Contact Maps (RRdistance Maps) questions:
Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map. I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. ALSO: Anyone know of a way to map defined attributes onto a contact map? Thanks so much! Sincerely, Nicky
Hi Nicky, Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with “findclash” but that would entail some postprocessing, see the last part of this message. (A) Coloring applies across the whole value range, not just the unmasked part… e.g. even if you have masked everything above 6 A with some solid color (let’s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can’t really see any color differences…not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I’m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html> (B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you’d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image. One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible. Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map. (C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn’t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs. (D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color. If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts” or the “findclash” command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command: findclash #0@ca test self overlap -2.3 save ~/Desktop/protein1.txt <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> … would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option “bondsep 2” to include those as well. You can use “log true” instead of (or in addition to) the “save” option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command: findclash #0@ca test self overlap -2.3 log true … sends the following stuff to the Reply Log, primarily a list of the two atoms’ identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: ------------------- Allowed overlap: -2.3 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 620 contacts atom1 atom2 overlap distance ARG 158.A CA GLY 116.A CA -0.203 3.963 LYS 189.A CA GLY 217.A CA -0.321 4.081 ARG 292.A CA THR 110.A CA -0.372 4.132 GLY 297.A CA VAL 254.A CA -0.453 4.213 THR 180.A CA LYS 147.A CA -0.460 4.220 VAL 235.A CA ASN 211.A CA -0.480 4.240 GLY 120.A CA VAL 162.A CA -0.493 4.253 LEU 196.A CA ALA 201.A CA -0.572 4.332 GLY 116.A CA VAL 162.A CA -0.663 4.423 MET 182.A CA GLY 148.A CA -0.668 4.428 THR 185.A CA GLY 217.A CA -0.697 4.457 ASN 256.A CA ASP 236.A CA -0.732 4.492 MET 182.A CA GLU 149.A CA -0.748 4.508 GLY 234.A CA ASP 212.A CA -0.794 4.554 […. many lines …] PHE 266.A CA LYS 270.A CA -2.269 6.029 ALA 155.A CA THR 159.A CA -2.274 6.034 ASN 302.A CA GLU 305.A CA -2.277 6.037 ILE 9.A CA SER 41.A CA -2.283 6.043 VAL 206.A CA ILE 204.A CA -2.285 6.045 LYS 92.A CA LEU 67.A CA -2.286 6.046 ALA 264.A CA LEU 268.A CA -2.286 6.046 LYS 270.A CA ASP 274.A CA -2.288 6.048 PRO 86.A CA ALA 105.A CA -2.289 6.049 ASN 130.A CA HIS 126.A CA -2.292 6.052 PHE 89.A CA TYR 106.A CA -2.293 6.053 ALA 251.A CA VAL 245.A CA -2.298 6.058 620 contacts --------------- So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn’t give a more convenient solution. 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 22, 2017, at 12:44 PM, Nicole Persky <persky@broadinstitute.org> wrote:
Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map.
I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms.
Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way.
ALSO: Anyone know of a way to map defined attributes onto a contact map?
Thanks so much! Sincerely, Nicky
Oh Wow! Thanks so much Elaine! That command line was super helpful. I should definitely be able to work with this. Thank you so much! One quick followup question, you mentioned in (C) that there is an export button for giving value matrices for all pairs, where is that located? I wasn't able to locate it. Again, thank you so much for your help! It totally helped me get started. Sincerely, Nicky On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nicky, Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with “findclash” but that would entail some postprocessing, see the last part of this message.
(A) Coloring applies across the whole value range, not just the unmasked part… e.g. even if you have masked everything above 6 A with some solid color (let’s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can’t really see any color differences…not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I’m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ rrdistmaps/rrdistmaps.html>
(B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you’d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image.
One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible.
Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map.
(C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn’t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs.
(D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color.
If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts” or the “findclash” command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command:
findclash #0@ca test self overlap -2.3 save ~/Desktop/protein1.txt
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
… would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option “bondsep 2” to include those as well.
You can use “log true” instead of (or in addition to) the “save” option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command:
findclash #0@ca test self overlap -2.3 log true
… sends the following stuff to the Reply Log, primarily a list of the two atoms’ identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: ------------------- Allowed overlap: -2.3 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True
620 contacts atom1 atom2 overlap distance ARG 158.A CA GLY 116.A CA -0.203 3.963 LYS 189.A CA GLY 217.A CA -0.321 4.081 ARG 292.A CA THR 110.A CA -0.372 4.132 GLY 297.A CA VAL 254.A CA -0.453 4.213 THR 180.A CA LYS 147.A CA -0.460 4.220 VAL 235.A CA ASN 211.A CA -0.480 4.240 GLY 120.A CA VAL 162.A CA -0.493 4.253 LEU 196.A CA ALA 201.A CA -0.572 4.332 GLY 116.A CA VAL 162.A CA -0.663 4.423 MET 182.A CA GLY 148.A CA -0.668 4.428 THR 185.A CA GLY 217.A CA -0.697 4.457 ASN 256.A CA ASP 236.A CA -0.732 4.492 MET 182.A CA GLU 149.A CA -0.748 4.508 GLY 234.A CA ASP 212.A CA -0.794 4.554 […. many lines …] PHE 266.A CA LYS 270.A CA -2.269 6.029 ALA 155.A CA THR 159.A CA -2.274 6.034 ASN 302.A CA GLU 305.A CA -2.277 6.037 ILE 9.A CA SER 41.A CA -2.283 6.043 VAL 206.A CA ILE 204.A CA -2.285 6.045 LYS 92.A CA LEU 67.A CA -2.286 6.046 ALA 264.A CA LEU 268.A CA -2.286 6.046 LYS 270.A CA ASP 274.A CA -2.288 6.048 PRO 86.A CA ALA 105.A CA -2.289 6.049 ASN 130.A CA HIS 126.A CA -2.292 6.052 PHE 89.A CA TYR 106.A CA -2.293 6.053 ALA 251.A CA VAL 245.A CA -2.298 6.058 620 contacts --------------- So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn’t give a more convenient solution. 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 22, 2017, at 12:44 PM, Nicole Persky <persky@broadinstitute.org> wrote:
Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map.
I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms.
Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way.
ALSO: Anyone know of a way to map defined attributes onto a contact map?
Thanks so much! Sincerely, Nicky
Hi Nicky, Great! I worried that my reply included too many words before the actual solution. :-) There is an Export button near the bottom of the RR Distance Maps dialog, as shown in the image: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html> If you don’t see this button in your Chimera, it must be an older version… according to the release notes, export was added sometime before the version 1.11 release. Either get the Chimera 1.11.2 production release or a 1.12 daily build to obtain this feature. Download: <http://www.rbvi.ucsf.edu/chimera/download.html> Best, Elaine
On Mar 23, 2017, at 2:31 PM, Nicole Persky <persky@broadinstitute.org> wrote:
Oh Wow! Thanks so much Elaine! That command line was super helpful. I should definitely be able to work with this. Thank you so much! One quick followup question, you mentioned in (C) that there is an export button for giving value matrices for all pairs, where is that located? I wasn't able to locate it. Again, thank you so much for your help! It totally helped me get started. Sincerely, Nicky
On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Nicky, Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with “findclash” but that would entail some postprocessing, see the last part of this message.
(A) Coloring applies across the whole value range, not just the unmasked part… e.g. even if you have masked everything above 6 A with some solid color (let’s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can’t really see any color differences…not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I’m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html>
(B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you’d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image.
One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible.
Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map.
(C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn’t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs.
(D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color.
If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts” or the “findclash” command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command:
findclash #0@ca test self overlap -2.3 save ~/Desktop/protein1.txt
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
… would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option “bondsep 2” to include those as well.
You can use “log true” instead of (or in addition to) the “save” option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command:
findclash #0@ca test self overlap -2.3 log true
… sends the following stuff to the Reply Log, primarily a list of the two atoms’ identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: ------------------- Allowed overlap: -2.3 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True
620 contacts atom1 atom2 overlap distance ARG 158.A CA GLY 116.A CA -0.203 3.963 LYS 189.A CA GLY 217.A CA -0.321 4.081 ARG 292.A CA THR 110.A CA -0.372 4.132 GLY 297.A CA VAL 254.A CA -0.453 4.213 THR 180.A CA LYS 147.A CA -0.460 4.220 VAL 235.A CA ASN 211.A CA -0.480 4.240 GLY 120.A CA VAL 162.A CA -0.493 4.253 LEU 196.A CA ALA 201.A CA -0.572 4.332 GLY 116.A CA VAL 162.A CA -0.663 4.423 MET 182.A CA GLY 148.A CA -0.668 4.428 THR 185.A CA GLY 217.A CA -0.697 4.457 ASN 256.A CA ASP 236.A CA -0.732 4.492 MET 182.A CA GLU 149.A CA -0.748 4.508 GLY 234.A CA ASP 212.A CA -0.794 4.554 […. many lines …] PHE 266.A CA LYS 270.A CA -2.269 6.029 ALA 155.A CA THR 159.A CA -2.274 6.034 ASN 302.A CA GLU 305.A CA -2.277 6.037 ILE 9.A CA SER 41.A CA -2.283 6.043 VAL 206.A CA ILE 204.A CA -2.285 6.045 LYS 92.A CA LEU 67.A CA -2.286 6.046 ALA 264.A CA LEU 268.A CA -2.286 6.046 LYS 270.A CA ASP 274.A CA -2.288 6.048 PRO 86.A CA ALA 105.A CA -2.289 6.049 ASN 130.A CA HIS 126.A CA -2.292 6.052 PHE 89.A CA TYR 106.A CA -2.293 6.053 ALA 251.A CA VAL 245.A CA -2.298 6.058 620 contacts --------------- So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn’t give a more convenient solution. 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 22, 2017, at 12:44 PM, Nicole Persky <persky@broadinstitute.org> wrote:
Hi All, I've just found the RRdistance Map function on Chimera and would like to compare between structures. I would like to: 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms 3- compare these two contact maps using the colors available for the whole contact map.
I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms.
Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way.
ALSO: Anyone know of a way to map defined attributes onto a contact map?
Thanks so much! Sincerely, Nicky
Hi Again! So sorry to bother you again, do you by any chance know if there is a command line similar to findclash #0@ca test self overlap -2.3 log true but instead of finding Ca-Ca distances that are less than 6 angstrom to use all of the atoms in a residue and look for other atoms/residues that come within 4 angstroms? Thanks so much!! Sincerely, Nicky On Thu, Mar 23, 2017 at 6:24 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nicky, Great! I worried that my reply included too many words before the actual solution. :-)
There is an Export button near the bottom of the RR Distance Maps dialog, as shown in the image: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ rrdistmaps/rrdistmaps.html>
If you don’t see this button in your Chimera, it must be an older version… according to the release notes, export was added sometime before the version 1.11 release. Either get the Chimera 1.11.2 production release or a 1.12 daily build to obtain this feature.
Download: <http://www.rbvi.ucsf.edu/chimera/download.html> Best, Elaine
On Mar 23, 2017, at 2:31 PM, Nicole Persky <persky@broadinstitute.org> wrote:
Oh Wow! Thanks so much Elaine! That command line was super helpful. I should definitely be able to work with this. Thank you so much! One quick followup question, you mentioned in (C) that there is an export button for giving value matrices for all pairs, where is that located? I wasn't able to locate it. Again, thank you so much for your help! It totally helped me get started. Sincerely, Nicky
On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Nicky, Unfortunately the RR Dist Maps tool is limited in just the ways you describe, so not that useful for what you want to do. A better way is with “findclash” but that would entail some postprocessing, see the last part of this message.
(A) Coloring applies across the whole value range, not just the unmasked part… e.g. even if you have masked everything above 6 A with some solid
color (let’s say dark blue) and specified showing short-long distances with a white-black gradient, white is 0 angstroms and black is longest residue-residue distance in the protein, typically >50 A. So the unmasked part of 0-6 A is only white to very light gray and you can’t really see any color differences…not that helpful if you are only interested in smaller differences between these shorter-range contacts. (I realize you understand this problem, I’m just laying it out in case anybody else is following along.) This problem is mentioned in the technical notes at the bottom of the help page for this tool: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ rrdistmaps/rrdistmaps.html> > > (B) Cannot show two RR Dist Maps dialogs at the same time. So to see two maps side by side, you’d have to either run two Chimera sessions concurrently or within a single session, do one calculation, save image, do another, save image again or compare current dialog with previously saved image. > > One way to compare the below-6-angstrom contacts only is to show side-by-side images of the distance map calculated for each protein separately with the distances >6 A masked out. However, this will only show differences of where there is a contact <6A in one protein and not the other, but because of the coloring issue, subtleties in different distances within that range will not be perceptible. > > Another way is to compare the individual distance maps (or a single map of average distance) with a difference map. However, it would be difficult to tell exactly where the unmasked parts of the distance maps would be on the difference map and only look at those latter areas of the difference map. > > (C) the Export button gives all the values of RR distance, and (if a comparison) standard deviation in RR distance and difference in RR distance. There isn’t an option to give only the residue IDs for contact pairs within some distance; it only gives value matrices for all pairs. > > (D) RR DIst Maps visualization is also focused on those 3 quantities, not attribute values. Chimera attributes are assigned to individual atoms, residues, or models, not a pair of residues. The RR distance map shows residue-pair values with color. > > If you want to use Chimera, for your purposes I think the best approach would be to use "Find Clashes/Contacts” or the “findclash” command to measure (intraprotein) CA-CA distances, and then filter to list only the pairs within 6 A. Then you could do that for the other protein as well, then compare the two lists. For example, if you had one of your proteins already open as #0, command: > > findclash #0@ca test self overlap -2.3 save ~/Desktop/protein1.txt > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> > > … would save a text file listing all CA-CA pairs with VDW surfaces within 2.3 angstroms. The distance from atom center to atom center will be larger, but the output file will also give that distance and you can delete the pairs for which it is >6 angstroms. I chose -2.3 because that should give you all the pairs within 6 angstroms and only a few with larger distances, using the VDW radii of CA atoms in structures without hydrogen atoms. You may need to use a larger distance to get them all if your protein has hydrogens, but in any case, you will be able to tell by looking at the center-center distances included in the output. The list is sorted by decreasing overlap so that longer distances willl be near the end. This example command will automatically exclude residues that are adjacent in sequence (separated by no more than 4 bonds), but you could add the findclash command option “bondsep 2” to include those as well. > > You can use “log true” instead of (or in addition to) the “save” option to show the output in the Reply Log. For example, if I have PDB 2gbp open as model #0, command: > > findclash #0@ca test self overlap -2.3 log true > > … sends the following stuff to the Reply Log, primarily a list of the two atoms’ identifiers, atom-atom VDW overlap (negative value = separation between VDW surfaces of the two atoms), and atom-atom center-to-center distance: > ------------------- > Allowed overlap: -2.3 > H-bond overlap reduction: 0.4 > Ignore contacts between atoms separated by 4 bonds or less > Detect intra-residue contacts: False > Detect intra-molecule contacts: True > > 620 contacts > atom1 atom2 overlap distance > ARG 158.A CA GLY 116.A CA -0.203 3.963 > LYS 189.A CA GLY 217.A CA -0.321 4.081 > ARG 292.A CA THR 110.A CA -0.372 4.132 > GLY 297.A CA VAL 254.A CA -0.453 4.213 > THR 180.A CA LYS 147.A CA -0.460 4.220 > VAL 235.A CA ASN 211.A CA -0.480 4.240 > GLY 120.A CA VAL 162.A CA -0.493 4.253 > LEU 196.A CA ALA 201.A CA -0.572 4.332 > GLY 116.A CA VAL 162.A CA -0.663 4.423 > MET 182.A CA GLY 148.A CA -0.668 4.428 > THR 185.A CA GLY 217.A CA -0.697 4.457 > ASN 256.A CA ASP 236.A CA -0.732 4.492 > MET 182.A CA GLU 149.A CA -0.748 4.508 > GLY 234.A CA ASP 212.A CA -0.794 4.554 > […. many lines …] > PHE 266.A CA LYS 270.A CA -2.269 6.029 > ALA 155.A CA THR 159.A CA -2.274 6.034 > ASN 302.A CA GLU 305.A CA -2.277 6.037 > ILE 9.A CA SER 41.A CA -2.283 6.043 > VAL 206.A CA ILE 204.A CA -2.285 6.045 > LYS 92.A CA LEU 67.A CA -2.286 6.046 > ALA 264.A CA LEU 268.A CA -2.286 6.046 > LYS 270.A CA ASP 274.A CA -2.288 6.048 > PRO 86.A CA ALA 105.A CA -2.289 6.049 > ASN 130.A CA HIS 126.A CA -2.292 6.052 > PHE 89.A CA TYR 106.A CA -2.293 6.053 > ALA 251.A CA VAL 245.A CA -2.298 6.058 > 620 contacts > --------------- > So, you would need to do some minor postprocessing to remove pairs with distances >6 angstroms and probably the harder part would be figuring out how to compare the two lists. Sorry I couldn’t give a more convenient solution. > 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 22, 2017, at 12:44 PM, Nicole Persky <persky@broadinstitute.org> wrote: > > > > Hi All, > > I've just found the RRdistance Map function on Chimera and > > would like to compare between structures. > > I would like to: > > 1- make contact map of protein 1 to protein 1 with a cutoff of about 6 angstroms > > 2- make a contact map of protein 2 to protein 2 with a cutoff of about 6 angstroms > > 3- compare these two contact maps using the colors available for the whole contact map. > > > > I can only seem to compare the ENTIRE contact map of protein 1 to the ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6 angstroms. > > > > Alternatively, if anyone knows of a way to export residue lists of contacts from the contact map site I could just compare them that way. > > > > ALSO: > > Anyone know of a way to map defined attributes onto a contact map? > > > > Thanks so much! > > Sincerely, > > Nicky >
Hi Nicky, You could specify all protein atoms instead of just the CA atoms. #0 means model 0, @ca means atoms named CA, so "#0@ca” means CA atoms in model 0... “protein” means all protein atoms, or to limit it to only model 0 (if you had multiple models open) “#0&protein”. E.g. findclash #0&protein test self overlap -0.3 log true (which by default excludes atom pairs 4 or fewer bonds apart, or in the same residue, but these can be adjusted with command options) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I think I’d determined empirically when formulating my previous reply that overlap -2.3 gives the pairs within 6 angstroms, so I changed it in the example above to overlap -0.3 (VDW surfaces up to 0.3 angstroms apart) to give pairs within 4 angstroms. You could doublecheck using overlap -0.35 or -.4 to see if that gives you any more contacts within 4 angstroms if you want. Again, the last column in the output is the distance between atom centers. However, you’d have to parse the extremely copious output to find which residues' atoms are in contact with which. Another possibility is to use a separate command for each residue to get a separate list, but then making the command script is tedious. E.g. findclash #0:1 test #0&protein overlap -2.3 log true findclash #0:2 test #0&protein overlap -2.3 log true [etc.] A third possibility (beyond my skill set) is to use python to loop through the residues and generate essentially those commands. This page has some tips on python scripting of Chimera commands if you want to try that. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> 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 May 3, 2017, at 11:43 AM, Nicole Persky <persky@broadinstitute.org> wrote:
Hi Again! So sorry to bother you again, do you by any chance know if there is a command line similar to
findclash #0@ca test self overlap -2.3 log true
but instead of finding Ca-Ca distances that are less than 6 angstrom to use all of the atoms in a residue and look for other atoms/residues that come within 4 angstroms?
Thanks so much!! Sincerely, Nicky
Hi Nicky, Upon further examination of my testing results, at this shorter cutoff distance (less negative overlap) you should also set the H-bonding allowance to zero so as not to miss any pairs within 4 angstroms. So whether you use the single-command shotgun approach or a separate command for each residue, include “hb 0”, e.g. findclash #0:1 test #0&protein overlap -0.3 hb 0 log true At this shorter cutoff, a large proportion of the contact pairs will be H-bonding. The H-bond allowance is normally used to avoid identifying H-bonding pairs as a “clash” because they can come closer together as a favorable interaction than they can to other atoms with which they are not H-bonding. However, you are using the command to identify contacts in general, not only unfavorable clashes. The default criteria (in the FInd Clashes/Contacts GUI) for identifying contacts are overlap -0.4 and hb allowance 0. Best, Elaine
On May 3, 2017, at 1:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nicky, You could specify all protein atoms instead of just the CA atoms. #0 means model 0, @ca means atoms named CA, so "#0@ca” means CA atoms in model 0... “protein” means all protein atoms, or to limit it to only model 0 (if you had multiple models open) “#0&protein”. E.g.
findclash #0&protein test self overlap -0.3 log true
(which by default excludes atom pairs 4 or fewer bonds apart, or in the same residue, but these can be adjusted with command options) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
I think I’d determined empirically when formulating my previous reply that overlap -2.3 gives the pairs within 6 angstroms, so I changed it in the example above to overlap -0.3 (VDW surfaces up to 0.3 angstroms apart) to give pairs within 4 angstroms. You could doublecheck using overlap -0.35 or -.4 to see if that gives you any more contacts within 4 angstroms if you want. Again, the last column in the output is the distance between atom centers.
However, you’d have to parse the extremely copious output to find which residues' atoms are in contact with which.
Another possibility is to use a separate command for each residue to get a separate list, but then making the command script is tedious. E.g.
findclash #0:1 test #0&protein overlap -2.3 log true findclash #0:2 test #0&protein overlap -2.3 log true [etc.]
A third possibility (beyond my skill set) is to use python to loop through the residues and generate essentially those commands. This page has some tips on python scripting of Chimera commands if you want to try that. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
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 May 3, 2017, at 11:43 AM, Nicole Persky <persky@broadinstitute.org> wrote:
Hi Again! So sorry to bother you again, do you by any chance know if there is a command line similar to
findclash #0@ca test self overlap -2.3 log true
but instead of finding Ca-Ca distances that are less than 6 angstrom to use all of the atoms in a residue and look for other atoms/residues that come within 4 angstroms?
Thanks so much!! Sincerely, Nicky
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