pymol-users Mailing List for PyMOL Molecular Graphics System

Michael
I've run in to something like this before (early ubuntu 12.04) using just using build_seq to write small peptide .pdbs in a loop, the work around I used (I think it was in the wiki at the time -- can't find it now) was to add a short wait at the end of the loop, <0.1 sec was enough on my machine at the time but that may be device/content specific.

**not my skill set**
IF I recall correctly the issue was explained as having a new run on the loop before the buffer on the old cleared (memory:cycles racing)
 
Hope this helps

Jacob Pessin
Albert Einstein College of Medicine
Diabetes Research Center SIMC
Computational Chemistry & Molecular Modeling
jac...@ei...
1 718 839 7228

------------------------------

Message: 4
Date: Wed, 24 Jun 2015 00:13:26 +0200
From: Michael Banck <mb...@de...>
Subject: [PyMOL] Race condition when running scripts in "stdin" mode
To: pymol-users <pym...@li...>
Message-ID:
        <201...@ra...>
Content-Type: text/plain; charset=us-ascii

Hi,

on Debian, we got a bug report which looks like the bug reported here as
well: http://sourceforge.net/p/pymol/bugs/130/

Unfortunately, there has been no discussion of this bug so far.

There seems to be some race condition for scripts, does anybody a
work-around, and/or fix for this?  Or is this a platform-dependent (or
even Debian/Ubuntu dependent) issue?


Thanks,

Michael




Message: 6
Date: Tue, 23 Jun 2015 19:45:26 -0300
From: Osvaldo Martin <alo...@gm...>
Subject: Re: [PyMOL] Race condition when running scripts in "stdin"
        mode
To: Michael Banck <mb...@de...>
Cc: pymol-users <pym...@li...>
Message-ID:
        <CAG...@ma...>
Content-Type: text/plain; charset="utf-8"

Hi MIchael,

I can reproduce the error on a machine with Ubuntu 15.04 (64 bits) and
PyMOL 1.7.2



On Tue, Jun 23, 2015 at 7:13 PM, Michael Banck <mb...@de...> wrote:

> Hi,
>
> on Debian, we got a bug report which looks like the bug reported here as
> well: http://sourceforge.net/p/pymol/bugs/130/
>
> Unfortunately, there has been no discussion of this bug so far.
>
> There seems to be some race condition for scripts, does anybody a
> work-around, and/or fix for this?  Or is this a platform-dependent (or
> even Debian/Ubuntu dependent) issue?
>
>
> Thanks,
>
> Michael

Hi all,

If I create a string of double-strand DNA, or take a string of double-strand DNA or RNA from a structure, is there any automated way to have the bases link, AT, UA, GC, so when I manually sculpt or deform the DNA those bases would stay together?

I could go through the structure and manually create physical bonds where the hydrogen bonds would be, and I’m guessing that would work, but I’m wondering if anyone has a script or is there a function that I am unaware of?

Thanks!

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

Hi MIchael,

I can reproduce the error on a machine with Ubuntu 15.04 (64 bits) and
PyMOL 1.7.2





On Tue, Jun 23, 2015 at 7:13 PM, Michael Banck <mb...@de...> wrote:

> Hi,
>
> on Debian, we got a bug report which looks like the bug reported here as
> well: http://sourceforge.net/p/pymol/bugs/130/
>
> Unfortunately, there has been no discussion of this bug so far.
>
> There seems to be some race condition for scripts, does anybody a
> work-around, and/or fix for this?  Or is this a platform-dependent (or
> even Debian/Ubuntu dependent) issue?
>
>
> Thanks,
>
> Michael
>
>
> ------------------------------------------------------------------------------
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>

Hi Jordan,

I think there are no drawbacks, I'm using this version for several months now and it works great. Of course such a question is hard to answer a-priori, that's why we didn't simply replace the regular bundle but offer the "syspython" version in addition.

Cheers,
  Thomas

On 23 Jun 2015, at 18:04, Jordan Willis <jwi...@gm...> wrote:

> Wow that is so cool. Is there any drawbacks I can expect?
> 
> 
>> On Jun 23, 2015, at 1:44 PM, Thomas Holder <tho...@sc...> wrote:
>> 
>> Hi Jordan,
>> 
>> if you want to use MacPyMOL with other libraries then I recommend to use the "syspython" version that we offer (installer named MacPyMOL-v1.7.x.x-syspython.dmg). It simply does not bundle a Python distribution, but uses /usr/bin/python2.7 to run MacPyMOL.
>> 
>> Related:
>> https://sourceforge.net/p/pymol/mailman/message/33531659/
>> 
>> Cheers,
>> Thomas
>> 
>> On 21 Jun 2015, at 21:44, Jordan Willis <jwi...@gm...> wrote:
>> 
>>> Hi,
>>> 
>>> I’m trying to use the pandas library with MacPymol 1.7.05 but get the following with import pandas. 
>>> 
>>> File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in <module>
>>>   from . import hashtable, tslib, lib
>>> File "numpy.pxd", line 157, in init pandas.hashtable (pandas/hashtable.c:22315)
>>> ValueError: numpy.dtype has the wrong size, try recompiling
>>> 
>>> Obviously there is some conflict with PyMOLs python interpreter and the interpreter I installed pandas with. That’s fine, I’ll just compile pandas against PyMOLs python library, but I don’t know how to do it.
>>> 
>>> I used pip within pymol 
>>> 
>>> python
>>> import pip
>>> pip.main([‘install’,’pandas’,’—reinstall’])
>>> python end
>>> 
>>> 
>>> but got something wrong with the certificate in the pypy server
>>> 
>>> /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL run on Sun Jun 21 18:35:15 2015
>>> Getting page https://pypi.python.org/simple/pandas/
>>> Could not fetch URL https://pypi.python.org/simple/pandas/: connection error: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
>>> 
>>> . I thought before I dug too deep, I would check with the list to see if anyone has added the pandas library that is compatible with pymol. Or more generally, how would one install third party libraries for use with pymol. If you don’t use pandas, I highly recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips.
>>> 
>>> Jordan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

on Debian, we got a bug report which looks like the bug reported here as
well: http://sourceforge.net/p/pymol/bugs/130/

Unfortunately, there has been no discussion of this bug so far.

There seems to be some race condition for scripts, does anybody a
work-around, and/or fix for this?  Or is this a platform-dependent (or
even Debian/Ubuntu dependent) issue?


Thanks,

Michael

Wow that is so cool. Is there any drawbacks I can expect?


> On Jun 23, 2015, at 1:44 PM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Jordan,
> 
> if you want to use MacPyMOL with other libraries then I recommend to use the "syspython" version that we offer (installer named MacPyMOL-v1.7.x.x-syspython.dmg). It simply does not bundle a Python distribution, but uses /usr/bin/python2.7 to run MacPyMOL.
> 
> Related:
> https://sourceforge.net/p/pymol/mailman/message/33531659/
> 
> Cheers,
>  Thomas
> 
> On 21 Jun 2015, at 21:44, Jordan Willis <jwi...@gm...> wrote:
> 
>> Hi,
>> 
>> I’m trying to use the pandas library with MacPymol 1.7.05 but get the following with import pandas. 
>> 
>>  File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in <module>
>>    from . import hashtable, tslib, lib
>>  File "numpy.pxd", line 157, in init pandas.hashtable (pandas/hashtable.c:22315)
>> ValueError: numpy.dtype has the wrong size, try recompiling
>> 
>> Obviously there is some conflict with PyMOLs python interpreter and the interpreter I installed pandas with. That’s fine, I’ll just compile pandas against PyMOLs python library, but I don’t know how to do it.
>> 
>> I used pip within pymol 
>> 
>> python
>> import pip
>> pip.main([‘install’,’pandas’,’—reinstall’])
>> python end
>> 
>> 
>> but got something wrong with the certificate in the pypy server
>> 
>> /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL run on Sun Jun 21 18:35:15 2015
>> Getting page https://pypi.python.org/simple/pandas/
>> Could not fetch URL https://pypi.python.org/simple/pandas/: connection error: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
>> 
>> . I thought before I dug too deep, I would check with the list to see if anyone has added the pandas library that is compatible with pymol. Or more generally, how would one install third party libraries for use with pymol. If you don’t use pandas, I highly recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips.
>> 
>> Jordan
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

Hi Jordan,

if you want to use MacPyMOL with other libraries then I recommend to use the "syspython" version that we offer (installer named MacPyMOL-v1.7.x.x-syspython.dmg). It simply does not bundle a Python distribution, but uses /usr/bin/python2.7 to run MacPyMOL.

Related:
https://sourceforge.net/p/pymol/mailman/message/33531659/

Cheers,
  Thomas

On 21 Jun 2015, at 21:44, Jordan Willis <jwi...@gm...> wrote:

> Hi,
> 
> I’m trying to use the pandas library with MacPymol 1.7.05 but get the following with import pandas. 
> 
>   File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in <module>
>     from . import hashtable, tslib, lib
>   File "numpy.pxd", line 157, in init pandas.hashtable (pandas/hashtable.c:22315)
> ValueError: numpy.dtype has the wrong size, try recompiling
> 
> Obviously there is some conflict with PyMOLs python interpreter and the interpreter I installed pandas with. That’s fine, I’ll just compile pandas against PyMOLs python library, but I don’t know how to do it.
> 
> I used pip within pymol 
> 
> python
> import pip
> pip.main([‘install’,’pandas’,’—reinstall’])
> python end
> 
> 
> but got something wrong with the certificate in the pypy server
> 
> /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL run on Sun Jun 21 18:35:15 2015
> Getting page https://pypi.python.org/simple/pandas/
> Could not fetch URL https://pypi.python.org/simple/pandas/: connection error: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
> 
> . I thought before I dug too deep, I would check with the list to see if anyone has added the pandas library that is compatible with pymol. Or more generally, how would one install third party libraries for use with pymol. If you don’t use pandas, I highly recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips.
> 
> Jordan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,

If I create a string of double-strand DNA, or take a string of double-strand DNA or RNA from a structure, is there any automated way to have the bases link AT, UA, GC, so when I manually sculpt or deform the DNA those bases would stay together?

I could go through the structure and manually create physical bonds where the hydrogen bonds would be, and that would work, but I’m wondering if anyone has a script or is there a function that I am unaware of?

Thanks!

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

Hello All.

I've just an hour ago installed the Suns plugin into my newly downloaded
Incentive MacPyMOL (which I've renamed PyMOLX11Hybrid to engage the
Plugin-supporting interface), and began the Suns tutorial (found here:
http://degradolab.org/suns/). I am running PyMOL on my Mac with OS X
Yosemite version 10.10.

I couldn't get very far with the Sun tutorial at all, and wonder if any of
you have insight you could offer. I need help proceeding past the
suns_query selection part. I've included a snapshot of my session with this
e-mail: I started the plugin, loaded PDB id 2GBP, selected a carboxyl group
as instructed in the tutorial that uses this PDB id, and hit 'Search'.
Nothing happened, except what you see on the screenshot herein. What I
expected would happen, given the tutorial instructions, was a population of
search results.

Can anyone help me get search results? I could very well be doing something
very naively wrong. I've posted to the Suns-search users group as well, but
am expanding my plea to the pymol-users group also.

Regards,
Emily.
[image: Inline image 1]
-- 
"The more one does, the more one can do."
- Amelia Earhart

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

Hi Andrew,

that's the same problem that Chiranjeev had with CMview last week. You can fix it by replacing "import cmd" with "from pymol import cmd" in the script (line 9).

Cheers,
  Thomas

On 22 Jun 2015, at 11:38, Andrew Johnathan Watkins <wa...@bg...> wrote:

> I have Mac PyMOL 1.7.4.4, and I have attempted to run the attached program. I know the program works on older versions, but I get the following error:
> 
> AttributeError: 'module' object has no attribute 'extend'
> 
> Does anyone know how to fix this?
> <RNA_coloring_pymol.py>

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I have Mac PyMOL 1.7.4.4, and I have attempted to run the attached program. I know the program works on older versions, but I get the following error:


AttributeError: 'module' object has no attribute 'extend'


Does anyone know how to fix this?

Hi,

I’m trying to use the pandas library with MacPymol 1.7.05 but get the following with import pandas. 

  File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in <module>
    from . import hashtable, tslib, lib
  File "numpy.pxd", line 157, in init pandas.hashtable (pandas/hashtable.c:22315)
ValueError: numpy.dtype has the wrong size, try recompiling

Obviously there is some conflict with PyMOLs python interpreter and the interpreter I installed pandas with. That’s fine, I’ll just compile pandas against PyMOLs python library, but I don’t know how to do it.

I used pip within pymol 

python
import pip
pip.main([‘install’,’pandas’,’—reinstall’])
python end


but got something wrong with the certificate in the pypy server

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL run on Sun Jun 21 18:35:15 2015
Getting page https://pypi.python.org/simple/pandas/
Could not fetch URL https://pypi.python.org/simple/pandas/: connection error: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed

. I thought before I dug too deep, I would check with the list to see if anyone has added the pandas library that is compatible with pymol. Or more generally, how would one install third party libraries for use with pymol. If you don’t use pandas, I highly recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips.

Jordan

Hi
What about Modevectors?

http://www.pymolwiki.org/index.php/Modevectors

Emilio

On Fri, Jun 19, 2015 at 10:23 AM, Command Line <g4c...@gm...> wrote:
> Hi, that works for me. Albeit I would be more happy if there would be an
> option directly inside pymol. Anyway, thanks.
>
> 2015-06-18 16:30 GMT-05:00 Osvaldo Martin <alo...@gm...>:
>>
>> Hi,
>>
>> Do you want to do something similar to porcupine plots? If so, check the
>> porcupine function in this Ipython notebook.
>>
>> Cheers,
>> Osvaldo.
>>
>> On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
>> wrote:
>>>
>>> Hi all,
>>> when visualizing motion or modes (like NMA), is it possible to show the
>>> velocities as small arrows on all the moving atoms? B-values are not an
>>> option, since I want to see the 3D motion of the atoms. Thanks
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi, that works for me. Albeit I would be more happy if there would be an
option directly inside pymol. Anyway, thanks.

2015-06-18 16:30 GMT-05:00 Osvaldo Martin <alo...@gm...>:

> Hi,
>
> Do you want to do something similar to porcupine plots? If so, check the
> porcupine function in this Ipython notebook
> <" rel="nofollow">https://github.com/aloctavodia/SBioA/blob/master/English/04_Comparing_structures.ipynb>
> .
>
> Cheers,
> Osvaldo.
>
> On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
> wrote:
>
> Hi all,
>> when visualizing motion or modes (like NMA), is it possible to show the
>> velocities as small arrows on all the moving atoms? B-values are not an
>> option, since I want to see the 3D motion of the atoms. Thanks
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
> ​
>

Thanks Jose, looking forward to the new CMview version!

There is a workaround to get current CMview and latest PyMOL to work together: Create a pymolrc file with the following content:

from pymol import cmd
__import__('sys').modules['cmd'] = cmd

FYI: In PyMOL 1.7.3 we changed the pymol namespace to do absolute imports only (https://www.python.org/dev/peps/pep-0328/) to avoid import conflicts with global modules. Since PyMOL's "run" command executes scripts in the "pymol" module namespace by default, it was actually possible to do relative imports of pymol submodules ("import cmd" instead of "from pymol import cmd").

Cheers,
  Thomas

On 19 Jun 2015, at 04:53, Jose Manuel Duarte <jos...@ps...> wrote:

> Hi Chiranjeev
> 
> It looks like this is an issue in CMview, not in PyMOL. The script used to interact with PyMOL contains an incompatible import on PyMOL versions 1.7.3+. Thanks to Thomas Holder this is now fixed in github. 
> 
> In the next weeks we are going to try to get out a new release of CMview that contains the patch. In the meantime you can try using an older PyMOL version, e.g. 1.7.2 (I've just tested it and it worked for me).
> 
> Cheers
> 
> Jose
> 
> 
> 
> On 17.06.2015 11:38, Chiranjeev Das wrote:
>> The problem appears while using MacPyMol with CMView 1.1.1
>> 
>> log:
>> 
>> Detected OpenGL version 2.0 or greater. Shaders available.
>>  Detected GLSL version 1.20.
>> PyMOL>log_open /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview_internal_pymol.log
>> PyMOL>@/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/CMView_pymol.cmd
>> PyMOL>run /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py
>> Traceback (most recent call last):
>>   File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py", line 256, in parse
>>     self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>   File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line 485, in run
>>     run_(path, ns_pymol, ns_pymol)
>>   File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line 535, in run_file
>>     execfile(file,global_ns,local_ns)
>>   File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line 530, in execfile
>>     b.execfile(filename, global_ns, local_ns)
>>   File "/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py", line 11, in <module>
>>     from cmd import lock,unlock,_cmd # for dist counter
>> ImportError: cannot import name lock
>> PyMOL>set dash_gap, 0
>>  Setting: dash_gap set to 0.00000.
>> PyMOL>set dash_width, 1.5
>>  Setting: dash_width set to 1.50000.
>> PyMOL>viewport 650, 650
>> PyMOL>callback /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.callback, 1
>> Traceback (most recent call last):
>>   File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py", line 419, in parse
>>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>>   File "<string>", line 1, in <module>
>> NameError: name 'callback' is not defined
>> 
>> All and any help is appreciated.
>> 
>> Brgds, 
>> Chiranjeev Das

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Chiranjeev

It looks like this is an issue in CMview, not in PyMOL. The script used 
to interact with PyMOL contains an incompatible import on PyMOL versions 
1.7.3+. Thanks to Thomas Holder this is now fixed in github.

In the next weeks we are going to try to get out a new release of CMview 
that contains the patch. In the meantime you can try using an older 
PyMOL version, e.g. 1.7.2 (I've just tested it and it worked for me).

Cheers

Jose



On 17.06.2015 11:38, Chiranjeev Das wrote:
> The problem appears while using MacPyMol with CMView 1.1.1
>
> log:
>
> Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 1.20.
> PyMOL>log_open 
> /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview_internal_pymol.log
> PyMOL>@/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/CMView_pymol.cmd
> PyMOL>run /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py
> Traceback (most recent call last):
>   File 
> "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py", 
> line 256, in parse
>     self.result=apply(layer.kw 
> <http://layer.kw>[0],layer.args,layer.kw_args)
>   File 
> "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", 
> line 485, in run
>     run_(path, ns_pymol, ns_pymol)
>   File 
> "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", 
> line 535, in run_file
>     execfile(file,global_ns,local_ns)
>   File 
> "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", 
> line 530, in execfile
>     b.execfile(filename, global_ns, local_ns)
>   File "/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py", 
> line 11, in <module>
>     from cmd import lock,unlock,_cmd # for dist counter
> ImportError: cannot import name lock
> PyMOL>set dash_gap, 0
>  Setting: dash_gap set to 0.00000.
> PyMOL>set dash_width, 1.5
>  Setting: dash_width set to 1.50000.
> PyMOL>viewport 650, 650
> PyMOL>callback 
> /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.callback, 1
> Traceback (most recent call last):
>   File 
> "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py", 
> line 419, in parse
>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "<string>", line 1, in <module>
> NameError: name 'callback' is not defined
>
> All and any help is appreciated.
>
> Brgds,
> Chiranjeev Das
>
>
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi,

Do you want to do something similar to porcupine plots? If so, check the
porcupine function in this Ipython notebook
<" rel="nofollow">https://github.com/aloctavodia/SBioA/blob/master/English/04_Comparing_structures.ipynb>
.

Cheers,
Osvaldo.

On Thu, Jun 18, 2015 at 5:07 PM, Command Line <g4c...@gm...>
wrote:

Hi all,
> when visualizing motion or modes (like NMA), is it possible to show the
> velocities as small arrows on all the moving atoms? B-values are not an
> option, since I want to see the 3D motion of the atoms. Thanks
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Hi all,
when visualizing motion or modes (like NMA), is it possible to show the
velocities as small arrows on all the moving atoms? B-values are not an
option, since I want to see the 3D motion of the atoms. Thanks

The problem appears while using MacPyMol with CMView 1.1.1

log:

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
PyMOL>log_open
/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview_internal_pymol.log
PyMOL>@/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/CMView_pymol.cmd
PyMOL>run /var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py
Traceback (most recent call last):
  File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py",
line 256, in parse
    self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File
"/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line
485, in run
    run_(path, ns_pymol, ns_pymol)
  File
"/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line
535, in run_file
    execfile(file,global_ns,local_ns)
  File
"/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parsing.py", line
530, in execfile
    b.execfile(filename, global_ns, local_ns)
  File "/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.py", line
11, in <module>
    from cmd import lock,unlock,_cmd # for dist counter
ImportError: cannot import name lock
PyMOL>set dash_gap, 0
 Setting: dash_gap set to 0.00000.
PyMOL>set dash_width, 1.5
 Setting: dash_width set to 1.50000.
PyMOL>viewport 650, 650
PyMOL>callback
/var/folders/j2/rc5hm8nx37vb6c2w1b6341dc0000gn/T/cmview.callback, 1
Traceback (most recent call last):
  File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py",
line 419, in parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
NameError: name 'callback' is not defined

All and any help is appreciated.

Brgds,
Chiranjeev Das

Hi Jordan et al.,

Yes one can use the alter command with a whole selection at once and
it is much faster. I hadn't realized that until Thomas Holder helped fix
my script that appears to do what you were wanting to do:

 http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/data2bfactor.py

The B-factor data is read in and assigned to a dictionary by the
"atom_data_extract" function elsewhere in the script (indexed either by
chain and residue number, or by chain and ID) and then it is applied
like this:

    b_dict = atom_data_extract(data_file)
    quiet = int(quiet) == 1

    def b_lookup(chain, resi, name, ID, b):
        def _lookup(chain, resi, name, ID):
            if resi in b_dict[chain] and isinstance(b_dict[chain][resi], dict):
                return b_dict[chain][resi][name][0]
            else:
                # find data by ID
                return b_dict[chain][int(ID)][0]
        try:
            if not chain in b_dict:
                chain = ''
            b = _lookup(chain, resi, name, ID)
            if not quiet: print '///%s/%s/%s new: %f' % (chain, resi, name, b)
        except KeyError:
            if not quiet: print '///%s/%s/%s keeping: %f' % (chain, resi, name, b)
        return b
    stored.b = b_lookup

    cmd.alter(mol, '%s=stored.b(chain, resi, name, ID, %s)' % (prop, prop))
    cmd.rebuild()

Hope that helps.

Cheers,
Rob

On Tue, 2015-06-16 11:10 EDT, Tsjerk Wassenaar <ts...@gm...>
wrote:

> Hi Jordan,
> 
> The answer is something like (assuming reading from a file):
> 
> newb=[float(i) for i in open("stuff.dat").read().split()]
> alter n. ca, b=newb.pop()
> spectrum b
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis
> <jwi...@gm...> wrote:
> 
> > Hi Tsjerk,
> >
> > It seems everyone is pointing to this (
> > http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
> > which I somehow missed. However, they seem to be altering one
> > residue at a time like I’m doing.
> >
> >
> > Jordan
> >
> > On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar <ts...@gm...>
> > wrote:
> >
> > Hi Jordan,
> >
> > Yes, although I don't have the answer at hand, it has been given on
> > the user list several times. You can find it in the archives.
> >
> > Cheers,
> >
> > Tsjerk
> > On Jun 16, 2015 08:16, "Jordan Willis" <jwi...@gm...>
> > wrote:
> >
> >> Hi,
> >>
> >> I have a dictionary that has a bunch of values I want to assign to
> >> b-factors in order to color by. In my script:
> >>
> >> for residue in data:
> >>    cmd.alter(“resi
> >> {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
> >>
> >> This executes the alter command for each residue. For some reason,
> >> its taking forever in my script. Is there something inherently
> >> inefficient about alter? And is there anyway to fix it? Perhaps,
> >> assign a bunch of b-factors at once.
> >>
> >> Jordan
> >>
> >>
> >> ------------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives:
> >> http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> 
> 




-- 
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
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

Hi all,

this is what I would do:

cmd.alter('all', 'b = mapping.get(resv, b)',
    space={'mapping': dict((r['resnum'], r['value']) for r in data)})

Cheers,
  Thomas

On 16 Jun 2015, at 05:10, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi Jordan,
> 
> The answer is something like (assuming reading from a file):
> 
> newb=[float(i) for i in open("stuff.dat").read().split()]
> alter n. ca, b=newb.pop()
> spectrum b
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis <jwi...@gm...> wrote:
> Hi Tsjerk,
> 
> It seems everyone is pointing to this (http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring) which I somehow missed. However, they seem to be altering one residue at a time like I’m doing. 
> 
> 
> Jordan
>> On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
>> 
>> Hi Jordan,
>> 
>> Yes, although I don't have the answer at hand, it has been given on the user list several times. You can find it in the archives.
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Jun 16, 2015 08:16, "Jordan Willis" <jwi...@gm...> wrote:
>> Hi,
>> 
>> I have a dictionary that has a bunch of values I want to assign to b-factors in order to color by. In my script:
>> 
>> for residue in data:
>>    cmd.alter(“resi {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
>> 
>> This executes the alter command for each residue. For some reason, its taking forever in my script. Is there something inherently inefficient about alter? And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.
>> 
>> Jordan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Jordan -

I think you're doing it exactly the way I would, given an existing dict containing the values.  Note, however, that if you have multiple loaded, or multiple chains with the same residue numbers, you may wish to be more specific with your selection string; your current script will alter every residue with the given resi # in all chains of all loaded objects.

If you're having to do this multiple times with the same structure and it's slow each time (e.g. while creating a figure from a script), maybe consider saving a new PDB file with the modified B-factors using PyMOL's `save` command, so you can just load it directly.

# After your `alter` script
save myfile_mod_b.pdb, myfile

# Then next time load the new version with the same name
# as before to avoid breaking the rest of the script. Now you can
# remove the `alter` for-loop from the script.
load myfile_mod_b.pdb, myfile

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 16, 2015, at 2:15 AM, Jordan Willis <jwi...@gm...<mailto:jwi...@gm...>> wrote:

Hi,

I have a dictionary that has a bunch of values I want to assign to b-factors in order to color by. In my script:

for residue in data:
   cmd.alter(“resi {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))

This executes the alter command for each residue. For some reason, its taking forever in my script. Is there something inherently inefficient about alter? And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.

Jordan
------------------------------------------------------------------------------
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Archives: http://www.mail-archive.com/pym...@li...

Hi Alsa,

In the line where you save the file, you need to specify a selection,
otherwise, everything will be saved
Look at http://www.pymolwiki.org/index.php/Save#PYMOL_API

So instead of
        cmd.save(filenameN + '.mol')
you want something like
        cmd.save(filenameN + '.mol', filename)

I haven't tested this myself though.

Hope this helps
Folmer


2015-06-06 11:53 GMT+02:00 AE <als...@ya...>:

> Good day,
>
> I have several thousands of files, which I upload using the loop:
>
> myDir = ‘/dirWithFiles'
> for filename in os.listdir(myDir):
>         cmd.load (filename)
>         filenameN = os.path.splitext(filename)[0]
>         cmd.save(filenameN + '.mol')
>         cmd.disable(filename)
>
> I am trying to save them one by one in a different (.mol) format. However,
> the files are saved together, i.e.: first file opened contains only
> molecule from the first file; second: first + second; third: first + second
> + third etc. But I want firstFile.readableFormat to be converted into
> firstFile.mol, secondFile.readableFormat - secondFile.mol etc, without any
> addition of other files. How can I do that?
>
> Thank you,
>
> Best Regards,
>
> Alsa
>
> Sorry I have sent it already, accidentally forgot to finish the question
> in subject(
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...




-- 
Folmer Fredslund

Hi Jordan,

The answer is something like (assuming reading from a file):

newb=[float(i) for i in open("stuff.dat").read().split()]
alter n. ca, b=newb.pop()
spectrum b

Hope it helps,

Tsjerk

On Tue, Jun 16, 2015 at 10:25 AM, Jordan Willis <jwi...@gm...>
wrote:

> Hi Tsjerk,
>
> It seems everyone is pointing to this (
> http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring)
> which I somehow missed. However, they seem to be altering one residue at a
> time like I’m doing.
>
>
> Jordan
>
> On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
>
> Hi Jordan,
>
> Yes, although I don't have the answer at hand, it has been given on the
> user list several times. You can find it in the archives.
>
> Cheers,
>
> Tsjerk
> On Jun 16, 2015 08:16, "Jordan Willis" <jwi...@gm...> wrote:
>
>> Hi,
>>
>> I have a dictionary that has a bunch of values I want to assign to
>> b-factors in order to color by. In my script:
>>
>> for residue in data:
>>    cmd.alter(“resi
>> {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
>>
>> This executes the alter command for each residue. For some reason, its
>> taking forever in my script. Is there something inherently inefficient
>> about alter? And is there anyway to fix it? Perhaps, assign a bunch of
>> b-factors at once.
>>
>> Jordan
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Tsjerk,

It seems everyone is pointing to this (http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring <)" rel="nofollow">http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring>) which I somehow missed. However, they seem to be altering one residue at a time like I’m doing. 


Jordan
> On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> 
> Hi Jordan,
> 
> Yes, although I don't have the answer at hand, it has been given on the user list several times. You can find it in the archives.
> 
> Cheers,
> 
> Tsjerk
> 
> On Jun 16, 2015 08:16, "Jordan Willis" <jwi...@gm... <mailto:jwi...@gm...>> wrote:
> Hi,
> 
> I have a dictionary that has a bunch of values I want to assign to b-factors in order to color by. In my script:
> 
> for residue in data:
>    cmd.alter(“resi {}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
> 
> This executes the alter command for each residue. For some reason, its taking forever in my script. Is there something inherently inefficient about alter? And is there anyway to fix it? Perhaps, assign a bunch of b-factors at once.
> 
> Jordan
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>