date:20170602

Re: [PyMOL] Problem with 'byring' selection

2017-06-02 Thread Tsjerk Wassenaar

Hi Vijay,

It is logic. 'byring elem N' selects all nitrogens and then expands the
selection to include the rings in which these participate. 'elem N and
byring elem N' does the same, but then intersects (and) to extract only
nitrogens. But that is the same as 'elem N'. If you want to have the
nitrogens from rings, you can do 'elem N and byring not elem N'. That
selects the non-nitrogen atoms and expands the selection over rings. So
only nitrogens in rings can be added to teh selection. Then intersecting to
get only nitrogens will yield only those that are members of rings.

Hope it helps,

Tsjerk

On Jun 3, 2017 5:45 AM, "Vijay Masand"  wrote:

> Dear PyMOL Users,
> I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
> was working with small molecule
> (ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN).
> When I tried to select all Nitrogen atoms which are exclusively in the
> ring only, I tried following command:
> abc=cmd.select('byring elem N')
> But, this selected not only Nitrogen atoms in the ring but Carbon
> atoms of the ring also.
> But, following command worked perfectly:
> abc=cmd.select('elem N & byring elem N')
> Is it a bug or something else?
> Cheers
> Vijay
>
> --
> Assistant Professor
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
> 
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[PyMOL] Problem with 'byring' selection

2017-06-02 Thread Vijay Masand

Dear PyMOL Users,
I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
was working with small molecule
(ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN).
When I tried to select all Nitrogen atoms which are exclusively in the
ring only, I tried following command:
abc=cmd.select('byring elem N')
But, this selected not only Nitrogen atoms in the ring but Carbon
atoms of the ring also.
But, following command worked perfectly:
abc=cmd.select('elem N & byring elem N')
Is it a bug or something else?
Cheers
Vijay

-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

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Re: [PyMOL] [External] Re: Unable to initialize plugin annocryst

2017-06-02 Thread Luo, Jonathan Z.

Hi Thomas,
Thanks for the reply. Didn't work, it just gave the same error message but with 
"idlelib.TreeWidget" instead of "modules.idlelib.TreeWidget"
Jon

From: Thomas Holder 
Sent: Friday, June 2, 2017 5:52 AM
To: Luo, Jonathan Z.
Cc: pymol-users@lists.sourceforge.net
Subject: [External] Re: [PyMOL] Unable to initialize plugin annocryst

Hi Jon,

try this: In file "annocryst.py" on line 22, replace:

from modules.idlelib.TreeWidget import TreeItem, TreeNode

with:

from idlelib.TreeWidget import TreeItem, TreeNode

Hope that works for you.

Cheers,
  Thomas


> On Jun 1, 2017, at 7:03 PM, Luo, Jonathan Z.  wrote:
>
> Hello,
> I've just installed pymol and am running into this error at startup:
> No module named modules.idlelib.TreeWidget
> Unable to initialize plugin 'annocryst' (pmg_tk.startup.annocryst)
>
> When I try to import:
> PyMOL>import pmg_tk.startup.annocryst
> Traceback (most recent call last):
>   File "/opt/pymol/modules/pymol/parser.py", line 262, in parse
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "", line 1, in 
>   File "/opt/pymol/Pymol-script-repo/plugins/annocryst.py", line 22, in 
> 
> from modules.idlelib.TreeWidget import TreeItem, TreeNode
> ImportError: No module named modules.idlelib.TreeWidget
>
> I see it exists at /opt/pymol/Pymol-script-repo/modules/idlelib/TreeWidget.py
> What should I do?
>
> Thank you!
> Jon

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Unable to initialize plugin annocryst

2017-06-02 Thread Thomas Holder

Hi Jon,

try this: In file "annocryst.py" on line 22, replace:

from modules.idlelib.TreeWidget import TreeItem, TreeNode

with:

from idlelib.TreeWidget import TreeItem, TreeNode

Hope that works for you.

Cheers,
  Thomas


> On Jun 1, 2017, at 7:03 PM, Luo, Jonathan Z.  wrote:
> 
> Hello,
> I've just installed pymol and am running into this error at startup: 
> No module named modules.idlelib.TreeWidget
> Unable to initialize plugin 'annocryst' (pmg_tk.startup.annocryst)
> 
> When I try to import:
> PyMOL>import pmg_tk.startup.annocryst
> Traceback (most recent call last):
>   File "/opt/pymol/modules/pymol/parser.py", line 262, in parse
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "", line 1, in 
>   File "/opt/pymol/Pymol-script-repo/plugins/annocryst.py", line 22, in 
> 
> from modules.idlelib.TreeWidget import TreeItem, TreeNode
> ImportError: No module named modules.idlelib.TreeWidget
> 
> I see it exists at /opt/pymol/Pymol-script-repo/modules/idlelib/TreeWidget.py
> What should I do?
> 
> Thank you!
> Jon

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Problem with 'byring' selection

[PyMOL] Problem with 'byring' selection

Re: [PyMOL] [External] Re: Unable to initialize plugin annocryst

Re: [PyMOL] Unable to initialize plugin annocryst

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