Hi Tsjerk,
Thanks you for your reply. Sorry for my late response, for some reasons the
mail went to the spam folder.
This is my log.pml file which I am trying to use to load all the simulation
generated pdb files.
for i in range(251,1000,100): cmd.load("prod_%d.pdb"%i,"traj")
hide all
show cartoon
create chainA, prod_251 and chain A
create chainB, prod_251 and chain B
create chainF, prod_251 and chain F
create chainU, prod_251 and chain U
create chainI, prod_251 and chain I
create chainE, prod_251 and chain E
cmd.color(6,"chainF")
cmd.disable('prod_251')
cmd.enable('prod_251',1)
cmd.color(8,"chainU")
cmd.color(5,"chainI")
cmd.color(13,"chainE")
cmd.disable('prod_251')
show sticks, chain*
util.cba(154,"chainA",_self=cmd)
util.cba(11,"chainB",_self=cmd)
util.cba(6,"chainF",_self=cmd)
util.cba(144,"chainU",_self=cmd)
util.cba(5,"chainI",_self=cmd)
util.cba(9,"chainE",_self=cmd)
hide sticks, resn HEME
remove hydrogens
set orthoscopic, on
get_view
_ set_view (\
_ 0.346752405, 0.364839107, 0.864089847,\
_ 0.836608529, -0.536830068, -0.109060325,\
_ 0.424081028, 0.760723948, -0.491375208,\
_ 0.000060976, -0.000058983, -180.212646484,\
_ 27.008840561, -10.384629250, -7.024227142,\
_ 99.177673340, 261.227661133, 20.000000000 )
I tried to run this script but nothing comes up. My question is:
a) How to I do the rendering, before loading the structures or after
issuing the "for i in range(0,1000,100): cmd.load("file%d.pdb"%i,"traj")"
command.
b) How to I modify my .pml file to take the "traj" object name?
Again thanks for your help.
Ritesh
On Fri, Jan 17, 2014 at 12:58 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote:
> Hi Ritesh,
>
> Assuming you want the PDB files to end up in one object and they are
> numbered like file0.pdb .. file1000.pdb
>
> for i in range(0,1000,100): cmd.load("file%d.pdb"%i,"traj")
>
> You can set the step size from 100 to 50, 25, ...
> One thing that you may want to ask yourself is whether you need all the
> water. The visualization will be a lot smoother without.
>
> @Jason, feature request: Adding a selection (or exclusion) argument to
> load :) That could prevent work and file-clutter when handling simulation
> data.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Jan 17, 2014 at 12:08 AM, Ritesh Kumar <ritesh1...@gmail.com>wrote:
>
>> Dear All,
>>
>> I have around 1000 PDB files generated from the MD simulation. Each file
>> is around 32 MB in size.
>>
>> What I am trying to do:
>>
>> a) Load every 100th pdb file automatically and analyze the data.
>>
>> b) I am also trying to customize the load list, for example from 100 to
>> say 50 or 25 or 10 like this.
>>
>> Any help would be greatly appreciated.
>>
>> Thanks
>> RK
>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
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