Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean
Hi Phil, If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command pwd <cxcmd:pwd>Current working directory is: /Users/goddard/Desktop To change the directory ChimeraX is currently in use the cd command cd ~/Documents <cxcmd:cd /Users/goddard/Documents>Current working directory is: /Users/goddard/Documents Lastly you can give a full path to the output file in your command alphafold contacts /B to /C output /Users/goddard/contact_pae.txt or alphafold contacts /B to /C output ~/contact_pae.txt where "~" means your user account home directory. Tom
On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone-
I used the following command to obtain a file with the contacts between two chains:
alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located.
Thanks for any help.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi Tom, Thanks. Found it on the desktop. A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file. And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort? Phil McClean ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file Hi Phil, If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command pwd Current working directory is: /Users/goddard/Desktop To change the directory ChimeraX is currently in use the cd command cd ~/Documents Current working directory is: /Users/goddard/Documents Lastly you can give a full path to the output file in your command alphafold contacts /B to /C output /Users/goddard/contact_pae.txt or alphafold contacts /B to /C output ~/contact_pae.txt where "~" means your user account home directory. Tom On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Philip, The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms. https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html> Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms). measure buriedarea /A with /B > Buried area between /A and /B = 484.71 To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface. Tom
On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Hi Tom,
Thanks. Found it on the desktop.
A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file.
And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort?
Phil McClean From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Phil,
If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command
pwd <applewebdata://91B35BD3-59DE-4B72-AC13-CF0B634EFF2F>Current working directory is: /Users/goddard/Desktop
To change the directory ChimeraX is currently in use the cd command
cd ~/Documents <applewebdata://91B35BD3-59DE-4B72-AC13-CF0B634EFF2F>Current working directory is: /Users/goddard/Documents
Lastly you can give a full path to the output file in your command
alphafold contacts /B to /C output /Users/goddard/contact_pae.txt
or
alphafold contacts /B to /C output ~/contact_pae.txt
where "~" means your user account home directory.
Tom
On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Everyone-
I used the following command to obtain a file with the contacts between two chains:
alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located.
Thanks for any help.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Thanks again Tom. The buried surface area was 1535 angstroms squared. Is that a "good" value? Also is that value calculated across the two proteins? There appears to be specific regions of the two proteins that are in contact. Is it possible to measure the buried area just for those two regions. A note on these two proteins. Both have specific structured regions (that are interacting) but also have disordered regions elsewhere that account for >50% of the proteins distances. I have looked at those regions using IUPred3. Phil ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 12:23 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file Hi Philip, The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms. https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms). measure buriedarea /A with /B
Buried area between /A and /B = 484.71
To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface. Tom On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean@ndsu.edu<mailto:phillip.mcclean@ndsu.edu>> wrote: Hi Tom, Thanks. Found it on the desktop. A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file. And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort? Phil McClean ________________________________ From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu<mailto:phillip.mcclean@ndsu.edu>> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] alphafold contacts output file Hi Phil, If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command pwd Current working directory is: /Users/goddard/Desktop To change the directory ChimeraX is currently in use the cd command cd ~/Documents Current working directory is: /Users/goddard/Documents Lastly you can give a full path to the output file in your command alphafold contacts /B to /C output /Users/goddard/contact_pae.txt or alphafold contacts /B to /C output ~/contact_pae.txt where "~" means your user account home directory. Tom On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Phil, I think for crystal packing contacts the minimum contact area for judging a biological interface was about 400 Angstroms. But this is all a matter of research judgement and I am not expert on assessing protein-protein interfaces. You can specify exactly the atoms you want to measure the buried area between in the command, for example, measure buriedarea /A:40-50 with /B:30-40 will measure between residue numbers 40-50 in chain A and residues numbers 30-40 in chain B. Another approach is to just delete parts of the proteins before doing the measurement delete /A:1-39 /B:1-29 Our ChimeraX mailing list is primarily for discussing how to the software works, not for advise on how analyze data in your research -- since we are software developers and not experts in your areas of research. Tom
On Oct 4, 2022, at 10:33 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Thanks again Tom.
The buried surface area was 1535 angstroms squared. Is that a "good" value? Also is that value calculated across the two proteins? There appears to be specific regions of the two proteins that are in contact. Is it possible to measure the buried area just for those two regions.
A note on these two proteins. Both have specific structured regions (that are interacting) but also have disordered regions elsewhere that account for >50% of the proteins distances. I have looked at those regions using IUPred3.
Phil From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 12:23 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Philip,
The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms.
https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html>
Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms).
measure buriedarea /A with /B
Buried area between /A and /B = 484.71
To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface.
Tom
On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean@ndsu.edu <mailto:phillip.mcclean@ndsu.edu>> wrote:
Hi Tom,
Thanks. Found it on the desktop.
A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file.
And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort?
Phil McClean From: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu <mailto:phillip.mcclean@ndsu.edu>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Phil,
If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command
pwd <applewebdata://D2B3CCE2-BDC9-46C4-99C2-F12E83214708>Current working directory is: /Users/goddard/Desktop
To change the directory ChimeraX is currently in use the cd command
cd ~/Documents <applewebdata://D2B3CCE2-BDC9-46C4-99C2-F12E83214708>Current working directory is: /Users/goddard/Documents
Lastly you can give a full path to the output file in your command
alphafold contacts /B to /C output /Users/goddard/contact_pae.txt
or
alphafold contacts /B to /C output ~/contact_pae.txt
where "~" means your user account home directory.
Tom
On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Everyone-
I used the following command to obtain a file with the contacts between two chains:
alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located.
Thanks for any help.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Yes, in agreement with Tom, how to interpret the modeling in the context of your specific research project depends on your own scientific judgment and knowledge of the proteins of interest, and what you are able to glean from the literature. I'm not an authority on protein-protein interfaces either, but thought I should mention that there have been a number of papers that survey or discuss the properties of known interfaces. Here are a couple of older examples, but you could probably find dozens more in Pubmed: Characterization of protein-protein interfaces. Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V. Protein J. 2008 Jan;27(1):59-70. doi: 10.1007/s10930-007-9108-x. PMID: 17851740 Analysis of protein-protein interaction sites using surface patches. Jones S, Thornton JM. J Mol Biol. 1997 Sep 12;272(1):121-32. doi: 10.1006/jmbi.1997.1234. PMID: 9299342 Keep in mind that it may be quite different for multidomain proteins vs. single domain, membrane proteins vs. soluble, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 4, 2022, at 10:44 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Phil,
I think for crystal packing contacts the minimum contact area for judging a biological interface was about 400 Angstroms. But this is all a matter of research judgement and I am not expert on assessing protein-protein interfaces.
You can specify exactly the atoms you want to measure the buried area between in the command, for example,
measure buriedarea /A:40-50 with /B:30-40
will measure between residue numbers 40-50 in chain A and residues numbers 30-40 in chain B. Another approach is to just delete parts of the proteins before doing the measurement
delete /A:1-39 /B:1-29
Our ChimeraX mailing list is primarily for discussing how to the software works, not for advise on how analyze data in your research -- since we are software developers and not experts in your areas of research.
Tom
On Oct 4, 2022, at 10:33 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Thanks again Tom.
The buried surface area was 1535 angstroms squared. Is that a "good" value? Also is that value calculated across the two proteins? There appears to be specific regions of the two proteins that are in contact. Is it possible to measure the buried area just for those two regions.
A note on these two proteins. Both have specific structured regions (that are interacting) but also have disordered regions elsewhere that account for >50% of the proteins distances. I have looked at those regions using IUPred3.
Phil From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 12:23 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Philip,
The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms.
https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html
Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms).
measure buriedarea /A with /B
Buried area between /A and /B = 484.71
To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface.
Tom
On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Hi Tom,
Thanks. Found it on the desktop.
A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file.
And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort?
Phil McClean From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Phil,
If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command
pwd Current working directory is: /Users/goddard/Desktop
To change the directory ChimeraX is currently in use the cd command
cd ~/Documents Current working directory is: /Users/goddard/Documents
Lastly you can give a full path to the output file in your command
alphafold contacts /B to /C output /Users/goddard/contact_pae.txt
or
alphafold contacts /B to /C output ~/contact_pae.txt
where "~" means your user account home directory.
Tom
On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone-
I used the following command to obtain a file with the contacts between two chains:
alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located.
Thanks for any help.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Thanks for the advice. I will start with the paper you mentioned. Phil ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, October 4, 2022 1:04 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file Yes, in agreement with Tom, how to interpret the modeling in the context of your specific research project depends on your own scientific judgment and knowledge of the proteins of interest, and what you are able to glean from the literature. I'm not an authority on protein-protein interfaces either, but thought I should mention that there have been a number of papers that survey or discuss the properties of known interfaces. Here are a couple of older examples, but you could probably find dozens more in Pubmed: Characterization of protein-protein interfaces. Yan C, Wu F, Jernigan RL, Dobbs D, Honavar V. Protein J. 2008 Jan;27(1):59-70. doi: 10.1007/s10930-007-9108-x. PMID: 17851740 Analysis of protein-protein interaction sites using surface patches. Jones S, Thornton JM. J Mol Biol. 1997 Sep 12;272(1):121-32. doi: 10.1006/jmbi.1997.1234. PMID: 9299342 Keep in mind that it may be quite different for multidomain proteins vs. single domain, membrane proteins vs. soluble, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 4, 2022, at 10:44 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Phil,
I think for crystal packing contacts the minimum contact area for judging a biological interface was about 400 Angstroms. But this is all a matter of research judgement and I am not expert on assessing protein-protein interfaces.
You can specify exactly the atoms you want to measure the buried area between in the command, for example,
measure buriedarea /A:40-50 with /B:30-40
will measure between residue numbers 40-50 in chain A and residues numbers 30-40 in chain B. Another approach is to just delete parts of the proteins before doing the measurement
delete /A:1-39 /B:1-29
Our ChimeraX mailing list is primarily for discussing how to the software works, not for advise on how analyze data in your research -- since we are software developers and not experts in your areas of research.
Tom
On Oct 4, 2022, at 10:33 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Thanks again Tom.
The buried surface area was 1535 angstroms squared. Is that a "good" value? Also is that value calculated across the two proteins? There appears to be specific regions of the two proteins that are in contact. Is it possible to measure the buried area just for those two regions.
A note on these two proteins. Both have specific structured regions (that are interacting) but also have disordered regions elsewhere that account for >50% of the proteins distances. I have looked at those regions using IUPred3.
Phil From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 12:23 PM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Philip,
The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues. But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms.
https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html
Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other. The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms).
measure buriedarea /A with /B
Buried area between /A and /B = 484.71
To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface.
Tom
On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:
Hi Tom,
Thanks. Found it on the desktop.
A follow-up Chimerax question (hopefully it shouldn't be a different thread). Is it possible to list the atoms that are in close contact in the output file.
And a general newbie question. You choose a distance of 3 as the default cutoff. In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins. The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold multimer along with its functional beta helix-loop-helix protein partner. If I see changes in distances might that suggest changes in interaction capacity of any sort?
Phil McClean From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 4, 2022 11:57 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] alphafold contacts output file
Hi Phil,
If you start ChimeraX by clicking an icon then it puts files on your desktop. If you start it from a shell (for example on Linux) it will put the files in the directory you started in. To find the directory ChimeraX is currently in use the ChimeraX pwd command
pwd Current working directory is: /Users/goddard/Desktop
To change the directory ChimeraX is currently in use the cd command
cd ~/Documents Current working directory is: /Users/goddard/Documents
Lastly you can give a full path to the output file in your command
alphafold contacts /B to /C output /Users/goddard/contact_pae.txt
or
alphafold contacts /B to /C output ~/contact_pae.txt
where "~" means your user account home directory.
Tom
On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone-
I used the following command to obtain a file with the contacts between two chains:
alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located.
Thanks for any help.
Phil McClean _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
McClean, Phillip -
Tom Goddard