[PyMOL] PyMOL 1.8.0 released

[Thomas Holder]

Greetings,

We are happy to announce the release of PyMOL v1.8.0! Official PyMOL sponsors 
can download ready-to-use installers from http://pymol.org/download . The 
open-source code has been pushed to sourceforge svn (revision 4142). This 
release finalizes our mmCIF support roadmap. 

Important: We changed the default of the “ignore_case” setting to off. This 
setting has effect on the selection language and atom sorting. While it’s 
convenient to select chain A with “chain a”, it’s not practical when you work 
with large structures and run out of uppercase chain identifiers (note: PyMOL 
does support multi-letter chain identifiers, but this doesn’t help when you 
want to export to PDB format). Be prepared that your old scripts might depend 
on ignore_case, in that case either fix them, or put an “set ignore_case” at 
the top of the script or in your pymolrc file.

The “fetch” command now by default downloads mmCIF files (type=cif).

This release fixes the issues with ATI R9 graphics cards on OS X.

Find the complete release notes on:
http://pymol.org/features

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] on coloring residues based on y values in the x y z coordinates

[Smith Liu]

Dear All,


Is any way we can colour the molecule by pymol based on the y values in the z y 
z coordinates, so that we can view easily the residues (or atoms) with 
equivalent position in the primary sequence but has a y-axis shift in the 3-D 
structure?


Smith
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

Assuming you are ok with overwriting the B-factors


stored.y=[]
iterate_state 1, prot, stored.y.append(y) % prot here should be replaced
with your pymol object name
alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object
name




On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu  wrote:

> Dear All,
>
> Is any way we can colour the molecule by pymol based on the y values in
> the z y z coordinates, so that we can view easily the residues (or atoms)
> with equivalent position in the primary sequence but has a y-axis shift in
> the 3-D structure?
>
> Smith
>
>
>
>
>
> --
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

I forgot:

spectrum b


at the end.



On Wed, Nov 18, 2015 at 8:11 AM, David Hall  wrote:

> Assuming you are ok with overwriting the B-factors
>
>
> stored.y=[]
> iterate_state 1, prot, stored.y.append(y) % prot here should be replaced
> with your pymol object name
> alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object
> name
>
>
>
>
> On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu  wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> 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] on coloring residues based on y values in the x y z coordinates

[Schubert, Carsten [JRDUS]]

If you have access to the incentive version, I would recommend looking at the 
new properties capabilities in Pymol. The distances can be nicely encoded in a 
property and rendered with spectrum w/o having to resort to messing with other 
properties like B-factors. I believe the docs at Schrodinger contain examples 
to that end.

HTH

Carsten

From: David Hall [mailto:li...@cowsandmilk.net]
Sent: Wednesday, November 18, 2015 8:13 AM
To: Smith Liu
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] on coloring residues based on y values in the x y z 
coordinates

I forgot:
spectrum b

at the end.


On Wed, Nov 18, 2015 at 8:11 AM, David Hall 
> wrote:
Assuming you are ok with overwriting the B-factors

stored.y=[]
iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with 
your pymol object name
alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name



On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu 
> wrote:
Dear All,

Is any way we can colour the molecule by pymol based on the y values in the z y 
z coordinates, so that we can view easily the residues (or atoms) with 
equivalent position in the primary sequence but has a y-axis shift in the 3-D 
structure?

Smith




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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

clearly shouldn’t write e-mails before having my morning coffee. Those %
symbols should have been pounds, I was aiming to make comments


As an example:

fetch 1acb, prot,  async=0
stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)
spectrum b



On Nov 18, 2015, at 9:12 AM, Smith Liu  wrote:

Dear David,

I am unfamiliar with the pymol scripts so I do not understands where your
scripts end at each line. Can we write this way,

stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)

which means those from % in your scripts will be not used in each line for
pymol reading?

Can you introduce a website to introduce the pymol scripts? For stored.y=，
following y= is it the file name of file stores y for each coordinates? Can
you introduce to me a server or software which can extract y coordinates
from the PDB and save it as another file? Can you introduce to me a server
of software which can delete the original b-factors in the original PDB and
have the ys pasted on the b-factors positions in the PDB file?

Smith











At 2015-11-18 21:13:05, "David Hall"  wrote:

I forgot:

spectrum b


at the end.



On Wed, Nov 18, 2015 at 8:11 AM, David Hall  wrote:

> Assuming you are ok with overwriting the B-factors
>
>
> stored.y=[]
> iterate_state 1, prot, stored.y.append(y) % prot here should be replaced
> with your pymol object name
> alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object
> name
>
>
>
>
> On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu  wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> 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] on coloring residues based on y values in the x y z coordinates

[Smith Liu]

Dear David,


I am unfamiliar with the pymol scripts so I do not understands where your 
scripts end at each line. Can we write this way,


stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)


which means those from % in your scripts will be not used in each line for 
pymol reading?


Can you introduce a website to introduce the pymol scripts? For stored.y=， 
following y= is it the file name of file stores y for each coordinates? Can you 
introduce to me a server or software which can extract y coordinates from the 
PDB and save it as another file? Can you introduce to me a server of software 
which can delete the original b-factors in the original PDB and have the ys 
pasted on the b-factors positions in the PDB file?


Smith


















At 2015-11-18 21:13:05, "David Hall"  wrote:

I forgot:


spectrum b



at the end.





On Wed, Nov 18, 2015 at 8:11 AM, David Hall  wrote:

Assuming you are ok with overwriting the B-factors



stored.y=[]

iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with 
your pymol object name

alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name







On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu  wrote:

Dear All,


Is any way we can colour the molecule by pymol based on the y values in the z y 
z coordinates, so that we can view easily the residues (or atoms) with 
equivalent position in the primary sequence but has a y-axis shift in the 3-D 
structure?


Smith





 



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Re: [PyMOL] problem of pymol 1.8

[Thomas Holder]

Hi Albert,

These messages come from third-party plugins that you have installed, see:
http://pymolwiki.org/index.php/MtsslDock
http://pymolwiki.org/index.php/MtsslTrilaterate

Cheers,
  Thomas

On 18 Nov 2015, at 17:08, Albert  wrote:

> Hello:
> 
> I've installed the open source code version pymol 1.8 in my Linux OS.
> 
> 
> However, when I start pymol, it always showed the following messages:
> 
> No module named tkintertable.Tables
> Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
> No module named wx
> Unable to initialize plugin 'mtsslTrilaterate'
> (pmg_tk.startup.mtsslTrilaterate).
> 
> I am just wondering how can we solve the problem? I've already installed 
> python PMW in my machine.
> 
> thank you very much.
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] problem of pymol 1.8

[Albert]

Hi Thomas:

thanks a lot for helpful advice.

HOwever, I got something new warnings:

No module named cPluginManager
Unable to initialize plugin 'xPyder' (pmg_tk.startup.xPyder).
No module named backend_wxagg
Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter).

I google it, and cannot find any helpful information


thanks again

ALbert


On 11/18/2015 11:16 PM, Thomas Holder wrote:
> Hi Albert,
>
> These messages come from third-party plugins that you have installed, see:
> http://pymolwiki.org/index.php/MtsslDock
> http://pymolwiki.org/index.php/MtsslTrilaterate
>
> Cheers,
>Thomas


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