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 <tsjerkw@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 <ritesh1612@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

------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net



--
Tsjerk A. Wassenaar, Ph.D.