Re: [PyMOL] Multiple pdb simulation data
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 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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[PyMOL] Multiple pdb simulation data
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
Re: [PyMOL] combining multiple objects into one multistate object
there is a "join_states" command in PSICO.
http://pymolwiki.org/index.php/psico
Cheers,
Thomas
On 16 Jan 2014, at 11:15, Jason Vertrees wrote:
> Jed,
>
> Yes, the create command should more intelligently handle the wildcard. In
> fact, I started out trying the same thing you did. I'll add this as a feature
> request.
>
> Cheers,
>
> -- Jason
>
>
> On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone wrote:
> Thanks! That works. I kept trying to avoid writing a script, figuring that it
> should just be an option in 'create'. That is, if the selection old_obj has a
> wild card, then
> create new_obj, old_obj*,1,-1
> should work. Clearly not; could this be a future feature?
>
> Jed
>
>
>
>
> On 1/16/2014 10:56 AM, Jason Vertrees wrote:
>> Jed,
>>
>> You are correct in that you should be using the "create" command:
>>
>> # creates new_obj from old_obj1 by copying old_obj1
>> # in state 1 to new_obj in state 1
>>
>> create new_obj, old_obj1, 1, 1
>>
>> # creates new_obj from old_obj2 by copying old_obj2
>> # in state 1 to new_obj in state 2
>>
>> create new_obj, old_obj2, 1, 2
>>
>> # creates new_obj from old_obj3 by copying old_obj3
>> # in state 1 to new_obj in state 3
>>
>> create new_obj, old_obj3, 1, 3
>>
>>
>>
>> If you have any empty session, this will automate the process:
>>
>> python
>>
>> for x in cmd.get_names():
>>
>> cmd.create("combined_models", x, 1, -1)
>>
>> python end
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>>
>> On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone wrote:
>> I know this seems silly, but I can't figure out how to combine multiple
>> separate objects into one multistate object. I have a set of Modeler
>> models loaded from a single pdb file, automagically separated into
>> separate objects that have been aligned, and I want to combine them into
>> one object in order to run Robert Cambell's rmsf_states script (and,
>> also since it's just easier to compare and manipulate).
>>
>> I've searched the manual, the sourceforge list, and the wiki. Somehow
>> the command 'create' with 'target_state=-1' and 'discrete=1' seems like
>> it should do this, but all the objects end up in the first state (and
>> the cartoon representation is a subset of what it should be (other
>> representations are fine).
>> I'm using incentive v1.6.0.0 on Windows 7.
>>
>> Jed
--
Thomas Holder
PyMOL Developer
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Re: [PyMOL] combining multiple objects into one multistate object
Jed,
Yes, the create command should more intelligently handle the wildcard. In
fact, I started out trying the same thing you did. I'll add this as a
feature request.
Cheers,
-- Jason
On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone wrote:
> Thanks! That works. I kept trying to avoid writing a script, figuring
> that it should just be an option in 'create'. That is, if the selection
> old_obj has a wild card, then
> create new_obj, old_obj*,1,-1
> should work. Clearly not; could this be a future feature?
>
> Jed
>
>
>
>
> On 1/16/2014 10:56 AM, Jason Vertrees wrote:
>
> Jed,
>
> You are correct in that you should be using the "create" command:
>
> # creates new_obj from old_obj1 by copying old_obj1
> # in state 1 to new_obj in state 1
>
> create new_obj, old_obj1, 1, 1
>
> # creates new_obj from old_obj2 by copying old_obj2
> # in state 1 to new_obj in state 2
>
> create new_obj, old_obj2, 1, 2
>
> # creates new_obj from old_obj3 by copying old_obj3
> # in state 1 to new_obj in state 3
>
> create new_obj, old_obj3, 1, 3
>
>
>
> If you have any empty session, this will automate the process:
>
> python
>
> for x in cmd.get_names():
>
>cmd.create("combined_models", x, 1, -1)
>
> python end
>
> Cheers,
>
> -- Jason
>
>
>
> On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone wrote:
>
>> I know this seems silly, but I can't figure out how to combine multiple
>> separate objects into one multistate object. I have a set of Modeler
>> models loaded from a single pdb file, automagically separated into
>> separate objects that have been aligned, and I want to combine them into
>> one object in order to run Robert Cambell's rmsf_states script (and,
>> also since it's just easier to compare and manipulate).
>>
>> I've searched the manual, the sourceforge list, and the wiki. Somehow
>> the command 'create' with 'target_state=-1' and 'discrete=1' seems like
>> it should do this, but all the objects end up in the first state (and
>> the cartoon representation is a subset of what it should be (other
>> representations are fine).
>> I'm using incentive v1.6.0.0 on Windows 7.
>>
>> Jed
>>
>> --
>>
>> Jed Goldstone, PhD
>> Research Specialist
>> Woods Hole Oceanographic Institution
>> Redfield 3-52 MS#32
>> Woods Hole, MA 02543
>> http://www.whoi.edu/hpb/Site.do?id=481
>> Phone: 508-289-4823
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
>
> --
>
> Jed Goldstone, PhD
> Research Specialist
> Woods Hole Oceanographic Institution
> Redfield 3-52 MS#32
> Woods Hole, MA 02543http://www.whoi.edu/hpb/Site.do?id=481
> Phone: 508-289-4823
>
>
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
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Re: [PyMOL] combining multiple objects into one multistate object
Thanks! That works. I kept trying to avoid writing a script, figuring
that it should just be an option in 'create'. That is, if the selection
old_obj has a wild card, then
create new_obj, old_obj*,1,-1
should work. Clearly not; could this be a future feature?
Jed
On 1/16/2014 10:56 AM, Jason Vertrees wrote:
Jed,
You are correct in that you should be using the "create" command:
# creates new_obj from old_obj1 by copying old_obj1
# in state 1 to new_obj in state 1
create new_obj, old_obj1, 1, 1
# creates new_obj from old_obj2 by copying old_obj2
# in state 1 to new_obj in state 2
create new_obj, old_obj2, 1, 2
# creates new_obj from old_obj3 by copying old_obj3
# in state 1 to new_obj in state 3
create new_obj, old_obj3, 1, 3
If you have any empty session, this will automate the process:
python
for x in cmd.get_names():
cmd.create("combined_models", x, 1, -1)
python end
Cheers,
-- Jason
On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone > wrote:
I know this seems silly, but I can't figure out how to combine
multiple
separate objects into one multistate object. I have a set of Modeler
models loaded from a single pdb file, automagically separated into
separate objects that have been aligned, and I want to combine
them into
one object in order to run Robert Cambell's rmsf_states script (and,
also since it's just easier to compare and manipulate).
I've searched the manual, the sourceforge list, and the wiki. Somehow
the command 'create' with 'target_state=-1' and 'discrete=1' seems
like
it should do this, but all the objects end up in the first state (and
the cartoon representation is a subset of what it should be (other
representations are fine).
I'm using incentive v1.6.0.0 on Windows 7.
Jed
--
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823
--
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
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)
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Archives:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823
--
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.
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Re: [PyMOL] combining multiple objects into one multistate object
Hi Jed, On Thu, 2014-01-16 10:28 EST, Jed Goldstone wrote: > I know this seems silly, but I can't figure out how to combine multiple > separate objects into one multistate object. I have a set of Modeler > models loaded from a single pdb file, automagically separated into > separate objects that have been aligned, and I want to combine them into > one object in order to run Robert Cambell's rmsf_states script (and, > also since it's just easier to compare and manipulate). You probably have a reason for loading the models into separate objects, but my first suggestion would be to just load all of the models into a single object in the first place. You can align them using the "intra_fit" command. I normally load my modeller models into one object with my load_models.py script or my load_best.py script if I want them sorted by modeller's objective function value (both scripts are also on my web site). I like being able to see the models individually or all at once (with set all_states, 1). Cheers, Rob > > I've searched the manual, the sourceforge list, and the wiki. Somehow > the command 'create' with 'target_state=-1' and 'discrete=1' seems like > it should do this, but all the objects end up in the first state (and > the cartoon representation is a subset of what it should be (other > representations are fine). > I'm using incentive v1.6.0.0 on Windows 7. > > Jed > -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 http://pldserver1.biochem.queensu.ca/~rlc -- 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
Re: [PyMOL] combining multiple objects into one multistate object
Jed,
You are correct in that you should be using the "create" command:
# creates new_obj from old_obj1 by copying old_obj1
# in state 1 to new_obj in state 1
create new_obj, old_obj1, 1, 1
# creates new_obj from old_obj2 by copying old_obj2
# in state 1 to new_obj in state 2
create new_obj, old_obj2, 1, 2
# creates new_obj from old_obj3 by copying old_obj3
# in state 1 to new_obj in state 3
create new_obj, old_obj3, 1, 3
If you have any empty session, this will automate the process:
python
for x in cmd.get_names():
cmd.create("combined_models", x, 1, -1)
python end
Cheers,
-- Jason
On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone wrote:
> I know this seems silly, but I can't figure out how to combine multiple
> separate objects into one multistate object. I have a set of Modeler
> models loaded from a single pdb file, automagically separated into
> separate objects that have been aligned, and I want to combine them into
> one object in order to run Robert Cambell's rmsf_states script (and,
> also since it's just easier to compare and manipulate).
>
> I've searched the manual, the sourceforge list, and the wiki. Somehow
> the command 'create' with 'target_state=-1' and 'discrete=1' seems like
> it should do this, but all the objects end up in the first state (and
> the cartoon representation is a subset of what it should be (other
> representations are fine).
> I'm using incentive v1.6.0.0 on Windows 7.
>
> Jed
>
> --
>
> Jed Goldstone, PhD
> Research Specialist
> Woods Hole Oceanographic Institution
> Redfield 3-52 MS#32
> Woods Hole, MA 02543
> http://www.whoi.edu/hpb/Site.do?id=481
> Phone: 508-289-4823
>
>
>
> --
> 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
>
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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.
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[PyMOL] combining multiple objects into one multistate object
I know this seems silly, but I can't figure out how to combine multiple separate objects into one multistate object. I have a set of Modeler models loaded from a single pdb file, automagically separated into separate objects that have been aligned, and I want to combine them into one object in order to run Robert Cambell's rmsf_states script (and, also since it's just easier to compare and manipulate). I've searched the manual, the sourceforge list, and the wiki. Somehow the command 'create' with 'target_state=-1' and 'discrete=1' seems like it should do this, but all the objects end up in the first state (and the cartoon representation is a subset of what it should be (other representations are fine). I'm using incentive v1.6.0.0 on Windows 7. Jed -- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- 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
