I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students. Bobby Barnett Department of Chemistry University of Chemistry
Hi Bobby, We have quite a few Chimera tutorials, but the main issue for you is probably whether they are suitable for undergraduates. Maybe other undergraduate educators will have better suggestions or materials that they can send you; the tutorials that we provide do presuppose some knowledge of protein structure and organic chemistry, but you can take a look and see what you think... The User's Guide (included with Chimera download but also shown on our website) includes several tutorials, including "getting started" for Chimera beginners. You can get to the copies included in your download from the Chimera Help menu. The copies at our website are here, but if you stick with the downloaded ones (menu: Help… Tutorials) they are version-synchronized with the software. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> While "getting started" may be simplest in terms of Chimera, some of the others in the User's Guide that are more basic in terms of the science are the Surface Properties image tutorial and the Structure Analysis and Comparison tutorial. I usually suggest the latter for graduate students learning Chimera because it includes several common protein analysis tasks. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> There are also a bunch of tutorials on the website only, listed here: <http://www.rbvi.ucsf.edu/chimera/tutorials.html> The most basic of these Chimera-wise is the expanded "getting started" tutorial: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.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 Feb 26, 2015, at 9:32 AM, Bobby Barnett <bobby.barnett@gmail.com> wrote:
I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students.
Bobby Barnett
Department of Chemistry University of Chemistry
Dear Elaine, I meant to thank you earlier for the many tutorials you provided, but I got distracted. I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option? I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera. Thanks again for your help. I really appreciate all of the tutorials and the videos that you and your group provide. Bobby Barnett, semi-retired crystallographer On Thu, Feb 26, 2015 at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Bobby, We have quite a few Chimera tutorials, but the main issue for you is probably whether they are suitable for undergraduates. Maybe other undergraduate educators will have better suggestions or materials that they can send you; the tutorials that we provide do presuppose some knowledge of protein structure and organic chemistry, but you can take a look and see what you think...
The User's Guide (included with Chimera download but also shown on our website) includes several tutorials, including "getting started" for Chimera beginners. You can get to the copies included in your download from the Chimera Help menu. The copies at our website are here, but if you stick with the downloaded ones (menu: Help… Tutorials) they are version-synchronized with the software. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
While "getting started" may be simplest in terms of Chimera, some of the others in the User's Guide that are more basic in terms of the science are the Surface Properties image tutorial and the Structure Analysis and Comparison tutorial. I usually suggest the latter for graduate students learning Chimera because it includes several common protein analysis tasks. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
There are also a bunch of tutorials on the website only, listed here: <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
The most basic of these Chimera-wise is the expanded "getting started" tutorial: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.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 Feb 26, 2015, at 9:32 AM, Bobby Barnett <bobby.barnett@gmail.com> wrote:
I was wondering if anyone had interactive tutorial session(s) that can be used to educate a small class of undergraduate students.
Bobby Barnett
Department of Chemistry University of Chemistry
Dear Bobby, You’re welcome. We don’t have a tutorial for the Autodock Vina interface, but there is a manual page. It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera’s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area. See the manual page for explanations of the fields in the dialog: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera. They might be useful for explaining what the advanced parameters mean, but you wouldn’t want to try to follow them step by step. Also keep in mind that Autodock is a different program from Autodock Vina. 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 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett@gmail.com> wrote:
Dear Elaine,
I meant to thank you earlier for the many tutorials you provided, but I got distracted.
I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option? I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
Thanks again for your help. I really appreciate all of the tutorials and the videos that you and your group provide.
Bobby Barnett, semi-retired crystallographer
Dear Elaine, Thanks for the advice about using the Autodock Vina option under Surface/Binding Analysis. I have run this with both the web based option and the local option and get the same error "[Errno 13] Permission denied: 'trial.receptor.pdb'" I don't see a way around this error. Do I need to run the program as Administrator? Thanks again for your help. Bobby Barnett On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Bobby, You’re welcome.
We don’t have a tutorial for the Autodock Vina interface, but there is a manual page. It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera’s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area.
See the manual page for explanations of the fields in the dialog: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera. They might be useful for explaining what the advanced parameters mean, but you wouldn’t want to try to follow them step by step. Also keep in mind that Autodock is a different program from Autodock Vina.
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 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett@gmail.com> wrote:
Dear Elaine,
I meant to thank you earlier for the many tutorials you provided, but I got distracted.
I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option? I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
Thanks again for your help. I really appreciate all of the tutorials and the videos that you and your group provide.
Bobby Barnett, semi-retired crystallographer
Dear Bobby, It sounds like you need to make sure to specify an output location where you have permission to read and write files. For example, my directory (Mac) is /Users/meng and I can specify output as /Users/meng/test (or /Users/meng/Desktop/test , etc.) to create several files with filenames that start with “test”… but of course you would need to specify a different pathname according to however your computer is set up. Elaine On Mar 28, 2015, at 11:25 AM, Bobby Barnett wrote:
Dear Elaine,
Thanks for the advice about using the Autodock Vina option under Surface/Binding Analysis. I have run this with both the web based option and the local option and get the same error "[Errno 13] Permission denied: 'trial.receptor.pdb'" I don't see a way around this error. Do I need to run the program as Administrator?
Thanks again for your help.
Bobby Barnett
On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Bobby, You’re welcome.
We don’t have a tutorial for the Autodock Vina interface, but there is a manual page. It should be reasonably friendly if you open the ligand and receptor as two separate models (from two separate input PDB files) and just fill in the required fields in Chimera’s Autodock Vina dialog, including drawing a box with the mouse in the main window to define a search area.
See the manual page for explanations of the fields in the dialog: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
Looking at other (non-Chimera) tutorials might be confusing because they are not describing using this interface in Chimera. They might be useful for explaining what the advanced parameters mean, but you wouldn’t want to try to follow them step by step. Also keep in mind that Autodock is a different program from Autodock Vina.
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 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett@gmail.com> wrote:
Dear Elaine,
I meant to thank you earlier for the many tutorials you provided, but I got distracted.
I did have another question and i will post it on the regular way if it is needed, but is there a tutorial using the Autodock Vina under the tools Surface Binding Analysis option? I have tried several times to perform this with one of the autodock tutorials and can't get it to work under chimera.
Thanks again for your help. I really appreciate all of the tutorials and the videos that you and your group provide.
Bobby Barnett, semi-retired crystallographer
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Bobby Barnett -
Elaine Meng