Re: [chimerax-users] pseudobond between atom and center of a ring
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form: /a:1@c3' /a:1@n3 rgba(20,90,90,70) However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent: /a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
Oops, didn't read my own documentation carefully enough! When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1. So you would need something like the following, which also works. Tested in daily build and in release 0.92. rgba(20%,90%,90%,0.7) Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Well, it's good to know I'm the only one who sometimes fails to RTFM :) While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this: ; pseudo bonds for figure
; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Alexis, Use the "style" command to set number of dashes in pseudobonds. The pb file just allows setting color and radius (which can also be set with "color" and "size" commands after creation). Our website documentation is broken temporarily but you can use command "help style" to see your downloaded version of the "style" manual page. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Well, it's good to know I'm the only one who sometimes fails to RTFM :)
While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
; pseudo bonds for figure ; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
Hi Alexis, The pseudobond reader could be improved to set the dashes. But all the pseudobonds in a pseudobond model must have the same number of dashes. So your example of setting 2 different dashes values in the file won't work. Tom
On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Well, it's good to know I'm the only one who sometimes fails to RTFM :)
While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
; pseudo bonds for figure ; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com <mailto:a.rohou@gmail.com>> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks both. I'll just do separate files as needed and set the dashes via style. On Tue, Mar 10, 2020 at 10:14 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
The pseudobond reader could be improved to set the dashes. But all the pseudobonds in a pseudobond model must have the same number of dashes. So your example of setting 2 different dashes values in the file won't work.
Tom
On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Well, it's good to know I'm the only one who sometimes fails to RTFM :)
While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
; pseudo bonds for figure
; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Alexis, I added dashes, color and halfbond variables to the ChimeraX pseudobond file format, example below. The radius, color and halfbond settings can be set multiple times in the file, applying to the lines below them, while dashes is a global setting. Tom ; radius = 0.075 ; color = orange ; halfbond = false ; dashes = 13 /D:38@OD2 /C:436@OH /D:38@OD1 /C:482@CA ; color = yellow /D:38@OD1 /C:436@OH
On Mar 10, 2020, at 10:16 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks both. I'll just do separate files as needed and set the dashes via style.
On Tue, Mar 10, 2020 at 10:14 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote: Hi Alexis,
The pseudobond reader could be improved to set the dashes. But all the pseudobonds in a pseudobond model must have the same number of dashes. So your example of setting 2 different dashes values in the file won't work.
Tom
On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou@gmail.com <mailto:a.rohou@gmail.com>> wrote:
Well, it's good to know I'm the only one who sometimes fails to RTFM :)
While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
; pseudo bonds for figure ; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com <mailto:a.rohou@gmail.com>> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Wow, that's awesome, thanks! I'll install the daily build tomorrow to try it out. On Tue, Mar 10, 2020 at 11:08 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
I added dashes, color and halfbond variables to the ChimeraX pseudobond file format, example below. The radius, color and halfbond settings can be set multiple times in the file, applying to the lines below them, while dashes is a global setting.
Tom
; radius = 0.075 ; color = orange ; halfbond = false ; dashes = 13 /D:38@OD2 /C:436@OH /D:38@OD1 /C:482@CA ; color = yellow /D:38@OD1 /C:436@OH
On Mar 10, 2020, at 10:16 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks both. I'll just do separate files as needed and set the dashes via style.
On Tue, Mar 10, 2020 at 10:14 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
The pseudobond reader could be improved to set the dashes. But all the pseudobonds in a pseudobond model must have the same number of dashes. So your example of setting 2 different dashes values in the file won't work.
Tom
On Mar 10, 2020, at 9:51 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Well, it's good to know I'm the only one who sometimes fails to RTFM :)
While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:
; pseudo bonds for figure
; radius = 0.05 ; dashes = 3 #1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2) #1/L@O11 #1/A:840@HH dodgerblue #1/B:940@HE21 #1/B:887@OG dodgerblue ; dashes = 8 #10841 #1/A:840@CD2 yellow #10884 #1/A:840@CE1 yellow #10840 #1/B:940@HE22 yellow #10001 #1/B:947@CZ yellow #10002 #1/A:841@CZ yellow
On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, didn't read my own documentation carefully enough!
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.
So you would need something like the following, which also works. Tested in daily build and in release 0.92.
rgba(20%,90%,90%,0.7)
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70 Elaine
On Mar 9, 2020, at 2:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form:
/a:1@c3' /a:1@n3 rgba(20,90,90,70)
However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:
/a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine!
Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!
Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.
Thanks again for the help.
Cheers, Alexis
On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Here is the more detailed description of pseudobond file format:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
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participants (3)
-
Alexis Rohou -
Elaine Meng -
Tom Goddard