internal coordinates (z-matrix) in chimera
Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix). Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out. I have bunch of conformations, so I may not use the gui. Thank you. Chinh
Hi Chinh, For scripting measurements (distance, angle, torsion) you can use commands: distance, angle <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry. More info on writing Chimera scripts to process multiple data files: <http://www.cgl.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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:
Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).
Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.
I have bunch of conformations, so I may not use the gui. Thank you. Chinh
Hi Chinh, If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide to write a script to get the values. There is a programmer's example specifically about atomic-level measurements such as angles and distances: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeas... Also, Python is reasonably easy to learn, especially if you already know how to program in another language. There are links to Python tutorials in the Programmer's Guide. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:
Hi Chinh, For scripting measurements (distance, angle, torsion) you can use commands: distance, angle <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry.
More info on writing Chimera scripts to process multiple data files: <http://www.cgl.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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:
Hi, I have some results after running docking from DOCK. I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).
Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.
I have bunch of conformations, so I may not use the gui. Thank you. Chinh
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear all, Thank you very much for your help. I am coding it in python and will run in batch mode. I think it will work. Chinh On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Chinh, If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide
to write a script to get the values. There is a programmer's example specifically about atomic-level measurements such as angles and distances:
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeas...
Also, Python is reasonably easy to learn, especially if you already know how to program in another language. There are links to Python tutorials in the Programmer's Guide.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:
Hi Chinh, For scripting measurements (distance, angle, torsion) you can use commands: distance, angle <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry.
More info on writing Chimera scripts to process multiple data files: <http://www.cgl.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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:
Hi,
I have some results after running docking from DOCK.
I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).
Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.
I have bunch of conformations, so I may not use the gui.
Thank you.
Chinh
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello, I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want. With the piece of code: *confor = chimera.openModels.list()* it shows an empty list of models (for mol2 file)??? Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)? I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges. Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious. Thank you. Chinh On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Chinh, If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide
to write a script to get the values. There is a programmer's example specifically about atomic-level measurements such as angles and distances:
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeas...
Also, Python is reasonably easy to learn, especially if you already know how to program in another language. There are links to Python tutorials in the Programmer's Guide.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:
Hi Chinh, For scripting measurements (distance, angle, torsion) you can use commands: distance, angle <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
These measurements are specified individually. Chimera does not have an option to write out a Z-matrix, sorry.
More info on writing Chimera scripts to process multiple data files: <http://www.cgl.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 Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:
Hi,
I have some results after running docking from DOCK.
I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).
Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.
I have bunch of conformations, so I may not use the gui.
Thank you.
Chinh
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:
Hello,
I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want.
With the piece of code: confor = chimera.openModels.list()
it shows an empty list of models (for mol2 file)???
Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)?
I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges.
Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.
As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi, Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []). *import chimera* *confor = chimera.openModels.list()* *print confor*
[]
""" if I used *print confor[0]*
IndexError: list index out of range"""
Thank you. Chinh On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:
Hello,
I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want.
With the piece of code: *confor = chimera.openModels.list()*
it shows an empty list of models (for mol2 file)???
Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)?
I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges.
Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.
As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script...
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi, I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. Thank you very much. Chinh On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To <chinh.sutranto@gmail.com
wrote:
Hi,
Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []).
*import chimera* *confor = chimera.openModels.list()* *print confor*
[]
""" if I used *print confor[0]*
IndexError: list index out of range"""
Thank you.
Chinh
On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:
Hello,
I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want.
With the piece of code: *confor = chimera.openModels.list()*
it shows an empty list of models (for mol2 file)???
Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)?
I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges.
Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.
As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script...
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Great! --Eric On Mar 20, 2013, at 11:22 PM, Chinh Su Tran To wrote:
Hi,
I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. Thank you very much.
Chinh
On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To <chinh.sutranto@gmail.com> wrote: Hi,
Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []).
import chimera confor = chimera.openModels.list() print confor
[]
""" if I used print confor[0]
IndexError: list index out of range"""
Thank you.
Chinh
On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:
Hello,
I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want.
With the piece of code: confor = chimera.openModels.list()
it shows an empty list of models (for mol2 file)???
Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)?
I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges.
Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.
As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script...
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Dear Dr. Pettersen, Greatly thank you for the help from you and Dr. Meng. Regards, Chinh On Mar 22, 2013, at 2:50 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Great!
--Eric
On Mar 20, 2013, at 11:22 PM, Chinh Su Tran To wrote:
Hi,
I fixed my silly mistake and solved the problem. Btw, I also found how to convert mol2 back to pdb in chimera. Chimera is interesting. Thank you very much.
Chinh
On Thu, Mar 21, 2013 at 11:12 AM, Chinh Su Tran To <chinh.sutranto@gmail.com> wrote:
Hi,
Attached is my mol2 file. It is the DOCK result containing 10 conformations of docked ligand. It does show 10 conformations using GUI Chimera (they're sub-model, aint they?), but when I run the piece of code below (just for testing), the result was an empty list (i.e. []).
import chimera confor = chimera.openModels.list() print confor
[]
""" if I used print confor[0]
IndexError: list index out of range"""
Thank you.
Chinh
On Thu, Mar 21, 2013 at 2:12 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Mar 20, 2013, at 2:28 AM, Chinh Su Tran To wrote:
Hello,
I managed to get the torsion angles from scripting, but I encountered one problem that my code works for pdb file ONLY. When I ran it for Mol2 input, I could not get the angles I want.
With the piece of code: confor = chimera.openModels.list()
it shows an empty list of models (for mol2 file)???
Please anyone help show me some hints how to convert Mol2 back to PDB or anyway that I can directly deal with mol2 format)?
I greatly appreciate if you please show me references about how chimera works with Models. I guess I have not understood yet the differences between pdb and mol2. It seems to me that mol2 contains the same info (in terms of ATOM and coordinates), but an extra column of charges.
Does that MODEL here mean conformations? Why the docked_conformer (results from DOCK with various conformations) contains NO models according to chimera? I am sorry that I did not mean questioning, but curious.
As far as Chimera is concerned, there is very little difference between a model opened from a PDB file and one opened from a Mol2 file. chimera.openModels.list() cannot be empty if Chimera is actually showing any structures. Is it? (when you open the Mol2 file normally)? Maybe you need to send along your Mol2 file and your script...
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (4)
-
Chinh Su Tran To -
Chinh Sutran
-
Elaine Meng -
Eric Pettersen