[Chimera-users] turning kdssp off

Mateusz Sikora masikora at biophys.mpg.de
Mon Jul 16 11:36:00 PDT 2018

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 at numpy converter... ?


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 at 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 at 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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