show stands' arrows a little werid
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much!
Best regards, Meinan CWRU
Hi Meinan, It looks like the cartoon style “arrowScale” factor was changed to a large value, maybe by an accidental command? You could try this command to put it back to the default value:
cartoon style arrowScale 2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 12, 2019, at 1:44 PM, Meinan Lyu mxl1032@case.edu wrote:
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much!
Best regards, Meinan CWRU
<fig3-aroudresi-ery.tif>
Thank you very much!
Elaine Meng meng@cgl.ucsf.edu于2019年10月14日 周一12:39写道:
Hi Meinan, It looks like the cartoon style “arrowScale” factor was changed to a large value, maybe by an accidental command? You could try this command to put it back to the default value:
cartoon style arrowScale 2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 12, 2019, at 1:44 PM, Meinan Lyu mxl1032@case.edu wrote:
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide
when using chimeraX to draw some figures, could you please tell me how to make it normal?
The problem showed after I put into these two command(not quite sure
yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true.
Thank you very much!
Best regards, Meinan CWRU
<fig3-aroudresi-ery.tif>
The zone command makes ribbons thinner outside the zone by default and it was not making the arrows smaller.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/zone.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/zone.html
I have fixed it in tonight's ChimeraX builds.
Tom
On Oct 14, 2019, at 9:39 AM, Elaine Meng wrote:
Hi Meinan, It looks like the cartoon style “arrowScale” factor was changed to a large value, maybe by an accidental command? You could try this command to put it back to the default value:
cartoon style arrowScale 2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 12, 2019, at 1:44 PM, Meinan Lyu wrote:
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much!
Best regards, Meinan CWRU
<fig3-aroudresi-ery.tif>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Meinan, If you just want to show residues within 5 angstroms of your ligand, you could do it directly with “show” instead of “zone.” For example, if your ligand in #3 has the residue name LIG:
show #3:lig & :<5
http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
…meaning show any residues within 5A of residue LIG in #3. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 14, 2019, at 11:06 AM, Tom Goddard goddard@sonic.net wrote:
The zone command makes ribbons thinner outside the zone by default and it was not making the arrows smaller.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/zone.html
I have fixed it in tonight's ChimeraX builds.
Tom
On Oct 14, 2019, at 9:39 AM, Elaine Meng wrote:
Hi Meinan, It looks like the cartoon style “arrowScale” factor was changed to a large value, maybe by an accidental command? You could try this command to put it back to the default value:
cartoon style arrowScale 2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 12, 2019, at 1:44 PM, Meinan Lyu wrote:
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much!
Best regards, Meinan CWRU
<fig3-aroudresi-ery.tif>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Oops! Should be
show #3:lig :<5
(no &)
Sorry about that, Elaine
On Oct 14, 2019, at 12:02 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Meinan, If you just want to show residues within 5 angstroms of your ligand, you could do it directly with “show” instead of “zone.” For example, if your ligand in #3 has the residue name LIG:
show #3:lig & :<5
http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
…meaning show any residues within 5A of residue LIG in #3. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 14, 2019, at 11:06 AM, Tom Goddard goddard@sonic.net wrote:
The zone command makes ribbons thinner outside the zone by default and it was not making the arrows smaller.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/zone.html
I have fixed it in tonight's ChimeraX builds.
Tom
On Oct 14, 2019, at 9:39 AM, Elaine Meng wrote:
Hi Meinan, It looks like the cartoon style “arrowScale” factor was changed to a large value, maybe by an accidental command? You could try this command to put it back to the default value:
cartoon style arrowScale 2
http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 12, 2019, at 1:44 PM, Meinan Lyu wrote:
Dear Dr.,
The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much!
Best regards, Meinan CWRU
<fig3-aroudresi-ery.tif>
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participants (3)
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Elaine Meng
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Meinan Lyu
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Tom Goddard