date:20150106

Re: [PyMOL] holes in isosurface representation

2015-01-06 Thread Spencer Bliven

Hey Jacob,

Are Lagging_A and Leading_B selections or objects? Generally for surfaces
to display right you have to create a new object for the part you want
(using either the create or extract commands). Otherwise you get holes in
the surface where the selection contacts the rest of the object.

-Spencer

On Tue, Dec 30, 2014 at 10:16 PM, Jacob Lewis  wrote:

> Hi all,
>
> I am using the maps and isosurface to represent a large protein protein
> complex, however whenever I generate a a map then isosurface it has holes
> in it areas that are not complete. I don’t understand as it surface
> representation it is a complete, closed surface? Anyone have any ideas as
> to why this is happening? Below is how I generate the maps and isosurface.
>
> remove solvent
> alter all, b=40
> alter all, q=1
> set gaussian_resolution,15
> set surface_quality, 2
>
> # Clamp Loader Maps
> # Lagging A
> map_new Lagging_A-MAP, gaussian, 1, Lagging_A, 3
> isosurface Lagging_A-SURF, Lagging_A-MAP
>
> # Leading B
> map_new Leading_B-MAP, gaussian, 1, Leading_B, 3
> isosurface Leading_B-SURF, Leading_B-MAP
>
> Any help is greatly appreciated,
>
> Cheers,
>
> Jacob
>
> --
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[PyMOL] How do I undo my last command I executed in the PyMOL command line and viewer?

2015-01-06 Thread Brenton Horne

Hi,

I thought that running "undo" from the PyMOL command line would do this 
but it didn't do anything that I could see visually in the viewer. I've 
also tried going to Edit->Undo and it didn't do anything visually 
apparent in the viewer.

Thanks for your time,
Brenton

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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Yarrow Madrona

Sorry,

I didn't read the other entries. Thanks for the "python end" code. I have
had this problem with loops a lot in pymol and this solves it.

-Yarrow

On Tue, Jan 6, 2015 at 9:21 AM, Yarrow Madrona 
wrote:

> Hi Brenton,
>
> I'm pretty sure you have to import python in your script. Otherwise the
> python commands will be ignored. Also you forgot to put colons after your
> 'for' statement. Either way, I think pymol got the first image then ignored
> the 'for statement' and just went straight to the second 'png.' which
> it named %4d because you didn't tell it to recognize python string
> formatting by importing python.
>
> -Yarrow
>
> On Tue, Jan 6, 2015 at 6:00 AM, Brenton Horne 
> wrote:
>
>> Hi,
>>
>> I've been executing the pml script I wrote:
>>
>> set ray_opaque_background, 0
>>
>> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
>> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>>
>> for i in range(2, 60)
>>
>>  rotate y, 6
>>
>>  png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
>> imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1
>>
>>
>> The desired result from this script is a series of 60 transparent pngs
>> taken at 6 degrees apart (rotated around the y axis) with name
>> Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly
>> however I only got two PNGs: Image0001.png and Image%4d.png. How do I
>> overcome this problem?
>>
>> Thanks for your time,
>> Brenton
>>
>>
>>
>> --
>> Dive into the World of Parallel Programming! The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
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>>
>
>
>
> --
> Yarrow Madrona, Ph.D.
> *Postdoctoral Scholar*
> University of California, San Francisco
> Department of Pharmaceutical Chemistry
> Rm N551, 600 16th street
> San Francisco CA, 94143
>



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*Postdoctoral Scholar*
University of California, San Francisco
Department of Pharmaceutical Chemistry
Rm N551, 600 16th street
San Francisco CA, 94143
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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Yarrow Madrona

Hi Brenton,

I'm pretty sure you have to import python in your script. Otherwise the
python commands will be ignored. Also you forgot to put colons after your
'for' statement. Either way, I think pymol got the first image then ignored
the 'for statement' and just went straight to the second 'png.' which
it named %4d because you didn't tell it to recognize python string
formatting by importing python.

-Yarrow

On Tue, Jan 6, 2015 at 6:00 AM, Brenton Horne 
wrote:

> Hi,
>
> I've been executing the pml script I wrote:
>
> set ray_opaque_background, 0
>
> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>
> for i in range(2, 60)
>
>  rotate y, 6
>
>  png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1
>
>
> The desired result from this script is a series of 60 transparent pngs
> taken at 6 degrees apart (rotated around the y axis) with name
> Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly
> however I only got two PNGs: Image0001.png and Image%4d.png. How do I
> overcome this problem?
>
> Thanks for your time,
> Brenton
>
>
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
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>



-- 
Yarrow Madrona, Ph.D.
*Postdoctoral Scholar*
University of California, San Francisco
Department of Pharmaceutical Chemistry
Rm N551, 600 16th street
San Francisco CA, 94143
--
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Re: [PyMOL] Dot representation

2015-01-06 Thread Yarrow Madrona

Thanks Jared.

On Mon, Jan 5, 2015 at 1:35 PM, Sampson, Jared 
wrote:

>  Hi Yarrow -
>
>  1. Yes, according to the wiki , the
> dots are located on the vdW surface unless the `dot_solvent` setting is
> turned on (in which case they’re on the solvent accessible surface).
>
>  2. Based on the settings listed with “dot” in their names, it doesn’t
> look like dot_transparency is currently available.
>
>  Hope that helps.
>
>  Cheers,
> Jared
>
>   --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Dec 30, 2014, at 6:48 PM, Yarrow Madrona 
> wrote:
>
>  Hell Pymolers,
>
>  1. Does anyone know what the dot representation for a residue
> represents? Is it the van der waals radii?
>
>  2. Is there a way to draw transparency for the dots?
>
>  -Yarrow
>
>
>  --
>Yarrow Madrona, Ph.D.
>   *Postdoctoral Scholar*
> University of California, San Francisco
>  Department of Pharmaceutical Chemistry
>  Rm N551, 600 16th street
> San Francisco CA, 94143
>
> --
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>
>
>
>
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-- 
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*Postdoctoral Scholar*
University of California, San Francisco
Department of Pharmaceutical Chemistry
Rm N551, 600 16th street
San Francisco CA, 94143
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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Matthew Baumgartner

I think that the problem is that python is interpreting part of your 
directories as special characters. This is due to the fact that Windows 
uses the backslash as the directory separator which is also a special 
character in python (and in *nix systems).


In a regular python terminal, if I do:

print "C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4))


I get:
C:\\Users\\Brenton\\Documents\\Chem Structures\\PDBs*\x02\x02*HYY - 
imatinib\\PyMOL movie\\Image0003.png


Which is not a directory. To fix this, make the string a raw string 
(https://docs.python.org/2/reference/lexical_analysis.html#string-literals) 
by adding a 'r' before the string like:


print *r*'C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image{}.png'.format(str(i).zfill(4))


Now we get the correct directory:
C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image0003.png



Matt Baumgartner

On 01/06/2015 11:14 AM, Brenton Horne wrote:
I checked, it's not the problem, sadly. Anyway, the first line, 
outside the loop, which has the same location saves to Image0001.png 
just fine in the correct location without that directory error.


On 7/01/2015 2:11 AM, Matthew Baumgartner wrote:
I think that is because that the directory there doesn't exist. I 
think I made a copy paste error of your directory structure.


Please double check, but from your earlier email, it was

C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\




On 1/6/15, 11:08 AM, Brenton Horne wrote:

I should add that this error occurs for each loop.

On 7/01/2015 2:05 AM, Brenton Horne wrote:
This script gives the error (after the first frame that occurs 
before the loop):


ScenePNG-Error: error writing "C:\Users\Brenton\Documents\Chem 
Structures\PDBsHYY - imatinib\PyMOL movie\Image0060.png"! Please 
check directory...



On 7/01/2015 1:52 AM, Matthew Baumgartner wrote:
Be sure to reply to the list so everyone can benefit from the 
questions and answers.


Ah, as Tsjerk mentioned, you need to wrap it in a python-python 
end block.



set ray_opaque_background, 0

png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1


python
for i in range(2,61):
cmd.rotate('y', 6)
cmd.png("C:\Users\Brenton\Documents\Chem 
Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)

python end


On 01/06/2015 10:40 AM, Brenton Horne wrote:

Sure is this is my code atm:

set ray_opaque_background, 0

png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1


for i in range(2,61):

rotate y, 6

cmd.png("C:\Users\Brenton\Documents\Chem 
Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)



On 7/01/2015 1:33 AM, Matthew Baumgartner wrote:

Is it in your for loop?

for i in range(2,61):
rotate y, 6
cmd.png("C:\Users\Brenton\Documents\Chem 
Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)


On 1/6/15, 10:13 AM, Brenton Horne wrote:

That gave the error:

cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY 
- imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), 
dpi=300, ray=1)

Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\pymol\parser.py", line 
464, in parse

exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "", line 1, in 
NameError: name 'i' is not defined

On 7/01/2015 1:03 AM, Matthew Baumgartner wrote:
cmd.png("C:\Users\Brenton\Documents\Chem 
Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)





















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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Tsjerk Wassenaar

Hey :)

"Image{}.png".format(str(i).zfill(4))

can also be written

Image{:04d}.png".format(i)

Cheers,

Tsjerk


On Tue, Jan 6, 2015 at 4:52 PM, Matthew Baumgartner  wrote:

> Be sure to reply to the list so everyone can benefit from the questions
> and answers.
>
> Ah, as Tsjerk mentioned, you need to wrap it in a python-python end block.
>
>
> set ray_opaque_background, 0
>
> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>
> python
> for i in range(2,61):
>  cmd.rotate('y', 6)
>  cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
> python end
>
>
> On 01/06/2015 10:40 AM, Brenton Horne wrote:
> > Sure is this is my code atm:
> >
> > set ray_opaque_background, 0
> >
> > png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> > imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
> >
> > for i in range(2,61):
> >
> > rotate y, 6
> >
> > cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> > imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300,
> > ray=1)
> >
> >
> > On 7/01/2015 1:33 AM, Matthew Baumgartner wrote:
> >> Is it in your for loop?
> >>
> >> for i in range(2,61):
> >> rotate y, 6
> >> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> >> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300,
> >> ray=1)
> >>
> >> On 1/6/15, 10:13 AM, Brenton Horne wrote:
> >>> That gave the error:
> >>>
> >>> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> >>> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300,
> >>> ray=1)
> >>> Traceback (most recent call last):
> >>>   File "C:\Python27\lib\site-packages\pymol\parser.py", line 464, in
> >>> parse
> >>> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
> >>>   File "", line 1, in 
> >>> NameError: name 'i' is not defined
> >>>
> >>> On 7/01/2015 1:03 AM, Matthew Baumgartner wrote:
>  cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
>  imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300,
>  ray=1)
> >>>
> >>
> >>
> >
>
>
>
> --
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> your
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>



-- 
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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Matthew Baumgartner

Be sure to reply to the list so everyone can benefit from the questions 
and answers.

Ah, as Tsjerk mentioned, you need to wrap it in a python-python end block.


set ray_opaque_background, 0

png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1

python
for i in range(2,61):
 cmd.rotate('y', 6)
 cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
python end


On 01/06/2015 10:40 AM, Brenton Horne wrote:
> Sure is this is my code atm:
>
> set ray_opaque_background, 0
>
> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>
> for i in range(2,61):
>
> rotate y, 6
>
> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
> ray=1)
>
>
> On 7/01/2015 1:33 AM, Matthew Baumgartner wrote:
>> Is it in your for loop?
>>
>> for i in range(2,61):
>> rotate y, 6
>> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
>> ray=1)
>>
>> On 1/6/15, 10:13 AM, Brenton Horne wrote:
>>> That gave the error:
>>>
>>> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>>> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
>>> ray=1)
>>> Traceback (most recent call last):
>>>   File "C:\Python27\lib\site-packages\pymol\parser.py", line 464, in 
>>> parse
>>> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>>>   File "", line 1, in 
>>> NameError: name 'i' is not defined
>>>
>>> On 7/01/2015 1:03 AM, Matthew Baumgartner wrote:
 cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
 imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
 ray=1)
>>>
>>
>>
>


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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Matthew Baumgartner

Is it in your for loop?

for i in range(2,61):
 rotate y, 6
 cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)

On 1/6/15, 10:13 AM, Brenton Horne wrote:
> That gave the error:
>
> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
> ray=1)
> Traceback (most recent call last):
>   File "C:\Python27\lib\site-packages\pymol\parser.py", line 464, in 
> parse
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "", line 1, in 
> NameError: name 'i' is not defined
>
> On 7/01/2015 1:03 AM, Matthew Baumgartner wrote:
>> cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
>> ray=1)
>


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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Tsjerk Wassenaar

Hi :)

You can use for-loops in pml files, but it's a bit tricky. Usually you will
want to enclose the code in a python .. python end block, indicating that
the lines are pure python:

python
for i in range(2,61):
  ...
python end

Also mind that range runs UP TO (excluding) the last number, so you'll need
to put 61 if you want the counter to run to 60. For cases like this, I tend
to use a trick, so I put the for-loop on one line, and thus avoid the
python block:

filename="C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image%04d.png"
rotate y, -6
for i in range(1,61): cmd.rotate("y",6) or cmd.png(filename%i, dpi=300,
ray=1)

Hope it helps,

Tsjerk



On Tue, Jan 6, 2015 at 4:09 PM, David Hall  wrote:

> (a) I'll let someone else say whether you can use range in pml files, not
> completely sure on that one and the formatting rules. personally, I would
> write this in python, and you would need a : after the range
>
> (b) you are missing any indication of what %4d refers to. See example 3.23
> on http://www.diveintopython.net/native_data_types/formatting_strings.html
> , you need to have a % i so that there's a variable corresponding to your
> %4d. I also think you want %04d . And again, not sure what the rules are in
> pml files, python is much better documented.
>
> On Tue, Jan 6, 2015 at 9:00 AM, Brenton Horne 
> wrote:
>
>> Hi,
>>
>> I've been executing the pml script I wrote:
>>
>> set ray_opaque_background, 0
>>
>> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
>> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>>
>> for i in range(2, 60)
>>
>>  rotate y, 6
>>
>>  png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
>> imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1
>>
>>
>> The desired result from this script is a series of 60 transparent pngs
>> taken at 6 degrees apart (rotated around the y axis) with name
>> Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly
>> however I only got two PNGs: Image0001.png and Image%4d.png. How do I
>> overcome this problem?
>>
>> Thanks for your time,
>> Brenton
>>
>>
>>
>> --
>> Dive into the World of Parallel Programming! The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net
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>>
>
>
>
> --
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> your
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>



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Re: [PyMOL] Scripting attempts

2015-01-06 Thread Matthew Baumgartner

Hi,
You may need to use the API instead of the command.
cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)

Matt Baumgartner

On 01/06/2015 10:01 AM, Brenton Horne wrote:
> Hi
>
> I received this error from your modified code:
>
> png "C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1
>
>  Ray: render time: 8.97 sec. = 401.4 frames/hour (1278.57 sec. accum.).
>
>  ScenePNG-Error: error writing ""C:\Users\Brenton\Documents\Chem 
> Structures\PDBs\2\2HYY - imatinib\PyMOL 
> movie\Image{}.png".format(str(i).zfill(4)).png"! Please check 
> directory...
>
> Thanks for your time,
> Brenton
>
> On 7/01/2015 12:33 AM, Matthew Baumgartner wrote:
>> The problem that you have is not a PyMOL problem, but a bug in your 
>> code. You didn't change the file name to include the index.
>>
>> Replace the png command with this:
>>
>> png "C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>> imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)), dpi=300, 
>> ray=1
>>
>>
>> HTH,
>> Matt Baumgartner
>>
>>
>> On 01/06/2015 09:00 AM, Brenton Horne wrote:
>>> Hi,
>>>
>>> I've been executing the pml script I wrote:
>>>
>>> set ray_opaque_background, 0
>>>
>>> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>>> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>>>
>>> for i in range(2, 60)
>>>
>>>   rotate y, 6
>>>
>>>   png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
>>> imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1
>>>
>>>
>>> The desired result from this script is a series of 60 transparent 
>>> pngs taken at 6 degrees apart (rotated around the y axis) with name
>>> Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. 
>>> Sadly however I only got two PNGs: Image0001.png and Image%4d.png. 
>>> How do I overcome this problem?
>>>
>>> Thanks for your time,
>>> Brenton
>>>
>>>
>>> --
>>>  
>>>
>>> Dive into the World of Parallel Programming! The Go Parallel Website,
>>> sponsored by Intel and developed in partnership with Slashdot Media, 
>>> is your
>>> hub for all things parallel software development, from weekly thought
>>> leadership blogs to news, videos, case studies, tutorials and more. 
>>> Take a
>>> look and join the conversation now. http://goparallel.sourceforge.net
>>> ___
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>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>


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Re: [PyMOL] Scripting attempts

2015-01-06 Thread David Hall

(a) I'll let someone else say whether you can use range in pml files, not
completely sure on that one and the formatting rules. personally, I would
write this in python, and you would need a : after the range

(b) you are missing any indication of what %4d refers to. See example 3.23
on http://www.diveintopython.net/native_data_types/formatting_strings.html
, you need to have a % i so that there's a variable corresponding to your
%4d. I also think you want %04d . And again, not sure what the rules are in
pml files, python is much better documented.

On Tue, Jan 6, 2015 at 9:00 AM, Brenton Horne 
wrote:

> Hi,
>
> I've been executing the pml script I wrote:
>
> set ray_opaque_background, 0
>
> png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
>
> for i in range(2, 60)
>
>  rotate y, 6
>
>  png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
> imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1
>
>
> The desired result from this script is a series of 60 transparent pngs
> taken at 6 degrees apart (rotated around the y axis) with name
> Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly
> however I only got two PNGs: Image0001.png and Image%4d.png. How do I
> overcome this problem?
>
> Thanks for your time,
> Brenton
>
>
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
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Re: [PyMOL] Selecting specific ligands for colouring

2015-01-06 Thread Matthew Baumgartner


Hi,
I just wanted to chime in and add to what Folmer said.
Your selection syntax was close, but not quite correct, you are missing 
a slash.
Following you example, you would do /2hyy//A/600 where 600 is the 
residue id of the ligand.


But in general, I would recommend using the syntax that Folmer suggested 
wherein you spell out the selections. In addition to being more 
readable, you can make more powerful and complex selections.


To answer your second question, you can check out the PyMOL Cheat Sheet 
which has a nice summary of commands. It is available here: 
http://www.pymolwiki.org/index.php/CheatSheet


It's not necessarily completely up to date though. The wiki page 
indicates that it was last updated in 2008. Perhaps one of the devs 
could comment on any changes.


Matt Baumgartner

On 01/06/2015 04:34 AM, Folmer Fredslund wrote:

Hi Brenton,

It seems 2HYY only has that one (type of) ligand present?
so:

fetch 2hyy
as cartoon
show sticks, organic
color black, elem c and organic
remove not chain a

gives me a cartoon representation of the protein, with a stick 
representation of the ligand. There are 4 copies of the complex in the 
asymmetric unit and they have chain ID's A-D, so the last command 
removes all atoms except the ones in chain a.


I am personally more comfortable with this kind of selections, instead 
of the 2hhy/something/something/something


In case you want to keep all molecules, but just select on of the 
ligands, you could do something like:


select ligandA, organic and chain a and resname STI


Hope this helps,
Folmer




2015-01-06 9:40 GMT+01:00 Brenton Horne >:


Hi,

I know I must be getting annoying, although I must say this
mailing list and its users have been very helpful for me so thank
you all. My question this time is how do I select specific
ligands? Like I am using PDB ID 2HYY and I'd like to set the
imatinib (STI600) ligand as the only visible ligand, plus I'd like
to colour it according to the CPK scheme, except with carbons
coloured black. Now I've tried:

select  2hyy/A/STI

based on the Selection Algebra
 page on PyMOL
Wiki but this returned the result:

Selector: selection "sele" defined with 0 atoms.


ps. is there are any PDF document showing complete up-to-date
command-line syntax for PyMOL because I think this will really
help me. PyMOL Wiki I find generally only gives a snippet of the
command-line syntax for a given topic. Plus I generally find the
really general format of the syntax (e.g.,

show reprentation [,object]

) with the square brackets PyMOL sometimes shows is confusing to
me, unless it's accompanied by an example of how that code appears
for a specific example.

Thanks for your time,
Brenton


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Re: [PyMOL] PyMOL png movie creation from command line

2015-01-06 Thread Matthew Baumgartner

Hi,
When you ray trace you can specify the dimensions of the resulting image 
in pixels, eg:
ray 600,800

You can also set the resolution when saving the png file:
png image.png, dpi=300

HTH,
Matt Baumgartner

On 01/06/2015 12:39 AM, Brenton Horne wrote:
> Hi,
>
> I'd like to know how to create a series of PNGs of customized width,
> height and dpi taken at a customizable angle between frames. I've tried
> using eMovie but I don't know how to set the image resolution for each
> frame using this extension. A command line-based way of creating these
> serial PNGs I think would be best with me, if it is possible.
>
> Thanks for your time,
> Brenton
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
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[PyMOL] Scripting attempts

2015-01-06 Thread Brenton Horne

Hi,

I've been executing the pml script I wrote:

set ray_opaque_background, 0

png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL 
movie\Image0001.png, dpi=300, ray=1

for i in range(2, 60)

 rotate y, 6

 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - 
imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1


The desired result from this script is a series of 60 transparent pngs taken at 
6 degrees apart (rotated around the y axis) with name
Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly however 
I only got two PNGs: Image0001.png and Image%4d.png. How do I overcome this 
problem?

Thanks for your time,
Brenton


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Re: [PyMOL] Selecting specific ligands for colouring

2015-01-06 Thread Folmer Fredslund

Hi Brenton,

It seems 2HYY only has that one (type of) ligand present?
so:

fetch 2hyy
as cartoon
show sticks, organic
color black, elem c and organic
remove not chain a

gives me a cartoon representation of the protein, with a stick
representation of the ligand. There are 4 copies of the complex in the
asymmetric unit and they have chain ID's A-D, so the last command removes
all atoms except the ones in chain a.

I am personally more comfortable with this kind of selections, instead of
the 2hhy/something/something/something

In case you want to keep all molecules, but just select on of the ligands,
you could do something like:

select ligandA, organic and chain a and resname STI


Hope this helps,
Folmer




2015-01-06 9:40 GMT+01:00 Brenton Horne :

>  Hi,
>
> I know I must be getting annoying, although I must say this mailing list
> and its users have been very helpful for me so thank you all. My question
> this time is how do I select specific ligands? Like I am using PDB ID 2HYY
> and I'd like to set the imatinib (STI600) ligand as the only visible
> ligand, plus I'd like to colour it according to the CPK scheme, except with
> carbons coloured black. Now I've tried:
>
> select 2hyy/A/STI
>
> based on the Selection Algebra
>  page on PyMOL Wiki but
> this returned the result:
>
> Selector: selection "sele" defined with 0 atoms.
>
>
> ps. is there are any PDF document showing complete up-to-date command-line
> syntax for PyMOL because I think this will really help me. PyMOL Wiki I
> find generally only gives a snippet of the command-line syntax for a given
> topic. Plus I generally find the really general format of the syntax (e.g.,
>
> show reprentation [,object]
>
> ) with the square brackets PyMOL sometimes shows is confusing to me,
> unless it's accompanied by an example of how that code appears for a
> specific example.
>
> Thanks for your time,
> Brenton
>
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net
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>



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[PyMOL] Selecting specific ligands for colouring

2015-01-06 Thread Brenton Horne


Hi,

I know I must be getting annoying, although I must say this mailing list 
and its users have been very helpful for me so thank you all. My 
question this time is how do I select specific ligands? Like I am using 
PDB ID 2HYY and I'd like to set the imatinib (STI600) ligand as the only 
visible ligand, plus I'd like to colour it according to the CPK scheme, 
except with carbons coloured black. Now I've tried:


select  2hyy/A/STI

based on the Selection Algebra 
 page on PyMOL Wiki 
but this returned the result:


   Selector: selection "sele" defined with 0 atoms.


ps. is there are any PDF document showing complete up-to-date 
command-line syntax for PyMOL because I think this will really help me. 
PyMOL Wiki I find generally only gives a snippet of the command-line 
syntax for a given topic. Plus I generally find the really general 
format of the syntax (e.g.,


show reprentation [,object]

) with the square brackets PyMOL sometimes shows is confusing to me, 
unless it's accompanied by an example of how that code appears for a 
specific example.


Thanks for your time,
Brenton
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Re: [PyMOL] Selecting specific ligands for colouring

[PyMOL] Selecting specific ligands for colouring

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