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
>
>
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> ------------------------------
>
> 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
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> ------------------------------
>
> 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
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> End of PyMOL-users Digest, Vol 85, Issue 16
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--
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
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