Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks!
Hi Alexander, I don't know how that error message occurs, maybe the others will have some idea. It sounds like you wouldn't be able to fetch anything from the PDB.
In Chimera, I can fetch that entry and others from the PDB without problem. I also tried turning off my internet connection first to see what error message results, but it is a different message from what you reported. You could try using Help... Report a Bug in the Chimera menu and describe how you got the message, and include your email address if you want feedback.
To be able to go through the tutorial now, however, you could just go to the PDB web site, http://www.rcsb.org/pdb/home/home.do search for entry 1d86, download the PDB file (text) to your computer in some location where you will be able to find it in a file browser, then open the file as a local file from Chimera (use File... Open in the menu and browse to its location). Then proceed with the tutorial.
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 24, 2011, at 5:10 PM, Alexander Spyros Maris wrote:
Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks!
Thank you Dr. Meng! Downloading the protein from the PDB worked, so I'll do this from now on.
On Fri, Feb 25, 2011 at 1:22 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Alexander, I don't know how that error message occurs, maybe the others will have some idea. It sounds like you wouldn't be able to fetch anything from the PDB.
In Chimera, I can fetch that entry and others from the PDB without problem. I also tried turning off my internet connection first to see what error message results, but it is a different message from what you reported. You could try using Help... Report a Bug in the Chimera menu and describe how you got the message, and include your email address if you want feedback.
To be able to go through the tutorial now, however, you could just go to the PDB web site, http://www.rcsb.org/pdb/home/home.do search for entry 1d86, download the PDB file (text) to your computer in some location where you will be able to find it in a file browser, then open the file as a local file from Chimera (use File... Open in the menu and browse to its location). Then proceed with the tutorial.
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 24, 2011, at 5:10 PM, Alexander Spyros Maris wrote:
Hi, I was attempting to start part of the tutorial by fetching "1d86"
from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this?
Thanks!
Hi Alexander, Since your original error was "Connection refused", that could be a temporary network problem so you might want to try fetching again and see if the problem has gone away on its own. If not, then Elaine's workaround would be the way to go.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 25, 2011, at 7:21 PM, Alexander Spyros Maris wrote:
Thank you Dr. Meng! Downloading the protein from the PDB worked, so I'll do this from now on.
On Fri, Feb 25, 2011 at 1:22 PM, Elaine Meng wrote: Hi Alexander, I don't know how that error message occurs, maybe the others will have some idea. It sounds like you wouldn't be able to fetch anything from the PDB.
In Chimera, I can fetch that entry and others from the PDB without problem. I also tried turning off my internet connection first to see what error message results, but it is a different message from what you reported. You could try using Help... Report a Bug in the Chimera menu and describe how you got the message, and include your email address if you want feedback.
To be able to go through the tutorial now, however, you could just go to the PDB web site, http://www.rcsb.org/pdb/home/home.do search for entry 1d86, download the PDB file (text) to your computer in some location where you will be able to find it in a file browser, then open the file as a local file from Chimera (use File... Open in the menu and browse to its location). Then proceed with the tutorial.
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 24, 2011, at 5:10 PM, Alexander Spyros Maris wrote:
Hi, I was attempting to start part of the tutorial by fetching
"1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this?
Thanks!
-- Alex Maris
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
It could be that you need to set the "Use HTTP proxy" setting, and the associated proxy server and proxy port, in your Web Access preferences for chimera to access the Internet.
-- Greg
On 02/25/2011 07:21 PM, Alexander Spyros Maris wrote:
Thank you Dr. Meng! Downloading the protein from the PDB worked, so I'll do this from now on.
On Fri, Feb 25, 2011 at 1:22 PM, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
Hi Alexander, I don't know how that error message occurs, maybe the others will have some idea. It sounds like you wouldn't be able to fetch anything from the PDB. In Chimera, I can fetch that entry and others from the PDB without problem. I also tried turning off my internet connection first to see what error message results, but it is a different message from what you reported. You could try using Help... Report a Bug in the Chimera menu and describe how you got the message, and include your email address if you want feedback. To be able to go through the tutorial now, however, you could just go to the PDB web site, <http://www.rcsb.org/pdb/home/home.do> search for entry 1d86, download the PDB file (text) to your computer in some location where you will be able to find it in a file browser, then open the file as a local file from Chimera (use File... Open in the menu and browse to its location). Then proceed with the tutorial. 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 24, 2011, at 5:10 PM, Alexander Spyros Maris wrote: > Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? > Thanks!-- Alex Maris
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Alexander Spyros Maris -
Elaine Meng -
Eric Pettersen -
Greg Couch