identify representatives from a trajectory.
ii) just show one representative but (similar to the B-factor stuff above) color and/or worm it to show the structural variability from the whole set of conformations. You would do this by superimposing all of the conformations, then associating all of them with a single sequence, hiding all of the conformations except one, and then using the per-residue RMSD values along the sequence to color/worm that structure. The basic steps are outlined in the previous post linked below, except now you have the choice of other RMSDs over more atoms, not just the CA-RMSD. Note, however, that RMSDs including sidechain atoms are not automatically symmetry-corrected… even though some phenylalanine ring could look exactly superimposed, for example, if the atoms with the same names are on opposite sides of the ring, Chimera is not smart enough to calculate the lowest RMSD given the chemical equivalences (it uses the names only).
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.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 Nov 19, 2016, at 1:22 PM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure?
Thanks so much for any suggestions!
James
Hi James, Depends what you mean by “merged within one model.” Normally something like an NMR ensemble is in a multi-model PDB file, and when you read it in, the individual members get “submodel" numbers like #0.1, 0.2, 0.3 …. etc. and you can either specify them individually in the command line with #0.1 etc. or select them individually, such as from the Model Panel (open from Favorites menu). Just look in the Model Panel. You may need to “ungroup” to see #0 really contains #0.1, 0.2, 0.3 etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> That is the most sensible way to “merge”, as a multi-model PDB file. If you actually combined them into a single model so that they didn’t get different submodel numbers, you would need to give them different residue number ranges and/or chain IDs. Either/both of those things could be used to specify them separately in the command line, see atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Also, the Select menu allows selecting by chain ID. Elaine
On Nov 25, 2016, at 11:48 AM, James Starlight <jmsstarlight@gmail.com> wrote:
update - on screen is the result which I have composed using morphing (B): <ensemble_1.png> my question - is it possible to select one of the conformer from the ensemble (assuming that all are merged within one model) end changes its popersties regardless of others? E.g I want to select "the middle" state, making it visual state as solid (call it reference) and set transparency to others states, eventually producing impression of the deformation of the reference state (shown as solied) where rest conformers (shown as transparent) indicate the collective directions of it.
James
2016-11-25 0:22 GMT+04:00 James Starlight <jmsstarlight@gmail.com>: Hi Elaine and thank you so much for the interesting ideas! (B) should works for me, however I will also play with NMR ensemble of another protein and write here whether (C) is also works for my case.
Regarding (A): I like visualisation in worm-style at least from the visual perspective, however it will be great idea to include in future Chimera realize some built-in Normal mode tool to i) calculate Hessian for specified structure ii) obtain normal modes via it diagonalisation and finally iii) deform initial structure along chosen sub-set of normal modes to obtain it alternative conformers which iv) after superimposition against reference might be interesting concept to produce perception of NMR ensemble.
James
2016-11-21 21:41 GMT+04:00 Elaine Meng <meng@cgl.ucsf.edu>: Hi James, (A) If you have only one conformation of the structure, Chimera does not include any simple way of producing additional conformations that show its structural fluctuations. To do that, people often use some kind of “normal mode analysis," for which there are several web servers, e.g.
elNemo <http://www.sciences.univ-nantes.fr/elnemo/> ANM web server <http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi> WEBnma <http://apps.cbu.uib.no/webnma/home>
… and probably many others. I don’t have experience using them, I just know of their existence and that they produce various different kinds of output and show results in different ways.
In Chimera, one possibility is to just color the structure and/or use “worm” fatness to show its B-factor. Of course, for that you would need to have a crystal structure that includes B-factor values. This type of coloring and showing worms is done with Render by Attribute (in menu under Tools… Structure Analysis), and for coloring ribbons and showing worms (which are special ribbons), you would need to use the residue attribute “average bfactor” (average value from the atoms in the residue). Here is an example image of PDB 2gbp with average bfactor per residue shown with ribbon colors and worms: <2gbp-bfactor.png>
(B) if you have two conformations of the structure, you can calculate a morph trajectory in Chimera with Morph Conformations (in menu under Tools… Structure Comparison). Essentially it interpolates and makes additional structures that are intermediates between the two input structures. Then if you save the trajectory as multiple PDB files (or a single multi-model PDB file) you can superimpose the starting structures with one or more of the intermediate structures, as I did when making the figure shown in the Morph Conformations manual page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> (if it is just a trajectory in the MD Movie tool, you can only see one conformation at a time, that’s why you’d have to save as PDB and reopen to see multiple conformations together)
See also general discussion of how to superimpose structures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
There is also a “ViewMotions” web server that will take the two structures as input, calculate intermediate structures, and show them all together as a rainbow. It creates a Chimera session, so you can open the results in Chimera and change the view etc. as you like before saving an image. <http://viewmotions.bc.edu/>
(C) if you already have multiple conformations of the structure, such as from a NMR ensemble multi-model PDB file, then there are a few different possibilities: i) just superimpose them or a subset of them (see also Ensemble Cluster for identifying representatives if there are too many to show all at once) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html> The MD Movie tool also includes a similar clustering function to identify representatives from a trajectory.
ii) just show one representative but (similar to the B-factor stuff above) color and/or worm it to show the structural variability from the whole set of conformations. You would do this by superimposing all of the conformations, then associating all of them with a single sequence, hiding all of the conformations except one, and then using the per-residue RMSD values along the sequence to color/worm that structure. The basic steps are outlined in the previous post linked below, except now you have the choice of other RMSDs over more atoms, not just the CA-RMSD. Note, however, that RMSDs including sidechain atoms are not automatically symmetry-corrected… even though some phenylalanine ring could look exactly superimposed, for example, if the atoms with the same names are on opposite sides of the ring, Chimera is not smart enough to calculate the lowest RMSD given the chemical equivalences (it uses the names only).
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009712.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 Nov 19, 2016, at 1:22 PM, James Starlight <jmsstarlight@gmail.com> wrote:
Dear Chimera Users!
I am interesting whether it possible to add some impression of the dynamics to some static elements of the pdb? Assuming that I am working with the visualisation of static x-ray structure and would like via some vizualisation trick to add some element of the conformational dynamism (like what can be obtained from the md trajectory or nmr ensemble) to the selected fragment of the structure (e.g loops or alpha-helix) eventually making impression of the several conformers superimposed on the structure?
Thanks so much for any suggestions!
James
participants (2)
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Elaine Meng -
James Starlight