Updated tutorial membrane-only system.

[ojeda-e]

After fixing #70 , the tutorial of the membrane-only system needed some updates. This version should close #74.

Changes in this PR:

• [x] Updated interpretation of mean curvature plots.
• [x] Changed units in H and K plots (from nm to Å).
• [x] Added ticks to color bars in curvature plots.

I'm tagging @lilyminium and @orbeckst who usually review my PRs, but more reviewers are welcome. :) Thanks.

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[ojeda-e]

@lilyminium @orbeckst would you please help me with a quick review here? Thanks :)

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hmacdope commented on 2021-09-29T04:29:19Z ----------------------------------------------------------------

Perhaps you can do this with a numpy or scipy function and get it to spit out 1% at the end. Something like np.std(axis=0)

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hmacdope commented on 2021-09-29T04:29:20Z ----------------------------------------------------------------

You can also do an equality check on the residues, should be illustrative for a user to see ==

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hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As noted above I would directly test for equality here. I would also remove the word "new" from variable names and be more specific eg leafletfinder_leaflets

ojeda-e commented on 2021-09-29T21:58:01Z ----------------------------------------------------------------

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

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hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As with other notebook a quick intro to what the nbins parameter is would be helpful.

ojeda-e commented on 2021-09-29T21:58:18Z ----------------------------------------------------------------

Yes, thanks for this, it's a very good point.

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

perhaps "curv_upper_leaflet_f47" -> "curv_upper_leaflet_f_4_and_7" as I thought it was 47.

ojeda-e commented on 2021-09-29T22:01:18Z ----------------------------------------------------------------

Thanks, will update.

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

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hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

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hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

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hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

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ojeda-e commented 2 years ago

Thanks, will update.

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ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:20Z ----------------------------------------------------------------

You can also do an equality check on the residues, should be illustrative for a user to see ==

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hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As noted above I would directly test for equality here. I would also remove the word "new" from variable names and be more specific eg leafletfinder_leaflets

ojeda-e commented on 2021-09-29T21:58:01Z ----------------------------------------------------------------

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As with other notebook a quick intro to what the nbins parameter is would be helpful.

ojeda-e commented on 2021-09-29T21:58:18Z ----------------------------------------------------------------

Yes, thanks for this, it's a very good point.

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

perhaps "curv_upper_leaflet_f47" -> "curv_upper_leaflet_f_4_and_7" as I thought it was 47.

ojeda-e commented on 2021-09-29T22:01:18Z ----------------------------------------------------------------

Thanks, will update.

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

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ojeda-e commented 2 years ago

Thanks, will update.

---

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ojeda-e commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As noted above I would directly test for equality here. I would also remove the word "new" from variable names and be more specific eg leafletfinder_leaflets

ojeda-e commented on 2021-09-29T21:58:01Z ----------------------------------------------------------------

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As with other notebook a quick intro to what the nbins parameter is would be helpful.

ojeda-e commented on 2021-09-29T21:58:18Z ----------------------------------------------------------------

Yes, thanks for this, it's a very good point.

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

perhaps "curv_upper_leaflet_f47" -> "curv_upper_leaflet_f_4_and_7" as I thought it was 47.

ojeda-e commented on 2021-09-29T22:01:18Z ----------------------------------------------------------------

Thanks, will update.

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Thanks, will update.

---

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ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:21Z ----------------------------------------------------------------

As with other notebook a quick intro to what the nbins parameter is would be helpful.

ojeda-e commented on 2021-09-29T21:58:18Z ----------------------------------------------------------------

Yes, thanks for this, it's a very good point.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

perhaps "curv_upper_leaflet_f47" -> "curv_upper_leaflet_f_4_and_7" as I thought it was 47.

ojeda-e commented on 2021-09-29T22:01:18Z ----------------------------------------------------------------

Thanks, will update.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Thanks, will update.

---

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ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

perhaps "curv_upper_leaflet_f47" -> "curv_upper_leaflet_f_4_and_7" as I thought it was 47.

ojeda-e commented on 2021-09-29T22:01:18Z ----------------------------------------------------------------

Thanks, will update.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Thanks, will update.

---

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ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:22Z ----------------------------------------------------------------

What is each matrix element representing.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Thanks, will update.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:23Z ----------------------------------------------------------------

Add detail about units for each curvature here.

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

View / edit / reply to this conversation on ReviewNB

hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

Thanks, will update.

---

View entire conversation on ReviewNB

ojeda-e commented 2 years ago

added

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hmacdope commented on 2021-09-29T04:29:24Z ----------------------------------------------------------------

Line #5.        MembraneCurvature is a tool to calculate membrane curvature.

Same here for general docstirng.

_ojeda-e commented on 2021-09-29T22:31:26Z_ ----------------------------------------------------------------

added

review-notebook-app[bot] commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

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ojeda-e commented 2 years ago

Thanks, will update.

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ojeda-e commented 2 years ago

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hmacdope commented on 2021-09-29T04:29:25Z ----------------------------------------------------------------

As with other PR is there a paper linking gauss curvature and elasticity?

ojeda-e commented 2 years ago

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

hmacdope commented 2 years ago

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

ojeda-e commented 2 years ago

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

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ojeda-e commented 2 years ago

Yes, thanks for this, it's a very good point.

---

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ojeda-e commented 2 years ago

Thanks, will update.

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ojeda-e commented 2 years ago

added

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[ojeda-e]

Thanks @hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst or @lilyminium to confirm I can merge.

[hmacdope]

I like that review. Perhaps linking to it as an introduction to curvature is a good idea. :)

On Wed, Sep 29, 2021 at 3:18 PM Estefania Barreto-Ojeda < @.***> wrote:

Thanks @hmacdope https://github.com/hmacdope! I added the suggested changes. A link to further reading of membrane curvature is still missing. There is not much material out there, but maybe linking this https://www.researchgate.net/figure/Measures-of-surface-curvature-a-The-principal-curvatures-are-calculated-from-the_fig6_321165318 may work? Not sure that's what you had in mind, though.

Will wait for @orbeckst https://github.com/orbeckst or @lilyminium https://github.com/lilyminium to confirm I can merge.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/MDAnalysis/membrane-curvature/pull/78#issuecomment-929844091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF3RHCYLS3T6CH3ZV4Z3XATUEKOR5ANCNFSM5EPZXWTQ .

-- Hugo MacDermott-Opeskin PhD Candidate, RSC ANU Email: @. @.>

[ojeda-e]

Thanks, I changed the name of the variables but left the equality test only for the previous comment. My intention here is more to read the elements of each leaflet. Hope this works too. :)

---

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[ojeda-e]

Yes, thanks for this, it's a very good point.

---

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[ojeda-e]

Thanks, will update.

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[ojeda-e]

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