Query regarding solvent accessible surface area of protein
Hi all, I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants? Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)? Kindly help me sir. Any other suggestions will be highly grateful. Thanks and regards Aditya.
Hi Aditya, If you display the molecular surface, the atoms and residues are automatically assigned their surface area values as the attributes named areaSAS (solvent-accessible surface area) and areaSES (solvent-excluded surface area). You get both values even though the surface displayed in Chimera is the SES. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces> You can see histograms of the per-atom or per-residue attribute values and show them with colors using the Render by Attribute tool (under Tools... Structure Analysis). You can also write out the values into a file using the File menu of that tool. Another way to do the coloring is with the command "rangecolor" <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render> It is not necessary to calculate an average. You can do it by showing a surface at each step, then saving the values or coloring to show them as described above. However, there are a few issues: (1) Bubbles inside the structure also have surface area. If you do not want to include these bubbles in the surface area calculations, use the Preferences (under Favorites menu), New Surface category, turn off "show disjoint surfaces" and click Save. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces> (2) Sometimes surface calculation has numerical failures, as discussed in this previous post and links theirein: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005689.html> (3) In MD Movie, you could use a per-model script to show the values with coloring. There is the rangecolor command as mentioned above, but no Chimera command for saving the attributes to a file. However, a python script for this purpose has been posted to the mailing list: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003531.html> (You would need to download "attachment.bin" from that page, which is a misnomer, as it is a python file in plain text. You could just paste the plain text as a Python script in the MD Movie per-frame script dialog.) 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 Oct 30, 2010, at 2:54 AM, Aditya Padhi wrote:
Hi all, I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants? Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)? Kindly help me sir. Any other suggestions will be highly grateful. Thanks and regards Aditya.
Thanks alot Elaine. I will try it up. If any problem still resides I will convey to you. Aditya. On Sun, Oct 31, 2010 at 12:00 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Aditya, If you display the molecular surface, the atoms and residues are automatically assigned their surface area values as the attributes named areaSAS (solvent-accessible surface area) and areaSES (solvent-excluded surface area). You get both values even though the surface displayed in Chimera is the SES. < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
You can see histograms of the per-atom or per-residue attribute values and show them with colors using the Render by Attribute tool (under Tools... Structure Analysis). You can also write out the values into a file using the File menu of that tool. Another way to do the coloring is with the command "rangecolor" < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
It is not necessary to calculate an average. You can do it by showing a surface at each step, then saving the values or coloring to show them as described above. However, there are a few issues:
(1) Bubbles inside the structure also have surface area. If you do not want to include these bubbles in the surface area calculations, use the Preferences (under Favorites menu), New Surface category, turn off "show disjoint surfaces" and click Save. < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfa...
(2) Sometimes surface calculation has numerical failures, as discussed in this previous post and links theirein: < http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005689.html
(3) In MD Movie, you could use a per-model script to show the values with coloring. There is the rangecolor command as mentioned above, but no Chimera command for saving the attributes to a file. However, a python script for this purpose has been posted to the mailing list: < http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003531.html
(You would need to download "attachment.bin" from that page, which is a misnomer, as it is a python file in plain text. You could just paste the plain text as a Python script in the MD Movie per-frame script dialog.)
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 Oct 30, 2010, at 2:54 AM, Aditya Padhi wrote:
Hi all, I have carried out molecular dynamics simulation of my protein of interest using AMBER 10. I need to calculate the "solvent accessible surface area (SASA)" of 6 amino acid residues in wild type and certain mutants. My query is regarding can I use chimera for the same. Is it possible to both visualize and get analytical data for the differences in solvent accessible surface area for wild type and mutants? Another query is, in chimera can I get the SASA for each and every trajectories or I have to generate average PDB (Is it correct)? Kindly help me sir. Any other suggestions will be highly grateful. Thanks and regards Aditya.
-- ******************************************** Aditya Kumar Padhi Ph.D Scholar School of Biological Sciences (SBS) Indian Institute of Technology Delhi New Delhi-110016, India Contact no:+91-9711539958 ********************************************
Hi Elaine, I have tried the tools that you have mentioned in detail but I am getting the .crd and .parm7 file in my MD simulation. So, when I am trying to open these, there is no file formats of these in Chimera. Can you suggest any solution for it? How can Chimera can read these files. Kindly help me as I have no idea. Thank you. Aditya.
Hi Aditya, To read in trajectory formats, you need to start MD Movie (choose Tools... MD/Ensemble Analysis... MD Movie). That gives a file browser for opening trajectory formats. As you said, these formats are not in the main "File... Open" dialog. It is because reading in a trajectory usually requires more than one file and sometimes additional user-specified parameters. MD Movie documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> Best, 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 Oct 31, 2010, at 10:12 PM, Aditya Padhi wrote:
Hi Elaine, I have tried the tools that you have mentioned in detail but I am getting the .crd and .parm7 file in my MD simulation. So, when I am trying to open these, there is no file formats of these in Chimera. Can you suggest any solution for it? How can Chimera can read these files. Kindly help me as I have no idea. Thank you. Aditya.
Dear Elaine, Thanks alot. I hope I can able to solve my problem now. I will try it up. Best of luck, Aditya. On Mon, Nov 1, 2010 at 9:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Aditya, To read in trajectory formats, you need to start MD Movie (choose Tools... MD/Ensemble Analysis... MD Movie). That gives a file browser for opening trajectory formats.
As you said, these formats are not in the main "File... Open" dialog. It is because reading in a trajectory usually requires more than one file and sometimes additional user-specified parameters.
MD Movie documentation: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
Best, 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 Oct 31, 2010, at 10:12 PM, Aditya Padhi wrote:
Hi Elaine, I have tried the tools that you have mentioned in detail but I am
getting the .crd and .parm7 file in my MD simulation. So, when I am trying to open these, there is no file formats of these in Chimera. Can you suggest any solution for it? How can Chimera can read these files.
Kindly help me as I have no idea. Thank you. Aditya.
-- ******************************************** Aditya Kumar Padhi Ph.D Scholar School of Biological Sciences (SBS) Indian Institute of Technology Delhi New Delhi-110016, India Contact no:+91-9711539958 ********************************************
Hi Elaine, As per your guidance, I am now able to calculate SASA for the trajectories of AMBER MD simulation of my protein. But I have 1200 frames and I need to calculate SASA for each and every frame. As u told, I can calculate by fixing each frame. But it seems to be very time taking and not favorable. Is there any way so that I can calculate SASA as an average among all the frames or most favorable would be to get SASA for all 1200 frames automatically rather going for individual ones. If you have any such script/relevant idea , kindly help me in this regard. Thanking you. Aditya.
Hi Aditya, There is no way to get the average without calculating it for each step first. Or, you could calculate average coordinates (with some other program, Chimera does not have this function now) and then calculate the SASA for those coordinates, but it would be different than the average of SASA over all the steps. The way to do anything automatically for a whole trajectory is to use the "per-frame scripting" in the MD Movie tool, as described in #3 of my earlier reply. That would not make it any faster, however, but it would automatically use the python script to save a file with SASA information at each step. See that earlier message for how to get and use the script. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005693.html> 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 2, 2010, at 8:43 PM, Aditya Padhi wrote:
Hi Elaine, As per your guidance, I am now able to calculate SASA for the trajectories of AMBER MD simulation of my protein. But I have 1200 frames and I need to calculate SASA for each and every frame. As u told, I can calculate by fixing each frame. But it seems to be very time taking and not favorable. Is there any way so that I can calculate SASA as an average among all the frames or most favorable would be to get SASA for all 1200 frames automatically rather going for individual ones. If you have any such script/relevant idea , kindly help me in this regard.
Thanking you. Aditya.
Hi Elaine, Thank you so much for answering all my doubts. I am now able to calculate SASA for all frames by modifying the code posted on the site. Thanks alot. Aditya On Wed, Nov 3, 2010 at 9:02 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Aditya, There is no way to get the average without calculating it for each step first. Or, you could calculate average coordinates (with some other program, Chimera does not have this function now) and then calculate the SASA for those coordinates, but it would be different than the average of SASA over all the steps.
The way to do anything automatically for a whole trajectory is to use the "per-frame scripting" in the MD Movie tool, as described in #3 of my earlier reply. That would not make it any faster, however, but it would automatically use the python script to save a file with SASA information at each step. See that earlier message for how to get and use the script. < http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-October/005693.html
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 2, 2010, at 8:43 PM, Aditya Padhi wrote:
Hi Elaine, As per your guidance, I am now able to calculate SASA for the trajectories of AMBER MD simulation of my protein. But I have 1200 frames and I need to calculate SASA for each and every frame. As u told, I can calculate by fixing each frame. But it seems to be very time taking and not favorable. Is there any way so that I can calculate SASA as an average among all the frames or most favorable would be to get SASA for all 1200 frames automatically rather going for individual ones. If you have any such script/relevant idea , kindly help me in this regard.
Thanking you. Aditya.
participants (2)
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Aditya Padhi -
Elaine Meng