Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off? I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it. I would appreciate some help. Best regards, Matt
Hi Matt, The slowness is probably the “chemical perception” rather than the secondary structure stuff. Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local> ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> Like Chimera, ChimeraX is free for noncommercial use. <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off?
I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
I would appreciate some help. Best regards, Matt
Hi Matt, What Elaine says is completely accurate. One thing you can try in Chimera itself is to open your file using the ‘noprefs’ keyword of the ‘open’ command (e.g. “open noprefs my-file”). This will make Chimera show the structure as simple wireframe and should sidestep the chemical perception step. If that doesn’t work, then ChimeraX will work! —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2018, at 10:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Matt, The slowness is probably the “chemical perception” rather than the secondary structure stuff.
Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
Like Chimera, ChimeraX is free for noncommercial use. <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off?
I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
I would appreciate some help. Best regards, Matt
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Thank you guys for prompt answers, I do not use the GUI at all, but I will try updating my script with noprefs. If this does not work I could split my system to sub-systems and sum up the maps - do you know any tool that could do that, without writing mrc@numpy converter... ? Matt On 16/07/18 19:48, Eric Pettersen wrote:
Hi Matt, What Elaine says is completely accurate. One thing you can try in Chimera itself is to open your file using the ‘noprefs’ keyword of the ‘open’ command (e.g. “open noprefs my-file”). This will make Chimera show the structure as simple wireframe and should sidestep the chemical perception step. If that doesn’t work, then ChimeraX will work!
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2018, at 10:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Matt, The slowness is probably the “chemical perception” rather than the secondary structure stuff.
Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
Like Chimera, ChimeraX is free for noncommercial use. <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off?
I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
I would appreciate some help. Best regards, Matt
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Matt, The “vop add” command in Chimera (“volume add” in ChimeraX) sums maps. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> Best, Elaine
On Jul 16, 2018, at 11:36 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Thank you guys for prompt answers,
I do not use the GUI at all, but I will try updating my script with noprefs.
If this does not work I could split my system to sub-systems and sum up the maps - do you know any tool that could do that, without writing mrc@numpy converter... ?
Matt
On 16/07/18 19:48, Eric Pettersen wrote:
Hi Matt, What Elaine says is completely accurate. One thing you can try in Chimera itself is to open your file using the ‘noprefs’ keyword of the ‘open’ command (e.g. “open noprefs my-file”). This will make Chimera show the structure as simple wireframe and should sidestep the chemical perception step. If that doesn’t work, then ChimeraX will work!
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 16, 2018, at 10:37 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Matt, The slowness is probably the “chemical perception” rather than the secondary structure stuff.
Although Chimera does not have an option to turn this off, ChimeraX does; see ChimeraX command “open” with “atomic false” option: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local>
ChimeraX is generally better (faster) with large data, and it also has the “molmap” command for transforming atomic coordinates to density: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
Like Chimera, ChimeraX is free for noncommercial use. <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 9:47 AM, Mateusz Sikora <masikora@biophys.mpg.de> wrote:
Dear Chimera users, is there any way to turn the secondary structure assignment (kdssp) off?
I am transforming a set of coordinates from a MD trajectory into electron density. I collapsed many frames of the trajectory into a single file, meaning there are many unphysical overlaps (I only care about the density). Problem is, that the PDB file I am opening is rather large (couple of millions of atoms) and kdssp gets absolutely stuck on it.
I would appreciate some help. Best regards, Matt
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Mateusz Sikora