Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.
Hi Oliver, You will be happy to hear that the nextgen program Chimera2 has 3D dashed pseudobonds! In the current Chimera, you can add custom pseudobonds by listing the pairs of atoms or markers in a text file and reading it in with the Pseudobond Reader tool. It also allows for labels, individual coloring, etc. See the manpage for file description and other details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....> Although there is nothing like the arrows/pointers that you mention for the 3D labels in current Chimera, you can specify 3D offsets in the label command, and (probably much friendlier) move them around in 3D with the mouse. You would just have to reassign one of the mouse buttons from its normal function to 3D label movement using the Preferences (in Favorites menu), category: Mouse. See “label-dragging” function: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse> 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 6, 2015, at 9:03 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful.
Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds.
Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues.
One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do.
Cheers, Oliver.
It does indeed Elaine, very much looking forward to trying out Chimera 2! Yes, I am aware of the pseudobond reader, and it’s great for scripting or when extensive per bond customization is required, but a single command allowing addition of a pseudo bond between two atoms would be handy in cases when one doesn’t need all the options that are available in the pseudobond reader. You know, that would actually also solve the third point - if I could create a single pseudobond easily, then I could associate dummy atoms (using ac mc) with the 3D labels and use pseudobonds as arrows. Cheers, Oli.
On Nov 6, 2015, at 12:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You will be happy to hear that the nextgen program Chimera2 has 3D dashed pseudobonds!
In the current Chimera, you can add custom pseudobonds by listing the pairs of atoms or markers in a text file and reading it in with the Pseudobond Reader tool. It also allows for labels, individual coloring, etc. See the manpage for file description and other details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....>
Although there is nothing like the arrows/pointers that you mention for the 3D labels in current Chimera, you can specify 3D offsets in the label command, and (probably much friendlier) move them around in 3D with the mouse. You would just have to reassign one of the mouse buttons from its normal function to 3D label movement using the Preferences (in Favorites menu), category: Mouse. See “label-dragging” function: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
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 6, 2015, at 9:03 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful.
Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds.
Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues.
One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do.
Cheers, Oliver.
Hi Oliver, I agree it would be very handy. What I do to fake it in Chimera now is just add a distance and then hide the distance label, for example with command: setattr p label “” sel (where sel is selected end atoms of the pseudobonds of interest, or you could give an actual atomspec that included all the end atoms of the pseudobonds of interest). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> Or you could do it using the GUI by selecting all the pseudobonds of interest with Ctrl-click, Shift-Ctrl-click and then in the Selection Inspector, setting the pseudobond label to blank. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Best, Elaine P.S. Regarding Eric’s suggestion, I personally have a hard time getting a good image out of the raytracing option, mainly that it often looks too dark and contrasty, and I find that the 3D dashes can look a lot different than in the Chimera window (e.g. very tiny short dashes), so I tend not to recommend it. However, you could take a look and see what you think. On Nov 6, 2015, at 10:06 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
It does indeed Elaine, very much looking forward to trying out Chimera 2!
Yes, I am aware of the pseudobond reader, and it’s great for scripting or when extensive per bond customization is required, but a single command allowing addition of a pseudo bond between two atoms would be handy in cases when one doesn’t need all the options that are available in the pseudobond reader.
You know, that would actually also solve the third point - if I could create a single pseudobond easily, then I could associate dummy atoms (using ac mc) with the 3D labels and use pseudobonds as arrows.
Cheers, Oli.
Thanks for the tips Elaine! Yes, I just tried the ray tracing and I agree, I *much* prefer Chimera rendering, which is also considerably faster. Oliver.
On Nov 6, 2015, at 1:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, I agree it would be very handy. What I do to fake it in Chimera now is just add a distance and then hide the distance label, for example with command:
setattr p label “” sel
(where sel is selected end atoms of the pseudobonds of interest, or you could give an actual atomspec that included all the end atoms of the pseudobonds of interest). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
Or you could do it using the GUI by selecting all the pseudobonds of interest with Ctrl-click, Shift-Ctrl-click and then in the Selection Inspector, setting the pseudobond label to blank. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
Best, Elaine
P.S. Regarding Eric’s suggestion, I personally have a hard time getting a good image out of the raytracing option, mainly that it often looks too dark and contrasty, and I find that the 3D dashes can look a lot different than in the Chimera window (e.g. very tiny short dashes), so I tend not to recommend it. However, you could take a look and see what you think.
On Nov 6, 2015, at 10:06 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
It does indeed Elaine, very much looking forward to trying out Chimera 2!
Yes, I am aware of the pseudobond reader, and it’s great for scripting or when extensive per bond customization is required, but a single command allowing addition of a pseudo bond between two atoms would be handy in cases when one doesn’t need all the options that are available in the pseudobond reader.
You know, that would actually also solve the third point - if I could create a single pseudobond easily, then I could associate dummy atoms (using ac mc) with the 3D labels and use pseudobonds as arrows.
Cheers, Oli.
That is supposed to be two double quotation marks straight from the keyboard, although they seem to have been fancified into open and close quotation marks, at least in my mail viewer. Two plain old single quotation marks would also work. Elaine On Nov 6, 2015, at 10:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p label “” sel
Hi Elaine, stupid question, but do you know how to change the pseudobond style to stick from the command line? I have tried "setattr p bond style stick” and variations thereof to no avail. Cheers, Oliver.
On Nov 6, 2015, at 1:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
That is supposed to be two double quotation marks straight from the keyboard, although they seem to have been fancified into open and close quotation marks, at least in my mail viewer. Two plain old single quotation marks would also work. Elaine
On Nov 6, 2015, at 10:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p label “” sel
Hi Oliver, You can find out the attribute names from the balloon help over the pseudobond attributes dialog opened from the Pseudobond Panel. So if I have a pseudobond selected and mouse over the “bond style” listing in the “Component PseudoBond Attributes” section of that dialog, it tells me the attribute name is “drawMode” with possible values 0,1,2 and what those values mean. So you could use setattr p drawMode 1 … to change all pseudobonds to stick, or if you just want only the ones with end atoms selected setattr p drawMode 1 sel I hope this helps, Elaine P.S. this kind of attribute name lookup is mentioned in the docs here (it’s also linked to “attribute name” in the “setattr” manpage) <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#attrn...> On Nov 6, 2015, at 12:49 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, stupid question, but do you know how to change the pseudobond style to stick from the command line? I have tried "setattr p bond style stick” and variations thereof to no avail.
Cheers, Oliver.
On Nov 6, 2015, at 1:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
That is supposed to be two double quotation marks straight from the keyboard, although they seem to have been fancified into open and close quotation marks, at least in my mail viewer. Two plain old single quotation marks would also work. Elaine
On Nov 6, 2015, at 10:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p label “” sel
Many thanks Elaine - I did do as you suggested initially, but I was typing drawmode, rather than drawMode, and Chimera attributes are case sensitive. It would be helpful I think if Chimera threw an error or exception of some kind when a user tries to use setattr with a nonexistent attribute - as it is it seems to fail silently, and it is hard to figure out sometimes whether this is because the attribute does not exist, or the wrong scope was used , e.g. p vs a etc. Cheers, Oliver.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p drawMode 1 sel
The rationale of silence was that you can use the command to create your own new attribute. But I’ve had the same thought occasionally. It depends what you’re trying to do! Best Elaine On Nov 6, 2015, at 1:21 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Many thanks Elaine - I did do as you suggested initially, but I was typing drawmode, rather than drawMode, and Chimera attributes are case sensitive.
It would be helpful I think if Chimera threw an error or exception of some kind when a user tries to use setattr with a nonexistent attribute - as it is it seems to fail silently, and it is hard to figure out sometimes whether this is because the attribute does not exist, or the wrong scope was used , e.g. p vs a etc.
Cheers, Oliver.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p drawMode 1 sel
I see the point - maybe not an error then, but a warning, something like “this attribute is not in the list of pre-defined attributes” or similar, in red text below the command line as per other chimera warnings? Oliver
On Nov 6, 2015, at 4:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
The rationale of silence was that you can use the command to create your own new attribute. But I’ve had the same thought occasionally. It depends what you’re trying to do! Best Elaine
On Nov 6, 2015, at 1:21 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Many thanks Elaine - I did do as you suggested initially, but I was typing drawmode, rather than drawMode, and Chimera attributes are case sensitive.
It would be helpful I think if Chimera threw an error or exception of some kind when a user tries to use setattr with a nonexistent attribute - as it is it seems to fail silently, and it is hard to figure out sometimes whether this is because the attribute does not exist, or the wrong scope was used , e.g. p vs a etc.
Cheers, Oliver.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p drawMode 1 sel
I’m thinking something like a “create” keyword that defaults to false. If “create” is false, then setting a non-existent attribute is an error… —Eric
On Nov 6, 2015, at 1:29 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
I see the point - maybe not an error then, but a warning, something like “this attribute is not in the list of pre-defined attributes” or similar, in red text below the command line as per other chimera warnings?
Oliver
On Nov 6, 2015, at 4:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
The rationale of silence was that you can use the command to create your own new attribute. But I’ve had the same thought occasionally. It depends what you’re trying to do! Best Elaine
On Nov 6, 2015, at 1:21 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Many thanks Elaine - I did do as you suggested initially, but I was typing drawmode, rather than drawMode, and Chimera attributes are case sensitive.
It would be helpful I think if Chimera threw an error or exception of some kind when a user tries to use setattr with a nonexistent attribute - as it is it seems to fail silently, and it is hard to figure out sometimes whether this is because the attribute does not exist, or the wrong scope was used , e.g. p vs a etc.
Cheers, Oliver.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p drawMode 1 sel
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
That would work. Incidentally, here is a mockup of the kind of thing I’m thinking about with regards to the creation of labels for stereo pairs - the labels are not quite offset correctly and so forth but I think the idea could work, for example for labeling every nth C-alpha in a stereo trace of a new fold. Cheers, Oli
On Nov 6, 2015, at 4:36 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
I’m thinking something like a “create” keyword that defaults to false. If “create” is false, then setting a non-existent attribute is an error…
—Eric
On Nov 6, 2015, at 1:29 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
I see the point - maybe not an error then, but a warning, something like “this attribute is not in the list of pre-defined attributes” or similar, in red text below the command line as per other chimera warnings?
Oliver
On Nov 6, 2015, at 4:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
The rationale of silence was that you can use the command to create your own new attribute. But I’ve had the same thought occasionally. It depends what you’re trying to do! Best Elaine
On Nov 6, 2015, at 1:21 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Many thanks Elaine - I did do as you suggested initially, but I was typing drawmode, rather than drawMode, and Chimera attributes are case sensitive.
It would be helpful I think if Chimera threw an error or exception of some kind when a user tries to use setattr with a nonexistent attribute - as it is it seems to fail silently, and it is hard to figure out sometimes whether this is because the attribute does not exist, or the wrong scope was used , e.g. p vs a etc.
Cheers, Oliver.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p drawMode 1 sel
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hmm, I just remembered that BILD format can include character strings along with 3D arrows: <plato.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>! However, there are limitations... the resulting text (while located in 3D) is flat and only horizontal in the unrotated orientation. You’d have to write out your structure(s) in transformed coordinates in the orientation for the image and then read them back in along with the BILD file with corresponding coordinates. Also, there seem to be serious bugs in this rarely (never?) used feature: - fontsize specification ignored - no compensation for supersampling so if you supersample, the text in the image is much bigger than in the Chimera window Nevertheless I attached text file ex.bild with some arrows and text as an example. Elaine attachments: BILD file, then non-supersampled image, then 3x3 supersampled image
Hi Elaine, using both of your suggestions, I have an alias that does pretty much what I originally wanted, I’m posting it here in case it is useful to anyone else: #pbond. Places black stick pseudobond between two selected atoms. #Usage: pbond alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel Cheers, Oli.
On Nov 6, 2015, at 4:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You can find out the attribute names from the balloon help over the pseudobond attributes dialog opened from the Pseudobond Panel. So if I have a pseudobond selected and mouse over the “bond style” listing in the “Component PseudoBond Attributes” section of that dialog, it tells me the attribute name is “drawMode” with possible values 0,1,2 and what those values mean.
So you could use
setattr p drawMode 1
… to change all pseudobonds to stick, or if you just want only the ones with end atoms selected
setattr p drawMode 1 sel
I hope this helps, Elaine
P.S. this kind of attribute name lookup is mentioned in the docs here (it’s also linked to “attribute name” in the “setattr” manpage) <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#attrn...>
On Nov 6, 2015, at 12:49 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Elaine, stupid question, but do you know how to change the pseudobond style to stick from the command line? I have tried "setattr p bond style stick” and variations thereof to no avail.
Cheers, Oliver.
On Nov 6, 2015, at 1:28 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
That is supposed to be two double quotation marks straight from the keyboard, although they seem to have been fancified into open and close quotation marks, at least in my mail viewer. Two plain old single quotation marks would also work. Elaine
On Nov 6, 2015, at 10:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
setattr p label “” sel
One last point of information is that if you use POV-ray rendering instead of the built-in rendering, then the pseudobonds will be 3D and dashed. —Eric
On Nov 6, 2015, at 9:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You will be happy to hear that the nextgen program Chimera2 has 3D dashed pseudobonds!
In the current Chimera, you can add custom pseudobonds by listing the pairs of atoms or markers in a text file and reading it in with the Pseudobond Reader tool. It also allows for labels, individual coloring, etc. See the manpage for file description and other details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....>
Although there is nothing like the arrows/pointers that you mention for the 3D labels in current Chimera, you can specify 3D offsets in the label command, and (probably much friendlier) move them around in 3D with the mouse. You would just have to reassign one of the mouse buttons from its normal function to 3D label movement using the Preferences (in Favorites menu), category: Mouse. See “label-dragging” function: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
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 6, 2015, at 9:03 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful.
Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds.
Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues.
One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
That I did not know - thanks Eric! Oli.
On Nov 6, 2015, at 1:09 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
One last point of information is that if you use POV-ray rendering instead of the built-in rendering, then the pseudobonds will be 3D and dashed.
—Eric
On Nov 6, 2015, at 9:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, You will be happy to hear that the nextgen program Chimera2 has 3D dashed pseudobonds!
In the current Chimera, you can add custom pseudobonds by listing the pairs of atoms or markers in a text file and reading it in with the Pseudobond Reader tool. It also allows for labels, individual coloring, etc. See the manpage for file description and other details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader....>
Although there is nothing like the arrows/pointers that you mention for the 3D labels in current Chimera, you can specify 3D offsets in the label command, and (probably much friendlier) move them around in 3D with the mouse. You would just have to reassign one of the mouse buttons from its normal function to 3D label movement using the Preferences (in Favorites menu), category: Mouse. See “label-dragging” function: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>
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 6, 2015, at 9:03 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all,
Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful.
Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds.
Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues.
One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do.
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke