Re: [PyMOL] PyMOLWiki: Quick Update

[H. Adam Steinberg]

Thank you Jason!

> On Oct 19, 2015, at 9:34 PM, Jason Vertrees  wrote:
> 
> Greetings Shane, et. al.,
> 
> The issue with the database connection should be fixed permanently now. 
> Search should also be consistently better.
> 
> I've independently owned and run the wiki for almost a decade now. It's 
> heading toward 22 million page views. Anyhow, it's now on good hardware (SSD, 
> lots of RAM, and a nice network) and should be stable. Let me know if not.
> 
> Cheers,
> 
> -- Jason
> 
> On Sun, Oct 18, 2015 at 6:35 PM Shane Caldwell  > wrote:
> Hi Jason, pymol-users list,
> 
> The pymolwiki seems to be down and has been for a few days now. It looks like 
> the server's down?
> 
> Any page returns:
> 
> (Can't contact the database server: Can't connect to local MySQL server 
> through socket '/var/run/mysqld/mysqld.sock' (111) (localhost))
> 
> Is there a mirror anywhere that can be used?
> 
> Shane Caldwell
> McGill University
> 
> On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees  > wrote:
> Greetings,
> 
> It's been a while, I hope this message finds everyone well. 
> 
> I'm writing to briefly let you know that I recently moved, upgraded, and 
> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast and 
> more useful. Feel free to report any bugs.
> 
> Back to the startup-life.
> 
> Cheers,
> 
> -- Jason
> 
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H. Adam Steinberg
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608/592-2366

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Re: [PyMOL] PyMOLWiki: Quick Update

[Jason Vertrees]

Greetings Shane, et. al.,

The issue with the database connection should be fixed permanently now.
Search should also be consistently better.

I've independently owned and run the wiki for almost a decade now. It's
heading toward 22 million page views. Anyhow, it's now on good hardware
(SSD, lots of RAM, and a nice network) and should be stable. Let me know if
not.

Cheers,

-- Jason

On Sun, Oct 18, 2015 at 6:35 PM Shane Caldwell 
wrote:

> Hi Jason, pymol-users list,
>
> The pymolwiki seems to be down and has been for a few days now. It looks
> like the server's down?
>
> Any page returns:
>
> (Can't contact the database server: Can't connect to local MySQL server
> through socket '/var/run/mysqld/mysqld.sock' (111) (localhost))
>
> Is there a mirror anywhere that can be used?
>
> Shane Caldwell
> McGill University
>
> On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees 
> wrote:
>
>> Greetings,
>>
>> It's been a while, I hope this message finds everyone well.
>>
>> I'm writing to briefly let you know that I recently moved, upgraded, and
>> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast
>> and more useful. Feel free to report any bugs.
>>
>> Back to the startup-life.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> --
>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
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>>
>>
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Re: [PyMOL] change electrostatic ramp color?

[Osvaldo Martin]

Great, I'm glad that you found the solution!


On Mon, Oct 19, 2015 at 7:10 PM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:

> Thank you Osvaldo for taking time to answer all the questions this morning!
>
> I tried but failed to recolor the ramp.
>
> Then an idea hit me, maybe the red in the ramp was changed to green so I
> opened the color setting panel and yes, the red was changed to green. I
> don’t remember why since that file was created 8 years back…
>
> So I changed it back to a “real” red and generated a new map - all is
> back!
>
> Thanks!
>
>
> On Oct 19, 2015, at 9:14 AM, Osvaldo Martin  wrote:
>
> Hi Adam,
>
> Now that the PyMOL wiki is back, did you find the solution at the Ramp_New
> Wiki page?
>
> Cheers,
>
> Osvaldo.
>
> On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg <
> h.adam.steinb...@gmail.com> wrote:
>
>
> I opened a complex .pse file I created back in 2007 and the electrostatic
>> ramp is showing as green to blue. Any ideas how to change it back to red to
>> blue?
>>
>> The wiki seems to be down.
>>
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>>
>>
>>
>> --
>>
>> ___
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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
>>
>
>
> ​
>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
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[PyMOL] how to enable 3D

[Albert]

Hello:

I just notice that nowadays the webGL and xml5 technology developed so 
fast that many new tools emerging these days. I am really impressed by 
the GLMOL tool for pymol recently. It is really powerful.

I am just wondering is it possible to enable anaglyph or side by side 
stereo for GLMOL tool? I just find a  a tool based in GLmol, called 
iview which support such kind of function. Is it possible for the 
developer integrate them into GLmol python script so that the generated 
.html file can also support some simple stereo view?

Here is the link of website:

http://istar.cse.cuhk.edu.hk/iview/

and here is script for this tool

https://github.com/HongjianLi/istar/tree/master/public/iview

Thank you very much.

Albert

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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] change electrostatic ramp color?

[H. Adam Steinberg]

Thank you Osvaldo for taking time to answer all the questions this morning!

I tried but failed to recolor the ramp. 

Then an idea hit me, maybe the red in the ramp was changed to green so I opened 
the color setting panel and yes, the red was changed to green. I don’t remember 
why since that file was created 8 years back…

So I changed it back to a “real” red and generated a new map - all is back! 

Thanks!


> On Oct 19, 2015, at 9:14 AM, Osvaldo Martin  wrote:
> 
> Hi Adam,
> 
> Now that the PyMOL wiki is back, did you find the solution at the Ramp_New <> 
> Wiki page?
> 
> Cheers,
> 
> Osvaldo.
> 
> On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg 
> mailto:h.adam.steinb...@gmail.com>> wrote:
> 
> 
> 
> I opened a complex .pse file I created back in 2007 and the electrostatic 
> ramp is showing as green to blue. Any ideas how to change it back to red to 
> blue?
> 
> The wiki seems to be down.
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366 
> 
> --
> 
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> 
> 
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Pymol Morph movie error

[Thomas Holder]

David, Incentive PyMOL does bundle mpeg_encode.exe and uses it for movie 
export. It is also available from http://freemol.org

Hans, what Windows version do you use? I can't reproduce this problem on 
Windows 7 or 8.

Cheers,
  Thomas

On 19 Oct 2015, at 10:44, David Hall  wrote:

> there is no mpeg_encode.exe binary.
> 
> mpeg_encode, as far as I am aware, has long been abandoned. You can find what 
> I believe is the last version of the source code (1.5c) at 
> https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode , you 
> can download by clicking the files with the up arrow (I know, those symbols 
> make no sense).
> 
> It uses an old version of libjpeg with apis that have been long abandoned.
> 
> Basically, you don't have a binary for what I think is a long abandoned 
> program that depends on old versions of libraries. 
> 
> Hopefully someone else will tell me there's some magical updated version 
> floating around out there, but I doubt it. Otherwise, no new features in 20 
> years and no bug/compatibility fixes in 13.
> 
> -David
> 
> 
> On Mon, Oct 19, 2015 at 8:36 AM,  wrote:
> Dear Pymol community,
> 
>  
> 
> Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
> 
> However when I tried to save the movie, I get an error:
> 
> --
> 
> produce: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in background)...
> 
> please wait ...
> 
> Error: mpeg_encode did not run
> 
> Traceback (most recent call last):
> 
>   File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py", line 
> 35, in run
> 
> mpeg_encode_in, mpeg_encode_out, mpeg_encode_err = 
> os.popen3(_mpeg_encode_exe)
> 
> WindowsError: [Error 2] The system cannot find the file specified: 'Ex: 
> C\\Temp /c "C:\\Program Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'
> 
> produce: compression failed
> 
> -
> 
> Anyone suggestions how to solve this?
> 
> Thanks in advance,
> 
> Hans van Leeuwen

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] lipid membrane help

[H. Adam Steinberg]

You could also do this in sections building up to the amount of lipids you need.
Create and Rotate 3 lipids.
Select, Duplicate and rotate one set of three so you now have 6 lipids.
Select, Duplicate and rotate on set of 6 so you now have 12 lipids.
Continue on…+



> On Oct 19, 2015, at 9:23 AM, Osvaldo Martin  wrote:
> 
> Hi Nhi,
> 
> You can use the Rotate . You just need 
> to specify the correct selection. If you have any other doubt, please ask.
> 
> Cheers,
> Osvaldo.
> 
> On Mon, Oct 12, 2015 at 9:45 PM, Tran,Nhi T  > wrote:
> 
> 
> 
> I want to rotate the lipid molecules in the outer leaflet to form a concave 
> surface. How do I do this without having to rotate each lipid individually?
> 
> Any suggestions would be greatly appreciated!
> 
> Best,
> Nhi
> --
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] on cartoon representation

[Osvaldo Martin]

Hi Smith,

There are several setting you could change to modify the way helices (and
loops and beta strands) are rendered. Try with this
 page and let us
know if you find something useful or you have further doubts.
Cheers,
Osvaldo.

On Wed, Oct 7, 2015 at 3:52 PM, Smith Liu  wrote:

Dear All,
>
> Recently I have noticed in Science and Nature paper, the author present
> the helix in cartoon as thin as that observed in VMD (and even similar in
> appearance). I do not know whether the author made the image by pymol or by
> VMD.
>
> Is any way for pymol to make helix in carton as  observed in VMD?
>
> Best regards.
>
> Smith
>
>
>
>
>
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Re: [PyMOL] Pymol Morph movie error

[David Hall]

there is no mpeg_encode.exe binary.

mpeg_encode, as far as I am aware, has long been abandoned. You can find
what I believe is the last version of the source code (1.5c) at
https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode , you
can download by clicking the files with the up arrow (I know, those symbols
make no sense).

It uses an old version of libjpeg with apis that have been long abandoned.

Basically, you don't have a binary for what I think is a long abandoned
program that depends on old versions of libraries.

Hopefully someone else will tell me there's some magical updated version
floating around out there, but I doubt it. Otherwise, no new features in 20
years and no bug/compatibility fixes in 13.

-David


On Mon, Oct 19, 2015 at 8:36 AM,  wrote:

> Dear Pymol community,
>
>
>
> Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
>
> However when I tried to save the movie, I get an *error*:
>
> --
>
> *produce**: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in
> background)...*
>
> *please wait ...*
>
> *Error**: mpeg_encode did not run*
>
> *Traceback (most recent call last):*
>
> *  File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py",
> line 35, in run*
>
> *mpeg_encode_in, mpeg_encode_out, mpeg_encode_err =
> os.popen3(_mpeg_encode_exe)*
>
> *WindowsError**: [Error 2] The system cannot find the file specified:
> 'Ex: C\\Temp /c "C:\\Program
> Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'*
>
> *produce: compression failed*
>
> -
>
>
>
> Anyone suggestions how to solve this?
>
>
>
> Thanks in advance,
>
>
>
> Hans van Leeuwen
>
>
>
>
>
>
>
>
> --
>
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Re: [PyMOL] lipid membrane help

[Osvaldo Martin]

Hi Nhi,

You can use the Rotate . You just
need to specify the correct selection. If you have any other doubt, please
ask.

Cheers,
Osvaldo.

On Mon, Oct 12, 2015 at 9:45 PM, Tran,Nhi T  wrote:

I want to rotate the lipid molecules in the outer leaflet to form a concave
> surface. How do I do this without having to rotate each lipid individually?
>
> Any suggestions would be greatly appreciated!
>
> Best,
> Nhi
>
> --
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Re: [PyMOL] volume measurement

[Osvaldo Martin]

Hi Smith,

I am not sure that there is an out-of-the-box function in PyMOL to compute
what you want. May be you would like to check the 3v website.


Cheers,
Osvaldo.

On Sat, Oct 10, 2015 at 10:40 AM, Smith Liu  wrote:

Dear All,
>
> If there is a cleft (looks like letter "C", which is not totally closed)
> formed by 2 subunits, will you please tell me by pymol how to measure the
> volume of the cleft formed?
>
> Best regards.
>
> Smith
>
>
>
>
>
> --
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Re: [PyMOL] change electrostatic ramp color?

[Osvaldo Martin]

Hi Adam,

Now that the PyMOL wiki is back, did you find the solution at the Ramp_New
Wiki page?

Cheers,

Osvaldo.

On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:

I opened a complex .pse file I created back in 2007 and the electrostatic
> ramp is showing as green to blue. Any ideas how to change it back to red to
> blue?
>
> The wiki seems to be down.
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
> --
>
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Re: [PyMOL] Remove my email

[Osvaldo Martin]

Hi Sabi,

Please follow this link
 or the link at
the bottom of every e-mail from the PyMOL mailing list.

Cheers,
Osvaldo.

On Mon, Oct 19, 2015 at 3:57 PM, Sabi  wrote:

How can I remove my email from the list I keep getting emails for something
> I don't use. At all pymol.
>
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[PyMOL] Remove my email

[Sabi]

How can I remove my email from the list I keep getting emails for something I 
don't use. At all pymol. 
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[PyMOL] Pymol Morph movie error

[H.C.van_Leeuwen]

Dear Pymol community,

Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
However when I tried to save the movie, I get an error:
--
produce: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in background)...
please wait ...
Error: mpeg_encode did not run
Traceback (most recent call last):
  File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py", line 35, 
in run
mpeg_encode_in, mpeg_encode_out, mpeg_encode_err = 
os.popen3(_mpeg_encode_exe)
WindowsError: [Error 2] The system cannot find the file specified: 'Ex: C\\Temp 
/c "C:\\Program Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'
produce: compression failed
-

Anyone suggestions how to solve this?

Thanks in advance,

Hans van Leeuwen



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