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 <neshat...@gmail.com> wrote:
> Thanks, thanks a lot Thomas it really helped
>
>
> On Mon, Jun 24, 2013 at 2:12 PM, <
> pymol-users-requ...@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.chap...@ibcp.fr>
>> Subject: [PyMOL] problem with "distance"
>> To: pymol-users@lists.sourceforge.net
>> Message-ID: <51c31b12.50...@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
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 20 Jun 2013 18:09:35 +0200
>> From: Thomas Holder <thomas.hol...@schrodinger.com>
>> Subject: Re: [PyMOL] problem with "distance"
>> To: pymol-users@lists.sourceforge.net
>> Message-ID: <51c3293f.4080...@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.hol...@schrodinger.com>
>> Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
>> To: pymol-users@lists.sourceforge.net
>> Message-ID: <51c3d4d7.5080...@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.hol...@schrodinger.com>
>> Subject: Re: [PyMOL] Problems with Pymol v 1.6.0.0
>> To: pymol-users@lists.sourceforge.net
>> Message-ID: <51c3e0e6.90...@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 <neshat...@gmail.com>
>> Subject: [PyMOL] Averaging a pdb file
>> To: pymol-users@lists.sourceforge.net
>> Message-ID:
>> <CAM3wsb1FiqVXXLK7Ea8R6xutztaC=
>> 5uzfhkrdpnhbvqmqro...@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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Sun, 23 Jun 2013 22:15:14 +0200
>> From: Thomas Holder <thomas.hol...@schrodinger.com>
>> Subject: Re: [PyMOL] Averaging a pdb file
>> To: pymol-users@lists.sourceforge.net
>> Message-ID: <51c75752.8060...@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" <scou...@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-dc54f01fe...@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
>> -------------- next part --------------
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>>
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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
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