Hello, everyone

Can anyone tell how to to find the "van der Waals"
radii of a non spherical molecule.
And how to find the residues in "van der Waals" contact of a ligand.


On Tue, Jun 25, 2013 at 2:49 PM, neshat haq <neshathaq@gmail.com> wrote:
Thanks, thanks a lot Thomas it really helped


On Mon, Jun 24, 2013 at 2:12 PM, <pymol-users-request@lists.sourceforge.net> wrote:
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Today's Topics:

   1.  problem with "distance" (vincent Chaptal)
   2. Re: problem with "distance" (Thomas Holder)
   3. Re: Problems with Pymol v 1.6.0.0 (Thomas Holder)
   4. Re: Problems with Pymol v 1.6.0.0 (Thomas Holder)
   5. Averaging a pdb file (neshat haq)
   6. Re: Averaging a pdb file (Thomas Holder)
   7. Fixed width font in gui on OSX w/ PyMOL 1.6.0
      (Alexander D. Scouras)


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

Message: 1
Date: Thu, 20 Jun 2013 17:09:06 +0200
From: vincent Chaptal <vincent.chaptal@ibcp.fr>
Subject: [PyMOL]  problem with "distance"
To: pymol-users@lists.sourceforge.net
Message-ID: <51C31B12.50805@ibcp.fr>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
I've just purchased v1.6 and installed it under MacOS 10.6.8.
I have a problem with using "distance" from a script, as well as via the
wizard.

my pdb has 12 chains.
when I type: distance d1, molA and chain a and resi 53 and name o, molA
and chain d and resi 8 and name n
the distance is drawn between: chain M and resi 7 and atom cg, and chain
I and resi 53 and atom o.

I don't understand the error. So I turned to the wizard ->measurement. I
click on the atoms that are in front of me, and the distance is drawn
again between  chain M and resi 7 and atom cg, and chain I and resi 53
and atom o.
For a proof, I'm pasting the top screen where the names of the atoms I
clicked is:
You clicked /molA//A/SER`53/O
Selector: selection "sele" defined with 1 atoms.
You clicked /molA//D/GLY`8/N)

I was previously under 1.3 and didn't have this problem.
Can you help me?
Vincent


--

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Prot?ines

Drug-resistance modulation and mechanism Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr


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Message: 2
Date: Thu, 20 Jun 2013 18:09:35 +0200
From: Thomas Holder <thomas.holder@schrodinger.com>
Subject: Re: [PyMOL] problem with "distance"
To: pymol-users@lists.sourceforge.net
Message-ID: <51C3293F.4080008@schrodinger.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Vincent,

we introduced dynamic_measures in PyMOL 1.4, which uses the atom ID and
is not robust against duplicated IDs. So the workaround here is to
switch dynamic_measures off:

PyMOL> unset dynamic_measures

Hope that helps.

Cheers,
  Thomas

vincent Chaptal wrote, On 06/20/13 17:09:
> Hi,
> I've just purchased v1.6 and installed it under MacOS 10.6.8.
> I have a problem with using "distance" from a script, as well as via the
> wizard.
>
> my pdb has 12 chains.
> when I type: distance d1, molA and chain a and resi 53 and name o, molA
> and chain d and resi 8 and name n
> the distance is drawn between: chain M and resi 7 and atom cg, and chain
> I and resi 53 and atom o.
>
> I don't understand the error. So I turned to the wizard ->measurement. I
> click on the atoms that are in front of me, and the distance is drawn
> again between  chain M and resi 7 and atom cg, and chain I and resi 53
> and atom o.
> For a proof, I'm pasting the top screen where the names of the atoms I
> clicked is:
> You clicked /molA//A/SER`53/O
> Selector: selection "sele" defined with 1 atoms.
> You clicked /molA//D/GLY`8/N)
>
> I was previously under 1.3 and didn't have this problem.
> Can you help me?
> Vincent

--
Thomas Holder
PyMOL Developer
Schr?dinger Contractor



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

Message: 3
Date: Fri, 21 Jun 2013 06:21:43 +0200
From: Thomas Holder <thomas.holder@schrodinger.com>
Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
To: pymol-users@lists.sourceforge.net
Message-ID: <51C3D4D7.5080506@schrodinger.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Matthew,

thanks for the report. We fixed and pushed this to SVN today.

Cheers,
  Thomas

Matthew Baumgartner wrote, On 06/20/13 15:54:
> Hi,
> Adding to thread.
>
> I'm using pymol 1.6 (built from svn yesterday) on Ubuntu 13.04.
> I've noticed that the selection indicators are not working properly.
>
> Steps to reproduce:
> #launch ignoring the config file
> pymol -k
>
> #in pymol
>>fetch 1YCR
>
> Then open sequence viewer and select a range of residues. Only the first
> residue is highlighed on the structure (pink squares).
>
> Is there some setting that I accidentally set somewhere?
>
> Thanks,
> Matt

--
Thomas Holder
PyMOL Developer
Schr?dinger Contractor



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

Message: 4
Date: Fri, 21 Jun 2013 07:13:10 +0200
From: Thomas Holder <thomas.holder@schrodinger.com>
Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
To: pymol-users@lists.sourceforge.net
Message-ID: <51C3E0E6.90307@schrodinger.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Stephen,

Stephen P. Molnar wrote, On 06/18/13 15:16:
> Two minor, but annoying, problems with the new version in Debian 7.0 64 bit/
>
> #1  The pull down menus in the graphics windows refuse to remain open
> when clicked, unless I left click and hold.  Is this normal behavior?

this is not normal behavior. Unfortunately I can't reproduce it. I don't
have a Debian system, but I tested on Ubuntu, Gentoo and CentOS. I'll
test on Debian when I get the change.

> #2.  Caver 2.1.2 will not save the location of the Directory with the
> plug-in .jar file.  The work around is rather cumbersome.

Caver is a third-party plugin and as far as I know will not save any
settings to disk. The easiest workaround is to edit PYMOL_LOCATION in
Caver2_1_2.py (the Plugin Manager can tell you where to find Caver2_1_2.py).

Actually, a nice way to reorganize the Caver plugin would be:

Caver2_1_2
|-- Caver2_1.jar
|-- __init__.py    (was: Caver2_1_2.py)
`-- lib
    |-- dt3d.jar
    |-- j3dcore.jar
    |-- j3dutils.jar
    |-- ujmp-complete-0.2.4.jar
    `-- vecmath.jar

And in Caver2_1_2/__init__.py, change:

  PYMOL_LOCATION = sys.modules[__name__].__path__[0]

Cheers,
  Thomas

--
Thomas Holder
PyMOL Developer
Schr?dinger Contractor



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

Message: 5
Date: Sun, 23 Jun 2013 22:52:10 +0530
From: neshat haq <neshathaq@gmail.com>
Subject: [PyMOL] Averaging a pdb file
To: pymol-users@lists.sourceforge.net
Message-ID:
        <CAM3wsb1FiqVXXLK7Ea8R6xutztaC=5UZFHkrdPnhBvqMqrOg_Q@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

How can we convert a 10 structure in apdb file to an approximate average.
Is there any plugin or tool?
I once tried average3d.py from mura lab but that average structure is
duplicate of the first structure we opt.

Anyways any suggestion will be appriciated.

--
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
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Message: 6
Date: Sun, 23 Jun 2013 22:15:14 +0200
From: Thomas Holder <thomas.holder@schrodinger.com>
Subject: Re: [PyMOL] Averaging a pdb file
To: pymol-users@lists.sourceforge.net
Message-ID: <51C75752.8060906@schrodinger.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Neshatul,

try "spheroid":

PyMOL> fetch 1nmr, async=0
PyMOL> spheroid 1nmr

To relax locally distorted structure, you can use sculpting:

PyMOL> fetch 1nmr, async=0
PyMOL> sculpt_activate 1nmr, 1
PyMOL> spheroid 1nmr
PyMOL> set sculpting, 1
# ... until you like it
PyMOL> set sculpting, 0

Hope that helps.

Cheers,
  Thomas

neshat haq wrote, On 06/23/13 19:22:
> How can we convert a 10 structure in apdb file to an approximate average.
> Is there any plugin or tool?
> I once tried average3d.py from mura lab but that average structure is
> duplicate of the first structure we opt.
>
> Anyways any suggestion will be appriciated.

--
Thomas Holder
PyMOL Developer
Schr?dinger Contractor



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

Message: 7
Date: Mon, 24 Jun 2013 01:41:47 -0700
From: "Alexander D. Scouras" <scouras@berkeley.edu>
Subject: [PyMOL] Fixed width font in gui on OSX w/ PyMOL 1.6.0
To: "pymol-users@lists.sourceforge.net"
        <pymol-users@lists.sourceforge.net>
Message-ID: <A17F62D4-449A-4405-BF35-DC54F01FE841@berkeley.edu>
Content-Type: text/plain; charset="us-ascii"

I'm wondering if it's possible to switch the MacPyMOL gui to use a fixed width font.

I've seen Jason's suggestion for the external Tk GUI and the FAQ.

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10847.html
http://pymol.sourceforge.net/faq.html#FONT

I've confirmed that they work fine if I launch the PyMOLX11Hybrid gui, but no luck with the OSX native one (_ext_gui = None), and haven't been able to introspect anything equivalent.

Thanks,

Alex Scouras
Postdoctoral Scholar
Alber Lab
UC Berkeley
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--
Best regards
Neshatul Haque 
PhD, Dpt of Biotechnology
university of hyderabad



--
Best regards
Neshatul Haque 
PhD, Dpt of Biotechnology
university of hyderabad