Interaction interface between two residues and measure buriedArea
Dear all, I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection. However I have a couple of questions about it: 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value? 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful? Any other feedback on the kind of measurement I am trying to do is more than welcome. Thanks a lot, Massimo
Dear chimera users, Is it possible to join the DNA bases? I could not find it in manual. best regards Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
On 3/11/15 1:33 PM, Urszula Uciechowska wrote:
Dear chimera users,
Is it possible to join the DNA bases? I could not find it in manual. What do you actually mean?
best regards Urszula
University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland
----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear chimera users, I was wondering if its possible to mutate DNA base pair (G-C etc.)in chimera using swapa command? Thank you in advance for any suggestions Urszula Uciechowska
Dear chimera users,
Is it possible to join the DNA bases? I could not find it in manual.
best regards Urszula
University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland
----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
Dear Urszula, The command for mutating a DNA base is “swapna” - you would have to use it twice, one time for each member of the pair. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html> For example, if your base pair was between residue 2 in chain A named DG and residue 23 in chain B named DC, to change them into DA-DT it would be something like: swapna A :2.A preserve true swapna T :23.B preserve true Or you could omit “preserve true” … see the manual page linked above for details. The pairing geometry might not be that good after the swap, but you could rotate the bonds manually if you wanted (see Build Structure tool, Adjust Torsions section): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> To get the heteroatom color-coding on the new bases (red oxygen and blue nitrogen) you could use command “color byhet” 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 Mar 11, 2015, at 7:25 AM, Urszula Uciechowska <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
I was wondering if its possible to mutate DNA base pair (G-C etc.)in chimera using swapa command?
Thank you in advance for any suggestions Urszula Uciechowska
Dear Urszula, If you just wanted to add a bond, you can use the “bond” command, for example “bond sel” if you have selected the two atoms, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> …or the Build Structure tool (in menu under Tools… Structure Editing), the Adjust Bonds section <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> 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 Mar 11, 2015, at 5:33 AM, Urszula Uciechowska <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users, Is it possible to join the DNA bases? I could not find it in manual. best regards Urszula
Dear chimera users, Is it possible to join the DNA bases? I could not find it in manual. I would like to join the Guanine with Thymine. I saw in the Build Structure/Join Models form other bond. However is not working for me in this case. best regards Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/
Dear Urszula, Build Structure/Join Models is only for when the two parts are in two different models (if you opened those parts from two separate files, for example). If the bases are in the same model already, you would instead use Build Structure/Adjust Bonds, or the "bond" command, as suggested in my previous reply: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-March/010766.html> Or, if you are building starting from nothing, use Build Structure/Start Structure. It can build helical DNA and/or RNA. 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 Mar 12, 2015, at 7:47 AM, "Urszula Uciechowska" <urszula.uciechowska@biotech.ug.edu.pl> wrote:
Dear chimera users,
Is it possible to join the DNA bases? I could not find it in manual. I would like to join the Guanine with Thymine. I saw in the Build Structure/Join Models form other bond. However is not working for me in this case.
best regards Urszula
Hi Massimo, (1) I am not aware of any clear-cut rules of which to use for what purposes. SES is where the probe sphere (crudely representing water) touches, SAS is where the probe sphere center can go. There have been some efforts to derive an energy value per unit area of hydrophobic surface buried, so if you were using that kind of multiplier you would of course use the measure for which it was developed. Otherwise, you could just think about the geometric definitions and see if one or the other fits what you are trying to measure. There are some pictures on the web illustrating the difference, e.g. Fig 3 here: <http://ieeexplore.ieee.org/ieee_pilot/articles/06/ttg2009061391/figures.html> (2) The fallback warning is something about certain calculations failing so that only a single component (e.g. outer envelope and not interior bubbles) is calculated, but it would still show up as a warning in the Reply Log, so I wouldn’t worry about the specifics. I believe it is rare, but sometimes there are errors or visible singularities in the surface that occur without a warning going to the Reply Log. I don’t think we can do or say much about this. In Chimera, molecular surfaces are created with embedded software from the MSMS package. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surface...> One issue is that you are stretching the functionality beyond its intended purposes. Measure buriedarea was mainly intended for looking at intermolecular or interdomain interfaces, not for measuring the area of single residues packing against each other within a protein. When you are using it on these smaller subparts, possibly with more tortuous shapes, I imagine there would be a greater chance of errors. 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 Mar 11, 2015, at 5:24 AM, ms <devicerandom@gmail.com> wrote:
Dear all, I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
However I have a couple of questions about it:
1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
Any other feedback on the kind of measurement I am trying to do is more than welcome. Thanks a lot, Massimo
Hi Massimo, I think buried solvent accessible area (SAS) is most often used when buried areas are reported. Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation, and if you see a case of that could you send me a Chimera session that demostrates it? Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct. I think buried SES can give a negative value in weird cases because the toroidal surface patches created by the probe sphere rolling between the two sets of atoms could be large (e.g. the buried area between two spheres whose surfaces are separate by a bit less than the probe radius). Tom
On Mar 11, 2015, at 5:24 AM, ms <devicerandom@gmail.com> wrote:
Dear all,
I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
However I have a couple of questions about it:
1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
Any other feedback on the kind of measurement I am trying to do is more than welcome.
Thanks a lot, Massimo _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Thanks for your reply. On 11/03/15 23:18, Tom Goddard wrote:
I think buried solvent accessible area (SAS) is most often used when buried areas are reported.
OK, thanks. Any justification in the literature for that, just to be on the safe side?
Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation,
OK.
and if you see a case of that could you send me a Chimera session that demostrates it?
I will do it tomorrow.
Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct.
Understood. If so, is there any sanity check I can do to see if a calculation has more or less chances of being meaningful? thanks, Massimo -- Massimo Sandal, Ph.D. http://devicerandom.org
Hi Massimo, I think the reason buried solvent accessible area is usually reported is because it is probably better correlated with the solvation energy, how much energy is related to the water / protein interface, then solvent excluded area. This makes some sense to me because the SAS surface is where the “probe” sphere representing a water molecule is centered so it roughly says how many spheres or water molecules you can pack against the protein. This is all just my guess. The only case where I have read literature on this topic is studies that try to identify biologically meaningful protein-protein interfaces in X-ray crystal structures by measuring buried areas. A sanity check on your buried area values (after checking that they are positive) is try changing the probe radius by a small bit and see if you get just a small change in buried area. This will cause different surfaces to be computed but should result in a small area change if the calculation is correct. The default probe radius is 1.4 Angstroms, so try “measure buried #0 #1 probe 1.45”. Tom
On Mar 11, 2015, at 3:48 PM, ms wrote:
Hi Tom,
Thanks for your reply.
On 11/03/15 23:18, Tom Goddard wrote:
I think buried solvent accessible area (SAS) is most often used when buried areas are reported.
OK, thanks. Any justification in the literature for that, just to be on the safe side?
Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation,
OK.
and if you see a case of that could you send me a Chimera session that demostrates it?
I will do it tomorrow.
Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct.
Understood. If so, is there any sanity check I can do to see if a calculation has more or less chances of being meaningful?
thanks, Massimo
-- Massimo Sandal, Ph.D. http://devicerandom.org
Hi all, Sorry for my late reply and many thanks, your comments really helped. Elaine Meng, your links really helped a lot. Two things: 1) I actually re-checked my dataset and it seems I have no negative SAS -only negative SES values sometimes. 2) Can someone confirm the SAS values are in units of angstrom squared? thanks, Massimo 2015-03-11 23:18 GMT+01:00 Tom Goddard <goddard@sonic.net>:
Hi Massimo,
I think buried solvent accessible area (SAS) is most often used when buried areas are reported. Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation, and if you see a case of that could you send me a Chimera session that demostrates it? Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct. I think buried SES can give a negative value in weird cases because the toroidal surface patches created by the probe sphere rolling between the two sets of atoms could be large (e.g. the buried area between two spheres whose surfaces are separate by a bit less than the probe radius).
Tom
On Mar 11, 2015, at 5:24 AM, ms <devicerandom@gmail.com> wrote:
Dear all,
I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection.
However I have a couple of questions about it:
1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value?
2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful?
Any other feedback on the kind of measurement I am trying to do is more than welcome.
Thanks a lot, Massimo _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Massimo, You're welcome! Yes, the SES and SAS values are in angstroms squared, given atomic coordinates in angstroms. Elaine On Mar 19, 2015, at 9:20 AM, massimo sandal <devicerandom@gmail.com> wrote:
Hi all,
Sorry for my late reply and many thanks, your comments really helped. Elaine Meng, your links really helped a lot. Two things:
1) I actually re-checked my dataset and it seems I have no negative SAS -only negative SES values sometimes. 2) Can someone confirm the SAS values are in units of angstrom squared?
thanks, Massimo
2015-03-19 17:40 GMT+01:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Massimo, You're welcome! Yes, the SES and SAS values are in angstroms squared, given atomic coordinates in angstroms.
Awesome, thanks a lot. M.
participants (5)
-
Elaine Meng -
massimo sandal -
ms
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Tom Goddard -
Urszula Uciechowska