On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina@gmail.com> wrote:
Hi Elaine, I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. Thanks! Juliana
Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.) One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances. You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection. In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command: name frozen blah sel See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like contacts #1/A:55 restrict blah overlap -1000 log true The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers: 1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...] The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance. The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Of course, if you only want to use alpha-carbons instead of all atoms of all residues, you could define the atom sets that way, e.g. name frozen blah #1/A:100-200@ca contacts #1/A:55@ca restrict blah overlap -1000 log true Also, I was using named selection because you asked about it. You do not need to use a named selection. Instead you can just specify both atom sets in "contacts," e.g. contacts #1/A:55@ca restrict #1/A:100-200@ca overlap -1000 log true Elaine
On Jun 15, 2021, at 10:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina@gmail.com> wrote:
Hi Elaine, I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. Thanks! Juliana
Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.)
One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances.
You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection.
In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command:
name frozen blah sel
See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like
contacts #1/A:55 restrict blah overlap -1000 log true
The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers:
1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...]
The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance.
The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you Elaine ! Sorry I didn't cc the list before. I think I need to be a little bit more specific. I am doing the following: open 1ycr name frozen pocket1 (#1/B:19 & sidechain) @<6 & (#1/A & sidechain) and I want to list the distances between the atoms of sel1 and sel2 that are lower than 6A I could use contacts, but it includes things that are over 6A. Thank you! Juliana El mar, 15 de jun. de 2021 a la(s) 14:59, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Of course, if you only want to use alpha-carbons instead of all atoms of all residues, you could define the atom sets that way, e.g.
name frozen blah #1/A:100-200@ca contacts #1/A:55@ca restrict blah overlap -1000 log true
Also, I was using named selection because you asked about it. You do not need to use a named selection. Instead you can just specify both atom sets in "contacts," e.g.
contacts #1/A:55@ca restrict #1/A:100-200@ca overlap -1000 log true
Elaine
On Jun 15, 2021, at 10:48 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina@gmail.com> wrote:
Hi Elaine, I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. Thanks! Juliana
Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.)
One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances.
You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection.
In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command:
name frozen blah sel
See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like
contacts #1/A:55 restrict blah overlap -1000 log true
The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers:
1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...]
The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance.
The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Juliana, Sure, you can do that, and it's not necessary to bother with selecting or naming the selection. You can specify using only the atom-atom center distances (instead of VDW overlap) with the "distanceOnly" option of the ChimeraX contacts command. Example: contacts (#1/B:19 & sidechain) restrict (#1/A & sidechain) distanceOnly 6 log true See options in the "contacts" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> Yes being more specific when you ask a question always helps! I hope this was what you needed, Elaine
On Jun 15, 2021, at 11:12 AM, Juliana Glavina via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine ! Sorry I didn't cc the list before.
I think I need to be a little bit more specific. I am doing the following:
open 1ycr name frozen pocket1 (#1/B:19 & sidechain) @<6 & (#1/A & sidechain)
and I want to list the distances between the atoms of sel1 and sel2 that are lower than 6A I could use contacts, but it includes things that are over 6A.
Thank you! Juliana
El mar, 15 de jun. de 2021 a la(s) 14:59, Elaine Meng (meng@cgl.ucsf.edu) escribió: Of course, if you only want to use alpha-carbons instead of all atoms of all residues, you could define the atom sets that way, e.g.
name frozen blah #1/A:100-200@ca contacts #1/A:55@ca restrict blah overlap -1000 log true
Also, I was using named selection because you asked about it. You do not need to use a named selection. Instead you can just specify both atom sets in "contacts," e.g.
contacts #1/A:55@ca restrict #1/A:100-200@ca overlap -1000 log true
Elaine
On Jun 15, 2021, at 10:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina@gmail.com> wrote:
Hi Elaine, I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. Thanks! Juliana
Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.)
One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances.
You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection.
In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command:
name frozen blah sel
See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like
contacts #1/A:55 restrict blah overlap -1000 log true
The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers:
1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...]
The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance.
The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different.
I hope this helps, Elaine
Yes! Exactly ! Thank you El mar, 15 de jun. de 2021 a la(s) 15:38, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hi Juliana, Sure, you can do that, and it's not necessary to bother with selecting or naming the selection. You can specify using only the atom-atom center distances (instead of VDW overlap) with the "distanceOnly" option of the ChimeraX contacts command. Example:
contacts (#1/B:19 & sidechain) restrict (#1/A & sidechain) distanceOnly 6 log true
See options in the "contacts" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
Yes being more specific when you ask a question always helps!
I hope this was what you needed, Elaine
On Jun 15, 2021, at 11:12 AM, Juliana Glavina via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine ! Sorry I didn't cc the list before.
I think I need to be a little bit more specific. I am doing the following:
open 1ycr name frozen pocket1 (#1/B:19 & sidechain) @<6 & (#1/A & sidechain)
and I want to list the distances between the atoms of sel1 and sel2 that are lower than 6A I could use contacts, but it includes things that are over 6A.
Thank you! Juliana
El mar, 15 de jun. de 2021 a la(s) 14:59, Elaine Meng (meng@cgl.ucsf.edu) escribió: Of course, if you only want to use alpha-carbons instead of all atoms of all residues, you could define the atom sets that way, e.g.
name frozen blah #1/A:100-200@ca contacts #1/A:55@ca restrict blah overlap -1000 log true
Also, I was using named selection because you asked about it. You do not need to use a named selection. Instead you can just specify both atom sets in "contacts," e.g.
contacts #1/A:55@ca restrict #1/A:100-200@ca overlap -1000 log true
Elaine
On Jun 15, 2021, at 10:48 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina@gmail.com> wrote:
Hi Elaine, I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. Thanks! Juliana
Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.)
One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances.
You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection.
In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command:
name frozen blah sel
See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html>
Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like
contacts #1/A:55 restrict blah overlap -1000 log true
The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers:
1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...]
The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance.
The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different.
I hope this helps, Elaine
participants (2)
-
Elaine Meng -
Juliana Glavina