[PyMOL] colouring states independently
Hi,
I have been fighting with this problem for some time now,
and I think it is time to try to ask to more experienced users.
What I want to achieve is really simple. I want to make a movie
with only spheres. At every frame each sphere has also a scalar
property (e.g. local density) which is used to color the sphere
accordingly.
So my input are a series of xyz files, and a corresponding series
of files holding the value of that scalar for each particle.
What I'm doing now is:
*) loading all the xyz file into different states
*) creating a frame from each of these states
*) loop on the different frames and color the spheres
according to the field
My problem is in this last point, as I cannot find a way to
tell pymol to colour each sphere only for that frame, and
I always end up with a movie where the colour of the spheres
is fixed by the last frame.
Here is some pseudo code for what I'm doing:
for file in file_list:
cmd.load(file,"movie")
cmd.mset("1 -%d" % cmd.count_states())
for i in range(1,cmd.count_states()+1):
name="%d" % (i)
cmd.frame(i)
scalar=readField(scalar_field[i])
for particle_index,s in enumerate(scalar):
cmd.select("particle","id "+str(particle_index+1))
cmd.color(custom_color[s],"particle")
cmd.scene(name,"store")
cmd.mview('store',name)
One last thing, the number of particles is not the same for every state.
I hope somebody can help me. Thanks,
John
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Re: [PyMOL] colouring states independently
Hi John,
what you need is a "discrete" object, not only because of the coloring,
but also because you say the number of particles is not the same for
each state.
Try to apply two modifications:
1) "discrete" argument for "load":
cmd.load(file, "movie", discrete=1)
2) "state" argument for "select":
cmd.select("particle", "id "+str(particle_index+1), state=i)
I hope this will work :)
Cheers,
Thomas
John Russo wrote, On 08/31/12 09:14:
> Hi,
> I have been fighting with this problem for some time now,
> and I think it is time to try to ask to more experienced users.
>
> What I want to achieve is really simple. I want to make a movie
> with only spheres. At every frame each sphere has also a scalar
> property (e.g. local density) which is used to color the sphere
> accordingly.
>
> So my input are a series of xyz files, and a corresponding series
> of files holding the value of that scalar for each particle.
>
> What I'm doing now is:
>
> *) loading all the xyz file into different states
> *) creating a frame from each of these states
> *) loop on the different frames and color the spheres
> according to the field
>
> My problem is in this last point, as I cannot find a way to
> tell pymol to colour each sphere only for that frame, and
> I always end up with a movie where the colour of the spheres
> is fixed by the last frame.
>
> Here is some pseudo code for what I'm doing:
>
>
> for file in file_list:
> cmd.load(file,"movie")
>
> cmd.mset("1 -%d" % cmd.count_states())
>
> for i in range(1,cmd.count_states()+1):
> name="%d" % (i)
>
> cmd.frame(i)
>
> scalar=readField(scalar_field[i])
>
> for particle_index,s in enumerate(scalar):
>
> cmd.select("particle","id "+str(particle_index+1))
> cmd.color(custom_color[s],"particle")
>
>
> cmd.scene(name,"store")
> cmd.mview('store',name)
>
>
> One last thing, the number of particles is not the same for every state.
>
> I hope somebody can help me. Thanks,
>
>John
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] colouring states independently
Thank you,
I didn't know that select has also a "state" option. That solved the
problem.
John
On 08/31/2012 04:57 PM, Thomas Holder wrote:
> Hi John,
>
> what you need is a "discrete" object, not only because of the
> coloring, but also because you say the number of particles is not the
> same for each state.
>
> Try to apply two modifications:
>
> 1) "discrete" argument for "load":
> cmd.load(file, "movie", discrete=1)
>
> 2) "state" argument for "select":
> cmd.select("particle", "id "+str(particle_index+1), state=i)
>
> I hope this will work :)
>
> Cheers,
> Thomas
>
> John Russo wrote, On 08/31/12 09:14:
>> Hi,
>> I have been fighting with this problem for some time now,
>> and I think it is time to try to ask to more experienced users.
>>
>> What I want to achieve is really simple. I want to make a movie
>> with only spheres. At every frame each sphere has also a scalar
>> property (e.g. local density) which is used to color the sphere
>> accordingly.
>>
>> So my input are a series of xyz files, and a corresponding series
>> of files holding the value of that scalar for each particle.
>>
>> What I'm doing now is:
>>
>> *) loading all the xyz file into different states
>> *) creating a frame from each of these states
>> *) loop on the different frames and color the spheres
>> according to the field
>>
>> My problem is in this last point, as I cannot find a way to
>> tell pymol to colour each sphere only for that frame, and
>> I always end up with a movie where the colour of the spheres
>> is fixed by the last frame.
>>
>> Here is some pseudo code for what I'm doing:
>>
>>
>> for file in file_list:
>> cmd.load(file,"movie")
>>
>> cmd.mset("1 -%d" % cmd.count_states())
>>
>> for i in range(1,cmd.count_states()+1):
>> name="%d" % (i)
>>
>> cmd.frame(i)
>>
>> scalar=readField(scalar_field[i])
>>
>> for particle_index,s in enumerate(scalar):
>>
>> cmd.select("particle","id "+str(particle_index+1))
>> cmd.color(custom_color[s],"particle")
>>
>>
>> cmd.scene(name,"store")
>> cmd.mview('store',name)
>>
>>
>> One last thing, the number of particles is not the same for every state.
>>
>> I hope somebody can help me. Thanks,
>>
>>John
>
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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