Re: [PyMOL] pymol to webGL?

[Albert]

Dear Osvaldo:

Thanks a lot for further information.

I just run the command

|set pse_export_version, 1.72 |


before I load anything to pymol, then followed the step for exporting. 
But it still failed with messages:


Traceback (most recent call last):
  File "/home/albert/install/pymol/modules/pymol/parser.py", line 256, 
in parse

self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "exportToWeb.py", line 119, in dump_rep
ret += parseObjMol(obj)
  File "exportToWeb.py", line 57, in parseObjMol
if (rep[7] == 1):
IndexError: list index out of range


Thank you very much.
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Re: [PyMOL] pymol to webGL?

[Osvaldo Martin]

Hi Takanori,

Thanks for joining the conversation.  I have been talking with Albert
(off-list) and as you wrote the problem seems to be related with the way
PyMOL save the session in the newer versions.

To export a pse file to an older PyMOl version you should do:

set pse_export_version, 1.72
save your_session.pse

where 1.72 is the PyMOL version 1.7.2 (you can set to other versions as
well)

Cheers,
Osvaldo.

On Sun, Oct 18, 2015 at 9:48 AM, Takanori Nakane <
takanori.nak...@bs.s.u-tokyo.ac.jp> wrote:

Hi,
>
> It looks like the structure of PyMOL session (what
> we got from cmd.get_session) has changed in recent upgrades.
> I have to rewrite the program.
>
> Does anyone know if there is a setting to export in the 'old' format?
>
> Best regards,
>
> Takanori Nakane
>
> On 2015/10/18 1:47, Osvaldo Martin wrote:
> > That really weird! the script is expecting a list but is getting an
> > integer. Could you send me the "my" molecule or a pse file with that
> > molecule? or at least other molecule that give you the same error?
> >
> > Cheers,
> > Osvaldo.
> >
> >
> >
> > On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:
> >
> >> Thanks a lot for further advice.
> >>
> >> Here is what I got:
> >>
> >> PyMOL> run exportToWeb.py
> >> PyMOL>exportToWeb my
> >> Traceback (most recent call last):
> >>File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
> >> 256, in parse
> >>  self.result=apply(layer.kw[0],layer.args,layer.kw_args)
> >>File "exportToWeb.py", line 118, in dump_rep
> >>  ret += parseObjMol(obj)
> >>File "exportToWeb.py", line 50, in parseObjMol
> >>  if (rep[5] == 1):
> >> TypeError: 'int' object has no attribute '__getitem__'
> >>
> >>
> >> If possible, would you please give me some suggestions?
> >>
> >> Thanks a lot
> >>
> >> Albert
> >>
> >>
> >>
> >>
> >> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
> >>
> >> Hi Albert,
> >>
> >> I do the following steps and I get a .html file as expected.
> >>
> >> 1. I download and unpack this
> >> <
> http://sourceforge.jp/projects/webglmol/downloads/54536/pymol-exporter-0.01.zip/
> >
> >> file. The script there seems to be similar to the one you attached.
> >> 2. Lauch PyMOL and do some stuff
> >> 3. cd to the folder creating during unpacking
> >> 4. run the script by doing
> >>
> >>  run exportToWeb.py
> >>
> >> 5. then run the commnand
> >>
> >>  exportToWeb PymolObjectName
> >>
> >> where PymolObjectName is the name of the pymol object you want to
> >> export
> >> 6. check the unpacked folder for a file with the name
> >> PymolObjectName.html
> >>
> >> Could you try to follow these steps and tell us what you get?
> >>
> >> Cheers,
> >>
> >> Osvaldo.
> >>
> >>
> >>
> >
> >
> >
> >
> --
> >
> >
> >
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Re: [PyMOL] pymol to webGL?

[David Hall]

You can set:

pse_export_version

to the 3-part version of pymol you would like to use as an export version.

-David

> On Oct 18, 2015, at 3:48 AM, Takanori Nakane 
>  wrote:
> 
> Hi,
> 
> It looks like the structure of PyMOL session (what
> we got from cmd.get_session) has changed in recent upgrades.
> I have to rewrite the program.
> 
> Does anyone know if there is a setting to export in the 'old' format?
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 2015/10/18 1:47, Osvaldo Martin wrote:
>> That really weird! the script is expecting a list but is getting an
>> integer. Could you send me the "my" molecule or a pse file with that
>> molecule? or at least other molecule that give you the same error?
>> 
>> Cheers,
>> Osvaldo.
>> 
>> 
>> 
>> On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:
>> 
>>> Thanks a lot for further advice.
>>> 
>>> Here is what I got:
>>> 
>>> PyMOL> run exportToWeb.py
>>> PyMOL>exportToWeb my
>>> Traceback (most recent call last):
>>>   File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
>>> 256, in parse
>>> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>>   File "exportToWeb.py", line 118, in dump_rep
>>> ret += parseObjMol(obj)
>>>   File "exportToWeb.py", line 50, in parseObjMol
>>> if (rep[5] == 1):
>>> TypeError: 'int' object has no attribute '__getitem__'
>>> 
>>> 
>>> If possible, would you please give me some suggestions?
>>> 
>>> Thanks a lot
>>> 
>>> Albert
>>> 
>>> 
>>> 
>>> 
>>> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
>>> 
>>> Hi Albert,
>>> 
>>> I do the following steps and I get a .html file as expected.
>>> 
>>>1. I download and unpack this
>>>
>>> 
>>>file. The script there seems to be similar to the one you attached.
>>>2. Lauch PyMOL and do some stuff
>>>3. cd to the folder creating during unpacking
>>>4. run the script by doing
>>> 
>>> run exportToWeb.py
>>> 
>>>5. then run the commnand
>>> 
>>> exportToWeb PymolObjectName
>>> 
>>>where PymolObjectName is the name of the pymol object you want to
>>>export
>>>6. check the unpacked folder for a file with the name
>>>PymolObjectName.html
>>> 
>>> Could you try to follow these steps and tell us what you get?
>>> 
>>> Cheers,
>>> 
>>> Osvaldo.
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> --
>> 
>> 
>> 
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Re: [PyMOL] pymol to webGL?

[Takanori Nakane]

Hi,

It looks like the structure of PyMOL session (what
we got from cmd.get_session) has changed in recent upgrades.
I have to rewrite the program.

Does anyone know if there is a setting to export in the 'old' format?

Best regards,

Takanori Nakane

On 2015/10/18 1:47, Osvaldo Martin wrote:
> That really weird! the script is expecting a list but is getting an
> integer. Could you send me the "my" molecule or a pse file with that
> molecule? or at least other molecule that give you the same error?
>
> Cheers,
> Osvaldo.
>
>
>
> On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:
>
>> Thanks a lot for further advice.
>>
>> Here is what I got:
>>
>> PyMOL> run exportToWeb.py
>> PyMOL>exportToWeb my
>> Traceback (most recent call last):
>>File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
>> 256, in parse
>>  self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>File "exportToWeb.py", line 118, in dump_rep
>>  ret += parseObjMol(obj)
>>File "exportToWeb.py", line 50, in parseObjMol
>>  if (rep[5] == 1):
>> TypeError: 'int' object has no attribute '__getitem__'
>>
>>
>> If possible, would you please give me some suggestions?
>>
>> Thanks a lot
>>
>> Albert
>>
>>
>>
>>
>> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
>>
>> Hi Albert,
>>
>> I do the following steps and I get a .html file as expected.
>>
>> 1. I download and unpack this
>> 
>> 
>> file. The script there seems to be similar to the one you attached.
>> 2. Lauch PyMOL and do some stuff
>> 3. cd to the folder creating during unpacking
>> 4. run the script by doing
>>
>>  run exportToWeb.py
>>
>> 5. then run the commnand
>>
>>  exportToWeb PymolObjectName
>>
>> where PymolObjectName is the name of the pymol object you want to
>> export
>> 6. check the unpacked folder for a file with the name
>> PymolObjectName.html
>>
>> Could you try to follow these steps and tell us what you get?
>>
>> Cheers,
>>
>> Osvaldo.
>>
>>
>>
>
>
>
> --
>
>
>
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Re: [PyMOL] pymol to webGL?

[Osvaldo Martin]

That really weird! the script is expecting a list but is getting an
integer. Could you send me the "my" molecule or a pse file with that
molecule? or at least other molecule that give you the same error?

Cheers,
Osvaldo.



On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:

> Thanks a lot for further advice.
>
> Here is what I got:
>
> PyMOL> run exportToWeb.py
> PyMOL>exportToWeb my
> Traceback (most recent call last):
>   File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
> 256, in parse
> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   File "exportToWeb.py", line 118, in dump_rep
> ret += parseObjMol(obj)
>   File "exportToWeb.py", line 50, in parseObjMol
> if (rep[5] == 1):
> TypeError: 'int' object has no attribute '__getitem__'
>
>
> If possible, would you please give me some suggestions?
>
> Thanks a lot
>
> Albert
>
>
>
>
> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
>
> Hi Albert,
>
> I do the following steps and I get a .html file as expected.
>
>1. I download and unpack this
>
> 
>file. The script there seems to be similar to the one you attached.
>2. Lauch PyMOL and do some stuff
>3. cd to the folder creating during unpacking
>4. run the script by doing
>
> run exportToWeb.py
>
>5. then run the commnand
>
> exportToWeb PymolObjectName
>
>where PymolObjectName is the name of the pymol object you want to
>export
>6. check the unpacked folder for a file with the name
>PymolObjectName.html
>
> Could you try to follow these steps and tell us what you get?
>
> Cheers,
>
> Osvaldo.
>
>
>
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Re: [PyMOL] pymol to webGL?

[Albert]

Thanks a lot for further advice.

Here is what I got:

PyMOL> run exportToWeb.py
PyMOL>exportToWeb my
Traceback (most recent call last):
  File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line 
256, in parse

self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "exportToWeb.py", line 118, in dump_rep
ret += parseObjMol(obj)
  File "exportToWeb.py", line 50, in parseObjMol
if (rep[5] == 1):
TypeError: 'int' object has no attribute '__getitem__'


If possible, would you please give me some suggestions?

Thanks a lot

Albert




On 10/17/2015 04:36 PM, Osvaldo Martin wrote:


Hi Albert,

I do the following steps and I get a .html file as expected.

 1. I download and unpack this


file. The script there seems to be similar to the one you attached.
 2. Lauch PyMOL and do some stuff
 3. cd to the folder creating during unpacking
 4. run the script by doing
|run exportToWeb.py |
 5. then run the commnand
|exportToWeb PymolObjectName |
where PymolObjectName is the name of the pymol object you want to
export
 6. check the unpacked folder for a file with the name
PymolObjectName.html

Could you try to follow these steps and tell us what you get?

Cheers,

Osvaldo.



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Re: [PyMOL] pymol to webGL?

[Osvaldo Martin]

Hi Albert,

I do the following steps and I get a .html file as expected.

   1. I download and unpack this
   

   file. The script there seems to be similar to the one you attached.
   2. Lauch PyMOL and do some stuff
   3. cd to the folder creating during unpacking
   4. run the script by doing

run exportToWeb.py

   5. then run the commnand

exportToWeb PymolObjectName

   where PymolObjectName is the name of the pymol object you want to export
   6. check the unpacked folder for a file with the name
   PymolObjectName.html

Could you try to follow these steps and tell us what you get?

Cheers,

Osvaldo.


On Sat, Oct 17, 2015 at 3:24 PM, Albert  wrote:

Dear Osvaldo:
>
> thanks a lot for the reply.
>
> I change the pymol2glmol.py as you sugguested, and rerun it with command:
>
> python pymol2glmol.py test.pse
>
> and there is still nothing new generated
>
> do you have any further comments? I've attached the files.
>
> Thanks again
>
> Albert
>
>
>
> On 10/17/2015 02:01 PM, Osvaldo Martin wrote:
>
> Hi Albert,
>
> I change the code to
>
> bgcolor = cmd.get_color_tuple(cmd.get_setting_tuple('bg_rgb')[1][0])
> ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
>   int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
>
> I think the code is correct, anyway when I export the scene I always get a
> black background.
>
> Cheers,
>
> Osvaldo,
>
>
> ​
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Re: [PyMOL] pymol to webGL?

[Osvaldo Martin]

Hi Albert,

I change the code to

bgcolor = cmd.get_color_tuple(cmd.get_setting_tuple('bg_rgb')[1][0])
ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
  int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))

I think the code is correct, anyway when I export the scene I always get a
black background.

Cheers,

Osvaldo,


On Sat, Oct 17, 2015 at 1:50 PM, Osvaldo Martin 
wrote:

Hi Albert,
>
> I get the following error
>
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 254, in parse
> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   File "exportToWeb.py", line 138, in dump_rep
> int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
>
> A quick and dirty workaround is to change
>
> ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
> int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
>
> to
>
> ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
> int(255 * float(bgcolor[0])), int(255 * float(bgcolor[0])))
>
> I guess Thomas could provide a proper solution to this problem. The
> problem, if I get it correctly, is that
>
> cmd.get_setting_tuple('bg_rgb')[1]
>
> is returning an integer-code for the colors, while the plugin is expecting
> and RGB-code.
>
> Cheers,
> Osvaldo.
>
>
>
> On Sat, Oct 17, 2015 at 10:35 AM, Albert  wrote:
>
> Hello:
>>
>> I noticed that there is a plugin called
>>
>>
>> exportToWeb.py
>>
>> I try to rum it with command:
>>
>> python exportToWeb.py test.pse
>>
>> However, no any new file generated I am just wondering how shall we
>> use this script correctly?
>>
>> thanks a lot
>>
>> Albert
>>
>>
>> --
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>>
> ​
>
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Re: [PyMOL] pymol to webGL?

[Osvaldo Martin]

Hi Albert,

I get the following error

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 254, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "exportToWeb.py", line 138, in dump_rep
int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))

A quick and dirty workaround is to change

ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))

to

ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
int(255 * float(bgcolor[0])), int(255 * float(bgcolor[0])))

I guess Thomas could provide a proper solution to this problem. The
problem, if I get it correctly, is that

cmd.get_setting_tuple('bg_rgb')[1]

is returning an integer-code for the colors, while the plugin is expecting
and RGB-code.

Cheers,
Osvaldo.



On Sat, Oct 17, 2015 at 10:35 AM, Albert  wrote:

Hello:
>
> I noticed that there is a plugin called
>
>
> exportToWeb.py
>
> I try to rum it with command:
>
> python exportToWeb.py test.pse
>
> However, no any new file generated I am just wondering how shall we
> use this script correctly?
>
> thanks a lot
>
> Albert
>
>
> --
>
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[PyMOL] pymol to webGL?

[Albert]

Hello:

I noticed that there is a plugin called

exportToWeb.py

I try to rum it with command:

python exportToWeb.py test.pse

However, no any new file generated I am just wondering how shall we 
use this script correctly?


thanks a lot

Albert

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