Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong? Kim
Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not. The Chimera tutorials are here and/or in the Chimera Help menu: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html> Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays. Kim On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
Hi Kim, Again, I do not know what instructions or python file you mean. If you just meant you were trying to download and install Chimera on Linux, the instructions say: "Some browsers may download the file as chimera-get.py. If yours does, rename the file to chimera-installer.bin” <http://www.rbvi.ucsf.edu/chimera/data/downloads/1.11/linux.html> (… and see also further instructions on that page, e.g. it mentions a “couldn’t get visual” error) However, Chimera doesn’t have any force field calculations that include Ag, and Ab isn’t even an element as far as I know, so you may be barking up the wrong tree. <https://en.wikipedia.org/wiki/Symbol_(chemistry)#Symbols_and_names_not_currently_used> Good luck, Elaine
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
Kim
On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
<Final Exam.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Kim, I think you have a typo- you are missing () after your object createAb Btw, like Dr. Meng said it is really confusing what you are trying to do because the script you provided is for a water molecule.
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
Kim
On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>> <http://www.rbvi.ucsf.edu/chimera/tutorials.html <http://www.rbvi.ucsf.edu/chimera/tutorials.html>>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu <mailto:knperry@go.olemiss.edu>> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
<Final Exam.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you for the response. Ab and Ag are not elements in this project-Ab not at all. They are referencing antigens and antibodies. I was creating a skeleton for my specific project but decided to try the template I found first to see what should happen. I wanted to see the interface of an antigen and an antibody. Kimberley N. Poland, AA, BA, BA, MS Doctoral Student Department of Chemistry & Biochemistry Coulter Hall Room 283 601-692-8577
On May 7, 2018, at 5:26 PM, David Gae <ddgae@ucdavis.edu> wrote:
Dear Kim,
I think you have a typo- you are missing () after your object createAb
Btw, like Dr. Meng said it is really confusing what you are trying to do because the script you provided is for a water molecule.
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
Kim
On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
<Final Exam.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kim, Not sure why you are using python here, but then again I’m not a python programmer myself. Generally for antibody-antigen modeling, you would just open the 3D structures from PDB or mmCIF files, then use the various analysis tools in Chimera (FindHBond, etc.). If you don’t already have 3D structures of these proteins, one approach is to “homology” model them from known structures of similar sequences. You could use Chimera’s Modeller interface for comparative modeling to do that. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> However, even if you had models of 3D structures of both proteins, Chimera will not predict how the two will interact. For that, you would need to use some other program for protein-protein docking. I hope this helps, Elaine
On May 7, 2018, at 7:48 PM, Kimberley Poland <knperry@go.olemiss.edu> wrote:
Thank you for the response. Ab and Ag are not elements in this project-Ab not at all. They are referencing antigens and antibodies. I was creating a skeleton for my specific project but decided to try the template I found first to see what should happen. I wanted to see the interface of an antigen and an antibody.
Kimberley N. Poland, AA, BA, BA, MS Doctoral Student Department of Chemistry & Biochemistry Coulter Hall Room 283 601-692-8577
On May 7, 2018, at 5:26 PM, David Gae <ddgae@ucdavis.edu> wrote:
Dear Kim,
I think you have a typo- you are missing () after your object createAb
Btw, like Dr. Meng said it is really confusing what you are trying to do because the script you provided is for a water molecule.
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
Kim
On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
<Final Exam.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I will look into that. I am a Physical Chemist now, and my PhD requires a Python Coding course. Everything just has to be done in there. So, I have to write a code to convert the .xyz file to a .pdb and have Chimera (I was hoping) to show the structures. On Tue, May 8, 2018 at 10:43 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kim, Not sure why you are using python here, but then again I’m not a python programmer myself.
Generally for antibody-antigen modeling, you would just open the 3D structures from PDB or mmCIF files, then use the various analysis tools in Chimera (FindHBond, etc.). If you don’t already have 3D structures of these proteins, one approach is to “homology” model them from known structures of similar sequences. You could use Chimera’s Modeller interface for comparative modeling to do that. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/modeller.html>
However, even if you had models of 3D structures of both proteins, Chimera will not predict how the two will interact. For that, you would need to use some other program for protein-protein docking.
I hope this helps, Elaine
On May 7, 2018, at 7:48 PM, Kimberley Poland <knperry@go.olemiss.edu> wrote:
Thank you for the response. Ab and Ag are not elements in this project-Ab not at all. They are referencing antigens and antibodies. I was creating a skeleton for my specific project but decided to try the template I found first to see what should happen. I wanted to see the interface of an antigen and an antibody.
Kimberley N. Poland, AA, BA, BA, MS Doctoral Student Department of Chemistry & Biochemistry Coulter Hall Room 283 601-692-8577
On May 7, 2018, at 5:26 PM, David Gae <ddgae@ucdavis.edu> wrote:
Dear Kim,
I think you have a typo- you are missing () after your object createAb
Btw, like Dr. Meng said it is really confusing what you are trying to do because the script you provided is for a water molecule.
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
Kim
On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kim, I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
The Chimera tutorials are here and/or in the Chimera Help menu:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
Good luck, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry@go.olemiss.edu> wrote:
Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
Kim
<Final Exam.py>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
participants (4)
-
David Gae -
Elaine Meng -
Kimberley Perry -
Kimberley Poland