Fwd: [Chimera-users] Can ChimeraX morph between two surfaces?
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB #2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. ============================= (2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, Thanks for your detailed explanation! What's the format of the pseudobond file? Should it look like this? =============================== #1/A:13@NE2 #1/A:502@MG =============================== All the best, Steve
On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Actually I’m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under “Atoms in Common”:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
For the case where composition changes, you could add in a fake Mg ion and water to the structure that’s missing them, but you’d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer.
Or if you don’t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou@gmail.com> wrote:
Thanks, Elaine! You command "rainbow structures" works beautifully. There is "a Mg ion" and "a water molecule" in the two conformations. (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. Is there a way to morph the specific components properly? Steve
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-- Steve Chou -- Steve Chou
Hi Steve, The problem with the pseudobond file is the blank line. The reader is not very smart. The pseudobonds (or distances) were just to have the HET atoms simply included in the morph at all, as I understood it and as written here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> How the HET atoms move along the trajectory is a separate matter, and it sounds like they are being handled poorly. Sorry about the limitations. You could use Help… Report a Bug and attach your session as an example for us if these structures are shareable (not private data). Elaine
On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB
#2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. =============================
(2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB
distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve
On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
I’m told that the pseudobonds may not be needed if: (A) the two endpoint structures have exactly and only the same atoms (with same names, res numbers, chain IDs) -or- (B) the “same true” option is used, when some atoms are different but the atoms in question have the same names, res numbers, and chain IDs. That may explain why your Mg was included in the first place if it wasn’t pseudobonded to the protein chain. However, that is orthogonal to the problem of poor movement path, which as far as I know is not solved. Sorry about that. Elaine
On Feb 15, 2019, at 3:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, The problem with the pseudobond file is the blank line. The reader is not very smart.
The pseudobonds (or distances) were just to have the HET atoms simply included in the morph at all, as I understood it and as written here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
How the HET atoms move along the trajectory is a separate matter, and it sounds like they are being handled poorly. Sorry about the limitations. You could use Help… Report a Bug and attach your session as an example for us if these structures are shareable (not private data).
Elaine
On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB
#2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. =============================
(2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB
distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve
On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
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… and now I’m told that currently in ChimeraX, adding pseudobonds wouldn’t help anyway, only covalent bonds. Sorry, the functionality and documentation were ported from Chimera (where this pseudobond bond stuff did apply), and I was not informed of the difference! Apologies for the red herring(s), Elaine
On Feb 15, 2019, at 4:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I’m told that the pseudobonds may not be needed if:
(A) the two endpoint structures have exactly and only the same atoms (with same names, res numbers, chain IDs) -or- (B) the “same true” option is used, when some atoms are different but the atoms in question have the same names, res numbers, and chain IDs.
That may explain why your Mg was included in the first place if it wasn’t pseudobonded to the protein chain.
However, that is orthogonal to the problem of poor movement path, which as far as I know is not solved. Sorry about that. Elaine
On Feb 15, 2019, at 3:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, The problem with the pseudobond file is the blank line. The reader is not very smart.
The pseudobonds (or distances) were just to have the HET atoms simply included in the morph at all, as I understood it and as written here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
How the HET atoms move along the trajectory is a separate matter, and it sounds like they are being handled poorly. Sorry about the limitations. You could use Help… Report a Bug and attach your session as an example for us if these structures are shareable (not private data).
Elaine
On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB
#2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. =============================
(2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB
distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve
On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
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By covalent bonds, do you mean that I should add the CONNECT keyword for an atom pair between a HETATM and an regular ATOM in the PDB? Steve On Fri, Feb 15, 2019 at 7:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
… and now I’m told that currently in ChimeraX, adding pseudobonds wouldn’t help anyway, only covalent bonds. Sorry, the functionality and documentation were ported from Chimera (where this pseudobond bond stuff did apply), and I was not informed of the difference!
Apologies for the red herring(s), Elaine
On Feb 15, 2019, at 4:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I’m told that the pseudobonds may not be needed if:
(A) the two endpoint structures have exactly and only the same atoms (with same names, res numbers, chain IDs) -or- (B) the “same true” option is used, when some atoms are different but the atoms in question have the same names, res numbers, and chain IDs.
That may explain why your Mg was included in the first place if it wasn’t pseudobonded to the protein chain.
However, that is orthogonal to the problem of poor movement path, which as far as I know is not solved. Sorry about that. Elaine
On Feb 15, 2019, at 3:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, The problem with the pseudobond file is the blank line. The reader is not very smart.
The pseudobonds (or distances) were just to have the HET atoms simply included in the morph at all, as I understood it and as written here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
How the HET atoms move along the trajectory is a separate matter, and it sounds like they are being handled poorly. Sorry about the limitations. You could use Help… Report a Bug and attach your session as an example for us if these structures are shareable (not private data).
Elaine
On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB
#2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. =============================
(2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB
distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve
On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
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-- Steve Chou
Hi Steve, First of all, if the atoms in question (ion, water) are already included in your morph trajectory, there is no need to do anything. This (pseudo)bonding stuff is merely to have them included the trajectory rather than omitted, and mainly applies to morphing in Chimera rather than ChimeraX. I think you told me that those atoms are already included in your morph trajectory, so none of the rest of this message is relevant to your situation. A poor path of movement is a separate issue that may not be solved. If those atoms are NOT included. There isn’t a good way to add covalent bonds in ChimeraX currently. That was just a statement that covalent ligands like glycosylations or retinal in rhodopsin would be included under certain circumstances. You would instead use “same true” morph option and make sure that all atoms to be included in the morph have the same atom names, chain IDs and residue numbers. If they don’t already have identical naming etc. it is generally hard to do for the protein part. One idea to avoid that is two stages: - morph the protein, write trajectory as PDB multiple files - take first and last morph trajectory structures and edit in the Mg, water, with same atom names, chain ID, residue numbers in their starting and ending positions - morph starting from those two structures Again, none of this solves the “path of movement” problem. For that, you could try messing with the morphing parameters, but it is possible that won’t help. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#morph-parameters> Elaine
On Feb 15, 2019, at 7:29 PM, Steve Chou <stevezchou@gmail.com> wrote:
By covalent bonds, do you mean that I should add the CONNECT keyword for an atom pair between a HETATM and an regular ATOM in the PDB? Steve
On Fri, Feb 15, 2019 at 7:32 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: … and now I’m told that currently in ChimeraX, adding pseudobonds wouldn’t help anyway, only covalent bonds. Sorry, the functionality and documentation were ported from Chimera (where this pseudobond bond stuff did apply), and I was not informed of the difference!
Apologies for the red herring(s), Elaine
On Feb 15, 2019, at 4:16 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I’m told that the pseudobonds may not be needed if:
(A) the two endpoint structures have exactly and only the same atoms (with same names, res numbers, chain IDs) -or- (B) the “same true” option is used, when some atoms are different but the atoms in question have the same names, res numbers, and chain IDs.
That may explain why your Mg was included in the first place if it wasn’t pseudobonded to the protein chain.
However, that is orthogonal to the problem of poor movement path, which as far as I know is not solved. Sorry about that. Elaine
On Feb 15, 2019, at 3:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, The problem with the pseudobond file is the blank line. The reader is not very smart.
The pseudobonds (or distances) were just to have the HET atoms simply included in the morph at all, as I understood it and as written here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
How the HET atoms move along the trajectory is a separate matter, and it sounds like they are being handled poorly. Sorry about the limitations. You could use Help… Report a Bug and attach your session as an example for us if these structures are shareable (not private data).
Elaine
On Feb 15, 2019, at 3:20 PM, Steve Chou <stevezchou@gmail.com> wrote:
Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB
#2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. =============================
(2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB
distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve
On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it.
You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
Elaine
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-- Steve Chou
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participants (2)
-
Elaine Meng -
Steve Chou