[PyMOL] Re: Need advice on graphic card
Hi, I have 2 monitors running out of an ATI Radeon 8500 on redhat 8.0 using the summit accelerated Xserver from Xig.com for hardware stereo on one of the monitors. I use the dual view function, so 1 big desktop (1 "screen" on 2 monitors) Very hardware accelerated! cheers Dan On 12 Nov 2003, at 06:25, pymol-users-requ...@lists.sourceforge.net wrote: --__--__-- Message: 3 Date: Tue, 11 Nov 2003 12:17:20 -0500 (EST) From: Yu Chen To: Marc Saric cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Need advice on graphic card the "merged mode" is just one framebuffer for both display, so fool the system thinking it's only a "single-head" presented. No, Xinerama won't work with DRI. That's why i used merged mode, but it messed up nmrview's font. Seems nobody else out there using two screens? Thanks anyway, Marc Chen Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
[PyMOL] Re:labeling atoms in GUI
Warren, I want to be able to use those useful
definations every time I load pymol. I wonder how to
edit the general startup script pymol in order to do
that? By the way, I also want pymol to show distance
when I click two atoms. Thank you.
Eric
> Quoting "Warren L. DeLano"
> :
>
> > Richard,
> >
> > It's not GUI, but you could simply bind a function
> key such as F1 to
> > that command:
> >
> > cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
> > %s"%(name,resn,resi)'))
> >
> > You might then want to bind 'F2' to something
> which hides all labels.
> >
> > cmd.set_key('F2',cmd.label)
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:war...@delanoscientific.com
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax (650)-593-4020
> >
> > > -Original Message-
> > > From: pymol-users-ad...@lists.sourceforge.net
> > > [mailto:pymol-users-ad...@lists.sourceforge.net]
> On Behalf Of
> > > rbax...@uchicago.edu
> > > Sent: Wednesday, October 29, 2003 5:14 PM
> > > To: pymol-users@lists.sourceforge.net
> > > Subject: [PyMOL] labeling atoms in GUI
> > >
> > >
> > > Dear All,
> > >
> > > I want to look at my structure in PyMOL and,
> having centered
> > > on something defined by my selection script,
> pick atoms
> > > nearby and see what residues they belong to.
> That is, I want
> > > to pick select an atom with the mouse and have
> its name,
> > > residue name and residue number appear on
> screen, like it does in O.
> > >
> > > I figured out that [Ctrl] + Left-Mouse-Button
> selects the
> > > atom as "lb", and that the command 'label
> (lb),"%s %s %s" %
> > > (name,resn,resi)' gives me the label I want. Now
> how could I
> > > get something like that to appear as a menu
> function in the
> > > GUI so I don't have type it in all the time? Can
> it be a
> > > command executed as part of my startup script?
> > >
> > > Maybe some function like this already exists,
> otherwise I
> > > think it is a very useful thing.
> > >
> > > regards,
> > >
> > > Richard Baxter
>
>
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Re: [PyMOL] Re: Need advice on graphic card
I just tried Summit Xserver, it is definitly a looot fast. But ... in single head mode. They claim they support Matrox Millennium G450 multihead. In dual view 1600x1200 mode, the pymol won't lanuch, gave out: GLUT: fatal error in pymol, visual with neccessary capbilities not found. But in dual view 1152x864 and under, it does lauch, but not as fast as in single head mode, and some of the screen goes out of the monitor. And the price for the Summit multi-head is more than the price for a new good graphic card. I just have ordered ATI radeon 9600 PRO and 9600, will see how it goes. Thanks for the informations. Chen > I have 2 monitors running out of an ATI Radeon 8500 on redhat 8.0 using > the summit accelerated Xserver from Xig.com for hardware stereo on one > of the monitors. > > I use the dual view function, so 1 big desktop (1 "screen" on 2 > monitors) > > Very hardware accelerated! > > cheers > > Dan > > > On 12 Nov 2003, at 06:25, pymol-users-requ...@lists.sourceforge.net > wrote: > > > --__--__-- > > > > Message: 3 > > Date: Tue, 11 Nov 2003 12:17:20 -0500 (EST) > > From: Yu Chen > > To: Marc Saric > > cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Need advice on graphic card > > > > the "merged mode" is just one framebuffer for both display, so fool the > > system thinking it's only a "single-head" presented. > > No, Xinerama won't work with DRI. That's why i used merged mode, but it > > messed up nmrview's font. > > > > Seems nobody else out there using two screens? > > > > Thanks anyway, Marc > > Chen > Dr. Daniel James White BSc. (Hons.) PhD > Cell Biology > Department of biological and environmental science > PO Box 35 > University of Jyväskylä > Jyväskylä FIN 40014 > Finland > +358 (0)14 260 4183 (work) > +358 (0)414740463 (mob) > > http://www.chalkie.org.uk > d...@chalkie.org.uk > wh...@cc.jyu.fi > > > > --- > This SF.Net email sponsored by: ApacheCon 2003, > 16-19 November in Las Vegas. Learn firsthand the latest > developments in Apache, PHP, Perl, XML, Java, MySQL, > WebDAV, and more! http://www.apachecon.com/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 182 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu ===
RE: [PyMOL] Re:labeling atoms in GUI
Eric,
PyMOL will source startup files in your home directory -- just
put your commands in there:
On Mac/Unix:
$HOME/.pymolrc (for PyMOL commands)
$HOME/.pymolrc.py (for Python code)
On Windows:
%HOMEPATH%\pymolrc(for PyMOL commands)
%HOMEPATH%\pymorc.py (for Python code)
To show distances, use the distance wizard:
wizard distance
then ctrl-middle-clock on two atoms in succession.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Eric Hu
> Sent: Wednesday, November 12, 2003 11:22 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Re:labeling atoms in GUI
>
>
> Warren, I want to be able to use those useful
> definations every time I load pymol. I wonder how to
> edit the general startup script pymol in order to do
> that? By the way, I also want pymol to show distance
> when I click two atoms. Thank you.
>
> Eric
>
>
> > Quoting "Warren L. DeLano"
> > :
> >
> > > Richard,
> > >
> > > It's not GUI, but you could simply bind a function
> > key such as F1 to
> > > that command:
> > >
> > > cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s
> > > %s"%(name,resn,resi)'))
> > >
> > > You might then want to bind 'F2' to something
> > which hides all labels.
> > >
> > > cmd.set_key('F2',cmd.label)
> > >
> > > Cheers,
> > > Warren
> > >
> > > --
> > > mailto:war...@delanoscientific.com
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax (650)-593-4020
> > >
> > > > -Original Message-
> > > > From: pymol-users-ad...@lists.sourceforge.net
> > > > [mailto:pymol-users-ad...@lists.sourceforge.net]
> > On Behalf Of
> > > > rbax...@uchicago.edu
> > > > Sent: Wednesday, October 29, 2003 5:14 PM
> > > > To: pymol-users@lists.sourceforge.net
> > > > Subject: [PyMOL] labeling atoms in GUI
> > > >
> > > >
> > > > Dear All,
> > > >
> > > > I want to look at my structure in PyMOL and,
> > having centered
> > > > on something defined by my selection script,
> > pick atoms
> > > > nearby and see what residues they belong to.
> > That is, I want
> > > > to pick select an atom with the mouse and have
> > its name,
> > > > residue name and residue number appear on
> > screen, like it does in O.
> > > >
> > > > I figured out that [Ctrl] + Left-Mouse-Button
> > selects the
> > > > atom as "lb", and that the command 'label
> > (lb),"%s %s %s" %
> > > > (name,resn,resi)' gives me the label I want. Now
> > how could I
> > > > get something like that to appear as a menu
> > function in the
> > > > GUI so I don't have type it in all the time? Can
> > it be a
> > > > command executed as part of my startup script?
> > > >
> > > > Maybe some function like this already exists,
> > otherwise I
> > > > think it is a very useful thing.
> > > >
> > > > regards,
> > > >
> > > > Richard Baxter
> >
> >
>
>
> __
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>
>
>
> ---
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest
> developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV,
> and more! http://www.apachecon.com/
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> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
[PyMOL] clipping
Robert Schwarzenbacher, PhD The Joint Center for Structural Genomics phone: 858 822 3637 Hi there, Is there a way to define the clipping planes for only one object in a scene. For example I only want to clip the surface while not affecting residues shown in stick. Or alternatively is there a way to extract the surface of an inside cavity. Many thanks robert
[PyMOL] surface area calculation
Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
Re: [PyMOL] surface area calculation
To calculate surface area for a defined object from the PyMOL command
line type:
print cmd.get_area("obj")
where obj is the name of your object.
for arginines:
create ARG, resn ARG
print cmd.get_area("ARG")
Kaushik.
On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:
Is it possible to get pymol to calculate surface area for a defined
object? For instance, can it calculate surface area occupied by
arginines.
Thanks,
Joel
Joel M. Harp
Vanderbilt University
RE: [PyMOL] surface area calculation
Joel, Yes, PyMOL does have this capability, but it is immature and not routinely validated. The basic concepts are: 1) "get_area selection" command will return the effective surface area of the dots that you would see from "show dots, selection". This is a discrete approximation -- not an exact calculation. 2) you can use the "dot_solvent" setting to control whether you get solvent surface area or a molecular surface area. 1=solvent, 0=molecular 3) the accuracy of the measurement depends on the density of dots, which is controlled by the "dot_density" setting (1-4). 4) the solvent radius is controlled by the "solvent_radius" setting (default 1.4). For example: PyMOL> load $TUT/1hpv.pdb PyMOL> show dots, resn arg PyMOL> get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOL>set dot_solvent, on PyMOL>get_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOL>set dot_density, 3 PyMOL>get_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOL>set dot_density, 4 PyMOL>get_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOL>get_area all cmd.get_area: 13837.804 Angstroms^2. This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface area calculation Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
RE: [PyMOL] surface area calculation
Close, but it depends on whether you want the surface area of the
residues alone, or in the context of the molecule.
load protein.pdb
get_area resn arg
will be less than
create arg_object, resn arg
get_area arg_object
This is because the first example will give you only the exposed area of
the arginines in the presence of the other atoms, whereas the second
gives the area of the arginines in isolation.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Kaushik
Raha
Sent: Wednesday, November 12, 2003 2:50 PM
To: Harp, Joel M
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] surface area calculation
To calculate surface area for a defined object from the PyMOL command
line type:
print cmd.get_area("obj")
where obj is the name of your object.
for arginines:
create ARG, resn ARG
print cmd.get_area("ARG")
Kaushik.
On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote:
Is it possible to get pymol to calculate surface area for a defined
object? For instance, can it calculate surface area occupied by
arginines.
Thanks,
Joel
Joel M. Harp
Vanderbilt University
[PyMOL] N-Terminal hydrogens with Chempy
Hi Warren, I found out that it is possible to write out AMBER style atom name formats with hydrogens added using the Chempy which is pretty neat. However it seems like this does not recognize the N-terminal residue for adding hydrogens. Is that still the case? I am still using PyMOL 088 (I will soon upgrade). Thanks, Kaushik. -- Graduate Student Penn State University University Park PA-16801
