pymol-users

[PyMOL] PyMOL 0.95 Released

[Warren D. <wa...@de...>]

PyMOLers:

Yesterday marked DeLano Scientific's one year anniversary as a full-time
business.  In addition to popping the cork on a bottle of champagne, we
celebrated with the release of version 0.95!

http://pymol.sf.net
http://pymol.sf.net/obtaining.html

Thank you to everyone who made the previous year possible with your
participation and support.  DeLano Scientific met exactly 99.92% of its
internal fundraising goal for the year, and we are now starting to plan for
some growth.  This year, in addition to continuing our PyMOL development and
support activites, we're hoping to secure some SBIR grant funding as well
project-specific monies from pharmaceutical companies.  The future looks
bright!

What's new in PyMOL 0.95?

   - Presets (in the Action menu) provide common views very quickly.
   - Context-specific pop-up menus now direct actions to where you point.
   - Mouse wheel can now control clipping slab width and position.
   - Improved look-and-feel, including bigger controls and longer names.
   - Appearance wizard facilitates color and representation control.
   - Labels can now be ray traced & with new fonts
(label_font_id=0,1,2,3,4).
   - Two new surface types: dots (surface_type=1) & tri-mesh
(surface_type=2) added.
   - Better handling of alpha-channel for semi-transparent figures.
   - Cartoons and spheres can now be "picked" using the mouse.
   - Roving origin behavior has been improved.
   - New cross-platform build for OS X uses Tcl/Tk under X11 without Fink.
   - Molecular picking and editing is now more general.
   - Numerous features and tweaks have been added.
   - Various major and minor bugs have been fixed.

An official 0.95 release of the MacPyMOL Incentive Product for OS X is also
available for download. 

http://delsci.com/macpymol

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
 

[PyMOL] MacPyMOL and USB controllers

[James R. G. <jam...@ma...>]

hello all,

i am trying to use an external USB device (belkin's nostromo52) to map 
keystrokes for use in MacPyMOL. However, it seems that MacPyMOL v.0.95 
does not allow this while the "native" os x version 0.93 does.

any suggestions on how to get this to work would be greatly appreciated!

james

Re: [PyMOL] PyMOL 0.95 Released

[Cameron M. <cm...@uc...>]

Hi PyMOLers,

I just downloaded and tried-out the new v0.95 -- very nice! 
(particularly the label-handling)...
Now I'm wondering -- has anyone seen the following OpenGL errors with 
this new version:

> OpenGL-Error: Where? During Rendering: invalid operation

This occurs when literally *any* operation is performed in the PyMOL 
Viewer graphics window -- whether it's doing complicated mouse tricks or 
just typing a single character (one can type the identical text in the 
Tcl/Tk GUI window without any errors). I'm running on a Red Hat 9 Linux 
box, having installed PyMOL via pymol-0.95-1.rh90.py22.i386.rpm...

Thanks for any info.,
Cameron



=== Warren DeLano wrote (on 04/04/2004 12:57 PM): ===

>PyMOLers:
>
>Yesterday marked DeLano Scientific's one year anniversary as a full-time
>business.  In addition to popping the cork on a bottle of champagne, we
>celebrated with the release of version 0.95!
>
>http://pymol.sf.net
>http://pymol.sf.net/obtaining.html
>
>Thank you to everyone who made the previous year possible with your
>participation and support.  DeLano Scientific met exactly 99.92% of its
>internal fundraising goal for the year, and we are now starting to plan for
>some growth.  This year, in addition to continuing our PyMOL development and
>support activites, we're hoping to secure some SBIR grant funding as well
>project-specific monies from pharmaceutical companies.  The future looks
>bright!
>
>What's new in PyMOL 0.95?
>
>   - Presets (in the Action menu) provide common views very quickly.
>   - Context-specific pop-up menus now direct actions to where you point.
>   - Mouse wheel can now control clipping slab width and position.
>   - Improved look-and-feel, including bigger controls and longer names.
>   - Appearance wizard facilitates color and representation control.
>   - Labels can now be ray traced & with new fonts
>(label_font_id=0,1,2,3,4).
>   - Two new surface types: dots (surface_type=1) & tri-mesh
>(surface_type=2) added.
>   - Better handling of alpha-channel for semi-transparent figures.
>   - Cartoons and spheres can now be "picked" using the mouse.
>   - Roving origin behavior has been improved.
>   - New cross-platform build for OS X uses Tcl/Tk under X11 without Fink.
>   - Molecular picking and editing is now more general.
>   - Numerous features and tweaks have been added.
>   - Various major and minor bugs have been fixed.
>
>An official 0.95 release of the MacPyMOL Incentive Product for OS X is also
>available for download. 
>
>http://delsci.com/macpymol
>
>Cheers,
>Warren
>
>--
>mailto:wa...@de...
>Warren L. DeLano, Ph.D.
>Principal Scientist
>DeLano Scientific LLC
>Voice (650)-346-1154 
>Fax   (650)-593-4020
> 
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>  
>

-- 
Cameron Mura
UCSD

RE: [PyMOL] PyMOL 0.95 Released

[Warren D. <wa...@de...>]

Cameron,

	This is an indication that PyMOL is experiencing OpenGL errors.  For
people with this problem, please email me your graphics hardware and driver
information.  Clearly, there are some drivers which don't like the new
version...

In the meantime, to alleviate this issue, you can issue the following
command 

   feedback disable, main, errors

(and perhaps put it in your $HOME/.pymolrc file.)

Cheers,
Warren
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Cameron Mura
> Sent: Monday, April 05, 2004 12:13 PM
> To: pym...@li...
> Subject: Re: [PyMOL] PyMOL 0.95 Released
> 
> Hi PyMOLers,
> 
> I just downloaded and tried-out the new v0.95 -- very nice! 
> (particularly the label-handling)...
> Now I'm wondering -- has anyone seen the following OpenGL 
> errors with this new version:
> 
> 
> 	OpenGL-Error: Where? During Rendering: invalid operation
> 	
> 
> This occurs when literally *any* operation is performed in 
> the PyMOL Viewer graphics window -- whether it's doing 
> complicated mouse tricks or just typing a single character 
> (one can type the identical text in the Tcl/Tk GUI window 
> without any errors).  I'm running on a Red Hat 9 Linux box, 
> having installed PyMOL via pymol-0.95-1.rh90.py22.i386.rpm...
> 
> Thanks for any info.,
>    Cameron
> 
> 
> 
> === Warren DeLano wrote (on 04/04/2004 12:57 PM): ===
> 
> 
> 	PyMOLers:
> 	
> 	Yesterday marked DeLano Scientific's one year 
> anniversary as a full-time
> 	business.  In addition to popping the cork on a bottle 
> of champagne, we
> 	celebrated with the release of version 0.95!
> 	
> 	http://pymol.sf.net
> 	http://pymol.sf.net/obtaining.html
> 	
> 	Thank you to everyone who made the previous year 
> possible with your
> 	participation and support.  DeLano Scientific met 
> exactly 99.92% of its
> 	internal fundraising goal for the year, and we are now 
> starting to plan for
> 	some growth.  This year, in addition to continuing our 
> PyMOL development and
> 	support activites, we're hoping to secure some SBIR 
> grant funding as well
> 	project-specific monies from pharmaceutical companies.  
> The future looks
> 	bright!
> 	
> 	What's new in PyMOL 0.95?
> 	
> 	   - Presets (in the Action menu) provide common views 
> very quickly.
> 	   - Context-specific pop-up menus now direct actions 
> to where you point.
> 	   - Mouse wheel can now control clipping slab width 
> and position.
> 	   - Improved look-and-feel, including bigger controls 
> and longer names.
> 	   - Appearance wizard facilitates color and 
> representation control.
> 	   - Labels can now be ray traced & with new fonts
> 	(label_font_id=0,1,2,3,4).
> 	   - Two new surface types: dots (surface_type=1) & tri-mesh
> 	(surface_type=2) added.
> 	   - Better handling of alpha-channel for 
> semi-transparent figures.
> 	   - Cartoons and spheres can now be "picked" using the mouse.
> 	   - Roving origin behavior has been improved.
> 	   - New cross-platform build for OS X uses Tcl/Tk 
> under X11 without Fink.
> 	   - Molecular picking and editing is now more general.
> 	   - Numerous features and tweaks have been added.
> 	   - Various major and minor bugs have been fixed.
> 	
> 	An official 0.95 release of the MacPyMOL Incentive 
> Product for OS X is also
> 	available for download. 
> 	
> 	http://delsci.com/macpymol
> 	
> 	Cheers,
> 	Warren
> 	
> 	--
> 	mailto:wa...@de...
> 	Warren L. DeLano, Ph.D.
> 	Principal Scientist
> 	DeLano Scientific LLC
> 	Voice (650)-346-1154 
> 	Fax   (650)-593-4020
> 	 
> 	
> 	
> 	
> 	
> 	-------------------------------------------------------
> 	This SF.Net email is sponsored by: IBM Linux Tutorials
> 	Free Linux tutorial presented by Daniel Robbins, 
> President and CEO of
> 	GenToo technologies. Learn everything from fundamentals 
> to system
> 	
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> 	_______________________________________________
> 	PyMOL-users mailing list
> 	PyM...@li...
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> 	
> 	  
> 
> 
> --
> Cameron Mura
> UCSD
> 

[PyMOL] add hydrogens using different hybridization

[S. F. Y. <fra...@ya...>]

Hi,

I was wondering if there is a way to add hydrogens to
a selected atom based on different hybridization,
e.g., sp2, sp3, etc., in which way different number of
hydrogens will be added with the corresponding
geometry.  

Thanks,
Frank


__________________________________
Do you Yahoo!?
Yahoo! Small Business $15K Web Design Giveaway 
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RE: [PyMOL] add hydrogens using different hybridization

[Warren D. <wa...@de...>]

Frank,

PyMOL adds hydrogens based on the hybridization and formal charge of an
atom...if you're not getting the right number of hydrogen, then you probably
need to adjust either the valences of the bonds it participates in, or the
formal charge.

A) To adjust valences:

1) enable "show valences" from the Display menu
2) put the mouse into editing mode
3) ctrl-right-click to pick a bond

and then

4) Type Ctrl-W or select Cycle-Valence from the Build menu to cycle through
the possible valences/

B) To change the formal charge of an atom:

(first make sure no other atoms are picked -- click Unpick if necessary)
Ctrl-middle-click to pick the atom

Ctrl-K -> makes atom positive
Ctrl-J -> makes atom negative
Ctrl-U -> makes atom neutral

C) To replace hydrogens on any atom:

(first make sure no other atoms are picked -- click Unpick if necessary)
Ctrl-middle-click to pick the atom
Ctrl-R or select Fill Hydrogens from the build menu to rebuild hydrogens on
that atom.

"remove hydro" can be used to remove all atoms
h_add will put them back.

Note that PyMOL doesn't yet know how to properly name hydrogens on standard
protein & dna residues.  That will come in time.

Cheers,
Warren


> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> S. Frank Yan
> Sent: Wednesday, April 07, 2004 12:10 PM
> To: pym...@li...
> Subject: [PyMOL] add hydrogens using different hybridization
> 
> Hi,
> 
> I was wondering if there is a way to add hydrogens to a 
> selected atom based on different hybridization, e.g., sp2, 
> sp3, etc., in which way different number of hydrogens will be 
> added with the corresponding geometry.  
> 
> Thanks,
> Frank
> 
> 
> __________________________________
> Do you Yahoo!?
> Yahoo! Small Business $15K Web Design Giveaway 
> http://promotions.yahoo.com/design_giveaway/
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>