Hi,
I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
Thank you, Caitlyn McCafferty
Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty@nih.gov
Hi Caitlyn, The users would have to have Chimera installed on their machines in order to open Chimera sessions. There is a “web data” mechanism for the browser to use Chimera as a helper app (analogous to Preview or Adobe for PDF files), but it requires Chimera on the end machine.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.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 Aug 15, 2016, at 8:14 AM, McCafferty, Caitlyn (NIH/NEI) [F] caitlyn.mccafferty@nih.gov wrote:
Hi,
I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
Thank you, Caitlyn McCafferty
Hi Caitlyn, Another possible option to be aware of is that Chimera can export to WebGL format, which can show the 3D structure in most modern web browsers and allow it to be manipulated with the mouse much in the same way it can in Chimera’s graphics window. Well, rotation and scaling at least. You can export to WebGL either with File…Export, or with the “export” command. The WebGL does lack some basic things, like showing text labels, so you would really need to try it out to see if it meets your needs.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 15, 2016, at 4:49 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Caitlyn, The users would have to have Chimera installed on their machines in order to open Chimera sessions. There is a “web data” mechanism for the browser to use Chimera as a helper app (analogous to Preview or Adobe for PDF files), but it requires Chimera on the end machine.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.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 Aug 15, 2016, at 8:14 AM, McCafferty, Caitlyn (NIH/NEI) [F] caitlyn.mccafferty@nih.gov wrote:
Hi,
I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
Thank you, Caitlyn McCafferty
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric,
Thank you for your quick response. I really want the labels for the amino acids to be present. I tried adding labels in the session and exporting to the html file and like you said no labels appeared. I did, however, notice that data that I added to the B-factor column appeared in the html file. Would it be possible to add the labels to another column and have them show up? Or do you have any other suggestions on how to approach this issue?
Thank you for your time,
Caitlyn McCafferty
Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty@nih.gov ________________________________ From: Eric Pettersen [pett@cgl.ucsf.edu] Sent: Monday, August 15, 2016 8:26 PM To: McCafferty, Caitlyn (NIH/NEI) [F] Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Integrating chimera into a database
Hi Caitlyn, Another possible option to be aware of is that Chimera can export to WebGL format, which can show the 3D structure in most modern web browsers and allow it to be manipulated with the mouse much in the same way it can in Chimera’s graphics window. Well, rotation and scaling at least. You can export to WebGL either with File…Export, or with the “export” command. The WebGL does lack some basic things, like showing text labels, so you would really need to try it out to see if it meets your needs.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 15, 2016, at 4:49 PM, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:
Hi Caitlyn, The users would have to have Chimera installed on their machines in order to open Chimera sessions. There is a “web data” mechanism for the browser to use Chimera as a helper app (analogous to Preview or Adobe for PDF files), but it requires Chimera on the end machine.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.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 Aug 15, 2016, at 8:14 AM, McCafferty, Caitlyn (NIH/NEI) [F] <caitlyn.mccafferty@nih.govmailto:caitlyn.mccafferty@nih.gov> wrote:
Hi,
I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
Thank you, Caitlyn McCafferty
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Caitlyn AFAIK, bfactor data does not appear in the WebGL html file, just geometry data, so I’m not sure what’s going on there. Anyway. I don’t have any great ideas. One possible thing is that you create one or more scenes showing various relevant positions of your structure, with labels, and then save them as an HTML “storyboard”:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/animation/f... (click on “Storyboard” on the left).
The scenes will be shown as thumbnails across the top, and a larger version of whichever one is chosen will be shown below, complete with labels. Just above the large image will be a “Load 3D Data” button which will allow the scene to be manipulated, just like the WebGL version, though labels will disappear (until the image is reloaded).
Like I said, not great, but maybe it’s something.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 25, 2016, at 9:28 AM, McCafferty, Caitlyn (NIH/NEI) [F] caitlyn.mccafferty@nih.gov wrote:
Hi Eric,
Thank you for your quick response. I really want the labels for the amino acids to be present. I tried adding labels in the session and exporting to the html file and like you said no labels appeared. I did, however, notice that data that I added to the B-factor column appeared in the html file. Would it be possible to add the labels to another column and have them show up? Or do you have any other suggestions on how to approach this issue?
Thank you for your time,
Caitlyn McCafferty
Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty@nih.gov mailto:caitlyn.mccafferty@nih.gov From: Eric Pettersen [pett@cgl.ucsf.edu] Sent: Monday, August 15, 2016 8:26 PM To: McCafferty, Caitlyn (NIH/NEI) [F] Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Integrating chimera into a database
Hi Caitlyn, Another possible option to be aware of is that Chimera can export to WebGL format, which can show the 3D structure in most modern web browsers and allow it to be manipulated with the mouse much in the same way it can in Chimera’s graphics window. Well, rotation and scaling at least. You can export to WebGL either with File…Export, or with the “export” command. The WebGL does lack some basic things, like showing text labels, so you would really need to try it out to see if it meets your needs.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 15, 2016, at 4:49 PM, Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote:
Hi Caitlyn, The users would have to have Chimera installed on their machines in order to open Chimera sessions. There is a “web data” mechanism for the browser to use Chimera as a helper app (analogous to Preview or Adobe for PDF files), but it requires Chimera on the end machine.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h... http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.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 Aug 15, 2016, at 8:14 AM, McCafferty, Caitlyn (NIH/NEI) [F] <caitlyn.mccafferty@nih.gov mailto:caitlyn.mccafferty@nih.gov> wrote:
Hi,
I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed?
Thank you, Caitlyn McCafferty
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear All,
When I scan my computer with antivirus software, it detects that the behaviour of Chimera 1.11\bin\DLLs\GLU32.dll likes that of a Trojan. Does it only behaves like a Trojan but not a Trojan, or there is the possibility that file was really invected by virus or Trojan?
I am looking forward to getting a reply from you.
Smith
The GLU32.dll that comes with Chimera is not infected. So if after reinstalling Chimera, you still get this error, you should report it as a false positive to your antivirus software company.
-- Greg
On 08/28/2016 06:28 PM, Smith Liu wrote:
Dear All,
When I scan my computer with antivirus software, it detects that the behaviour of Chimera 1.11\bin\DLLs\GLU32.dll likes that of a Trojan. Does it only behaves like a Trojan but not a Trojan, or there is the possibility that file was really invected by virus or Trojan?
I am looking forward to getting a reply from you.
Smith
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Elaine Meng -
Eric Pettersen -
Greg Couch -
McCafferty, Caitlyn (NIH/NEI) [F] -
Smith Liu