Re: [PyMOL] problems cloring sticks

2011-06-05 Thread David A. Horita
Ariel, 
I would just add to Andreas' reply that in my case (onboard intel GMA-HD, Suse 
linux, core i3) either using ray (and if you have a lot of memory, set 
setting-rendering-memory- use most) or saving the pse and making images on a 
windows PC (or a linux PC with an nvidia graphics card) are the workarounds I 
use.  Not a solution per se, but this seems to be an issue between OpenGL and 
Intel (although I've only seen problems with Pymol, and not vmd).

-David

David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston Salem, NC 27157, USA


From: Andreas Spitzmüller [andreas.spitzmuel...@staff.uni-marburg.de]
Sent: Sunday, June 05, 2011 11:09 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] problems cloring sticks

Hi Ariel,
I'm facing the same problem on my Ubuntu laptop with an onboard Intel
graphics chip. And as far as I know it is a problem of the linux graphics
driver.

 From my side this is a huge problem for making figures.

However, I found that ray tracing is not affected by this bug. I know that
this is for sure not convenient, but still it is possible to make figures
for publication or presentation slides. Just try the 'ray' command to see
if this yields correct coloring for you, too.

Regards,
Andreas


Am 05.06.2011, 08:29 Uhr, schrieb Ariel Talavera talav...@cim.sld.cu:

 Hi Jason,

 After some struggle, I finally compiled the last open source version,
 Pymol 1.4.1. Unfortunately, the same problem persist. I still not able
 to properly colored residues shown as sticks.

 From my side this is a huge problem for making figures.

 Best regards,
 Ariel


 On Wed, 2011-06-01 at 12:35 -0500, Jason Vertrees wrote:
 Hi Ariel,

 This is a known problem on some machines with ATI or Intel video
 cards.  You can try upgrading to a newer version of PyMOL.  Also,
 please check that your video driver is the newest for your video card.
  If I find a solution on our side that fixes this, I'll update the
 open-source.

 Cheers,

 -- Jason

 On Wed, Jun 1, 2011 at 12:04 PM, Ariel Talavera talav...@cim.sld.cu
 wrote:
  Hi Pymolers,
 
  I am having problems coloring residues when they are shown as stick.
 The
  coloring is properly working for the other representations like,
 lines,
  surface or spheres. I am using Pymol 1.2r2 under Ubuntu 11,04.
 
  Thanks in advanced,
  best regrads,
  Ariel
 
 
 
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[PyMOL] can't save pdb from within pymol

2011-01-27 Thread David A. Horita
Hi,
I've apparently managed to create a pse of a protein that loads fine but won't 
save the pdb coordinates (I get a file with END in it, and nothing else).
Any ideas how to get the coordinates out?

pymol 1.1b3 linux, windows (same pse has same result under both OS's)

Thanks,
Dave

-
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email:  dhor...@wfubmc.edumailto:dhor...@wfubmc.edu
web:  
http://www1.wfubmc.edu/biochem/faculty/Horita.htmhttp://www1.wfubmc.edu/biochem/faculty/Horita.htm/

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[PyMOL] cd in windows

2010-09-20 Thread David A. Horita
Hi,
How does one change directories in Windows when the directory name has a
space in it?  I've tried double and single quotes as well as backslash
space (I'd like to run a script that's in such a directory).
Thanks
David
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 
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Re: [PyMOL] cd in windows

2010-09-20 Thread David A. Horita
Thanks for the replies/suggestions.  Looks like I may need to upgrade from 
v1.1, but:

cd \program files, \program files, and \program?files give a variant of

PyMOLcd \program files
Traceback (most recent call last):
  File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\externing.py, 
line 46, in cd
os.chdir(dir)  # raises on error
OSError: [Errno 22] Invalid argument: '\\program files'


cd \progra~1 does work, however.
Pymol 1.1r1 running on Vista (32-bit) Business.

-David

-Original Message-
From: Edward A. Berry [mailto:ber...@upstate.edu]
Sent: Mon 9/20/2010 2:03 PM
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] cd in windows
 
David A. Horita wrote:
 Hi,
 How does one change directories in Windows when the directory name has a
 space in it? I've tried double and single quotes as well as backslash
 space (I'd like to run a script that's in such a directory).
 Thanks
 David

These all work for me:
 cd \program files

 cd \program files

 cd \program?files

 dir/x \prog*
06/05/2010  10:02p  DIR  PROGRA~1
 cd \progra~1

Or run in your data directory using full path of the executable:
 \program files\seamonkey\seamonkey.exe

(seamonkey is artemia the brine shrimp, you understand.
Diminutive alternative to thunderbird and firefox)

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Re: [PyMOL] Feature Request/Ideas

2010-01-21 Thread David A. Horita
Hi,
I would definitely not like to see a default representation to be any
more than lines (as it is now).  Opening one of my 100,000 atom MD
trajectory frames would take far longer than it's worth.

Regarding png output, I think this is in there already (but don't
remember) - I'd like to be able to specify one dimension (usually width)
and have the other automatically calculated.  If I'm trying to frame a
molecule and adjust the size of the screen window I'll want output to
keep the same aspect ratio.

Also, I see a major slowdown when running remotely as compared to VMD,
especially with regards to using the menus (top and right).  I get an
unable to create direct context rendering message, and while I don't
expect it to perform as well as when running locally, I get very
adequate performance running VMD over the same connection.  This is
useful when checking of MD or NMR calculations on a remote cluster from
my lab machines.  The slowdown (especially the view descriptor menu on
the right side) is apparent even over a gigE lan.

I'll add another voice for a better undo function.  In my specific case
I can think of a number of times where I've highlighted a collection of
residues as spheres and then accidentally added spheres to the whole
molecule instead of the next selection.  Being able to get back from
that (even one step) would be a time-saver.

Dave

- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-Original Message-
From: David Hall [mailto:dwash59_2...@yahoo.com] 
Sent: Thursday, January 21, 2010 9:20 AM
To: Jason Vertrees; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] PyMOL on the Mac

Alright, here's a feature request that might convince people who still
don't believe, despite your first commit to pymol trunk post-acquisition
including Fixed a GL build bug on OSX (see
http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 )

A Pymol Quicklook plugin.  My primary purpose would be for pses, but you
might as well pick up pdbs and other formats supported by pymol along
the way.
For pdb files, I wouldn't want the default pymol view of lines colored
by atom with green carbons being what I quicklook to, so either reading
.pymolrc to get a default view or some variant ( .pymolqlrc ?) would be
nice to allow users to customize their views.  Also, maybe default to a
cartoon representation colored by chains with het atoms as sticks and
metals as spheres, but that's probably just forcing the view I want on
others when I could just stick that in my personal .pymolqlrc type file.

Hopefully I'm out of ideas nows,
David




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Re: [PyMOL] How to plot residu with a number 9999

2009-06-09 Thread David A. Horita
Stephane, 

What I've done in these situations is broken the many-residue blocks
(typically water) into different chainID's and segid's.  Then select
with by both residue number and segid (or chainID or both).  That said,
I don't think segid's are a part of the official pdb specification
anymore (although pymol doesn't have a problem with them). 

As for getting around the 5-digit limit in overall atoms, I think
different packages have different tricks, including * (not
particularly useful) and hexadecimal (vmd/namd).  

Overall, this points out a glaring problem with fixed-width fields, but
that's another discussion...

Regards,
David

- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-Original Message-
From: Warren DeLano [mailto:war...@delsci.com] 
Sent: Monday, June 08, 2009 8:01 PM
To: Stephane Abel; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to plot residu with a number  

Stephane,

As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB
residue identifier field is only four characters wide.  

So how could you possibly have a PDB file with residue identifiers
larger than ?  

Cheers,
Warren

 -Original Message-
 From: Stephane Abel [mailto:stephane.a...@cea.fr]
 Sent: Monday, June 08, 2009 7:30 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] How to plot residu with a number  
 
 Hi pymol users
 
 
 It seems that the command select, residue xxx to plot residue xxx
where
 xxx is greater than  does not work in pymol version 0.99rc6
 
 
 Indeed for a pdb file with ~ 13800 residue, if i use the command:
 
 
 select water1846, residue 1846 - the water molecule with the residue 
 number 1846 is plotting
 
 
 But when i use the same command (say select water11100, residue 11100)
 
 
 for plotting the residue 11100 the previous command does not work
 
 
 How to tackle this problem. Thanks in advance for your help
 
 
 Stephane
 
 


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[PyMOL] hydrogen naming

2008-08-21 Thread David A. Horita
Hi,
How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add
(instead of H01, H02, ...)?  
 
Worst case I can build them in Xplor/CNS; second worst would be if there
is a uniform rule per residue that I could write a script to convert on
a residue type basis.
 
Thanks,
Dave
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 


[PyMOL] pymol nstall problems

2008-02-13 Thread David A. Horita
Hi,
I've been unable to install Pymol recently on an XP Pro-SP2 system.
I'll start setup.exe, and ntvdm.exe starts running but nothing
progresses from there (no error messages and installshield doesn't
start).  I'm not sure if it's a software conflict with something else
running, but it's likely (and the PC is managed/regulated by the IS
department, so I have limited ability to muck around with it, and they
like to push patches in the middle of the night).  At one time I
successfully installed 0.99rc6, but now that install also fails, so
something has changed.
 
I've seen other posts where people have had problems with the 5.10.130.0
version of installshield on xp; I've cleaned out my temp directory, and
tried running setup in various compatibility modes and with its own
memory space, and in safe mode.
 
Has anyone else seen/fixed this problem?
Thanks,
Dave
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 


[PyMOL] low-end graphics cards/laptops

2007-06-14 Thread David A. Horita
Hi,
While I've seen a number of examples of good graphics cards to use with
Pymol, I'd like some feedback on what an acceptable low-end is for a
Windows laptop computer.  Specifically, is the Intel GMA950 completely
useless or just not very good.  Likewise, does the X3100 help (this
seems to be weak on driver support)?  
 
My current system uses an ATI Mobility Radeon 9200, which is a few years
old and not a high-end gaming/workstation card, but lets me spin a
molecular cartoon or surface of a ~300 residue protein without any
problems (if the 950 or X3100 equal this level, I'll be satisfied).
Many of the current crop of 5 lb notebooks use integrated graphics for
price and battery life.  If these units don't provide sufficient
graphics power for Pymol/VMD/Deepview, the useful market shrinks
substantially.
 
Thanks,
David
 
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 


RE: [PyMOL] GUI

2006-01-20 Thread David A. Horita
Hi-
I'd second this; my brain doesn't do well keeping track of whether I'm,
for example, in maximum or reasonable performance mode. 
David

- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Mark A
Saper
Sent: Friday, January 20, 2006 3:01 PM
To: Pymol
Subject: [PyMOL] GUI

Hi Warren,

Why can't we have little check marks in the main menu that indicate the
current setting?
For example, SettingRenderingAntialias   gets a check, but  
selecting SettingRenderingShadowsNone doesn't give a check (as do any
of the other rendering options).

Mark
_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry Biophysics Research
Division, University of Michigan Chemistry Building Room 3040 930 N
University Ave Ann Arbor MI 48109-1055 U.S.A.

sa...@umich.edu(734) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html




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[PyMOL] Ray, png

2006-01-03 Thread David A. Horita
Hi,
On the subject of larger image sizes, I had a question a while back; I'd
like to know if it's been addressed or anyone has a quick(er)
workaround-
Basically, is there in inverse to the viewport command?  i.e., if I
manually resize the Pymol window to fit around the molecule I'm
displaying, how can I get the relative dimensions of the new window?
These dimensions are needed for the Ray command to keep proper
perspective.  What I've done in the past is save a small image of what's
displayed in the window, used a graphics program to determine the x  y
dimensions, and then used these to generate a high-resolution ray traced
image with the same x/y ratio.
I figure I'm missing something.
 
Regards,
 
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 


RE: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver

2005-03-29 Thread David A. Horita
Hi,
I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open
under the 71.84 drivers, but not the 70.78 drivers.  (Quadro 1300,
XP-Pro servicepack 2)
David Horita

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Stone
Sent: Monday, March 28, 2005 10:10 AM
To: Sabuj Pattanayek
Cc: pymol-users@lists.sourceforge.net; vm...@ks.uiuc.edu
Subject: Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167]
nvidia driver


Hi,
  Have you reported the crashes to NVidia?  I'd suggest sending an email
to their linux-b...@nvidia.com mail address.  The fact that multiple
packages crash with the new driver indicates that they may have a new
bug in their drivers.  You mentioned that making a licorice rep crashes
your VMD on that driver, what about VDW or bonds?  Do they have a
similar effect?

  John Stone
  v...@ks.uiuc.edu

On Sat, Mar 26, 2005 at 04:42:42PM -0600, Sabuj Pattanayek wrote:
 Yeah I have the same problem in the beta pymol, haven't tried the 
 stable
 version:
 
 OpenGL-based graphics engine:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW!
   GL_VERSION: 1.5.3 NVIDIA 71.67
  Hardware stereo capability detected.
  Adapting to Quadro hardware...
  Detected 2 CPUs.  Enabled multithreaded rendering.
 /usr/bin/pymol: line 14:  8852 Segmentation fault 
 $PYMOL_PATH/pymol.exe $*
 
 and 7167 won't compile on 2.6.10-11? kernels either, need 2.6.12-rc1, 
 haven't tested others. I get similar crashes in VMD 1.8.2+ using 7167 
 also. For instance, if you load a pdb and try to make a licorice
 representation, vmd just closes/crashes.
 
 I also think this maybe a Quadro problem and not a a problem with 
 GeForce cards. I have a GeForce 5500 FX on another machine and it 
 doesn't have these programs, and realtime GLSL rendering works very 
 nicely in vmd 1.8.3.
 
 Sorry for posting this on both mailing lists, just trying to avoid 
 reposting.
 
 ..Sabuj Pattanayek
 
 HuiZhe Li wrote:
 just upgraded nvidia driver from 6629 to 7167 (Linux, RHEL 4) and 
 pymol crashes when a molecule is load. is there a fix? (pymol worked 
 fine with 6629 driver).
 
  OpenGL-based graphics engine:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: Quadro FX 1400/PCI/SSE2
   GL_VERSION: 1.5.3 NVIDIA 71.67
  Adapting to Quadro hardware...
 /usr/local/bin/pymol: line 14:  4575 Segmentation
 fault  (core dumped) $PYMOL_PATH/pymol.exe $*
 
 
 
  
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Email: jo...@ks.uiuc.edu Phone: 217-244-3349

  WWW: http://www.ks.uiuc.edu/~johns/  Fax: 217-244-6078


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[PyMOL] rotating molecules

2004-10-27 Thread David A. Horita
Hi,
Let's say I load 4 molecules, A, B, C,  D.  A and B are a heterodimer
pair, as are C and D.  I'd like to move/rotate A and B together,
maintaining their respective orientations, while holding C and D fixed
(e.g., manually overlaying dimer structures).  
 
How do I do this?  I might have hit on the appropriate combination of
protecting/freezing/creating objects/etc. once, but can't seem to repeat
the routine.  
 
Thanks for any tips,
David Horita
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 


RE: [PyMOL] ray command

2004-04-05 Thread David A. Horita
Hi,
Regarding the use of the ray command, is there a way to automatically set 
either the x or y value to maintain the same aspect ratio as displayed in the 
window?  For that matter, how do you determine the number of x and y points 
displayed (other than making a bitmap and loading that into another program)?

-David Horita
 
 
 Mohammed,
 
   ray width, height
   png filename.png
 
 for example, for a 5x4 figure at 300 dpi:
 
   ray 1600,1200
   
   png hires.png
  (or use Save image... from the File menu after the ray command)
 
 Cheers,
 Warren

 



FW: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread David A. Horita
Warren,
Personally, I'd much rather have wild-card selections in atom names and have to 
deal individually with the ill-conceived PDB files than the other way around.
Regards,
David Horita

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net 
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano
Sent: Wednesday, February 18, 2004 10:56 AM
To: 'John Berrisford'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] selecting multiple atoms ie oxygen


John,
 
   color red, 5paa and elem o

The problem with using asterices as wildcards in atom names is that some 
ill-conceived PDB files actually use them in atom names. 

However, PyMOL does support the use of a terminal wildcard in some cases, such 
as with the delete command...

create obj01, none
create obj02, none
delete obj*

And with residue names

color red, as*
color blue, gl*
color pink, hi*

Cheers,
Warren


 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 John Berrisford
 Sent: Wednesday, February 18, 2004 3:42 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] selecting multiple atoms ie oxygen
 
 I wish to select multiple oxygens (labelled O1, O2 etc..
 within my pdb file) and colour them red for example. Is there 
 any easy way of doing this other than typing out a list of 
 all the oxygens I wish to select?
 
 eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p))
 
 I know in molscript its posible to use a o* label to select
 all oxygens, is such a switch possible in pymol. It doesn't 
 work, or I am using the wrong syntax if its possible.
 
 Any thoughts would be appreciated.
 
 John
 
 
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[PyMOL] unsetting cartoon_colors

2003-12-18 Thread David A. Horita
Hi all,
I have a collection of molecules and want to color a particular helix (in 
cartoon mode) a specific color different from other helices.  Unfortunately, I 
had previously set cartoon_color from default to another color, so now 
specifying a color for that helix (or even color red, ss h) has no impact.  
(it does change the color of the Calpha, but not the cartoon itself).  
So, the question is, how do I unset the cartoon_color variable (without wiping 
out my scene)?  The variable setting comes with the .pse file, set 
cartoon_color, default gives an error about not knowing what color default is.
Thanks,
Dave Horita
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 


[PyMOL] cartoons through nonstandard residues

2003-08-05 Thread David A. Horita
Hi,
When I try to draw a cartoon through the backbone of a nonstandard residue (in 
this case, phosphotyrosine), the cartoon strand stops prior to the PTR and 
starts after.  How do I get a continuous strand through the phosphotyrosine 
backbone (or other residues, in the general case)?  Ribbons seem to go through 
the PTR without problem, and selenomets don't seem to cause trouble, either.
Thanks,
David Horita
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 


[PyMOL] Nuvision stereo glasses?

2003-07-17 Thread David A. Horita
Hi,
Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or QuadroFX 500 
cards under linux?  Or any other non-nVidia card which supports quad-buffered 
stereo but doesn't have a mini-din connector on-board (i.e., not the 256 Mb 
FireGL X1).  It would be nice to avoid the problems with the nVidia stereo 
drivers, but I'd rather not buy the FX1000+/FireGL X1 level card, and FireGL2/4 
are getting old (and hard to find).  The Nuvision guys told me that their VGA 
passthrough (the -100 model, not the -NSR model), picks up the stereo sync from 
nVidia cards coming through the 15-pin VGA connector.  Is this signal present 
on ATI cards (or even on dual-DVI-I output cards)?
 
Thanks,
Dave Horita
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
 


[PyMOL] pkfrag

2003-05-08 Thread David A. Horita
Hi,
Is there a way to explicitly control which atoms end up in pkfrag1 and pkfrag2? 
 Specifically, I'd like to be able to move/rotate fragments which are made of 
multiple molecules or are internal loops.  Using pkbond or pkatom to break 
between fragments doesn't give me enough control.  Selecting and protecting 
atoms doesn't seem to help, in this case.
 
Thanks,
Dave Horita
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www.wfubmc.edu/biochem/faculty/Horita/