Hi David,
> Thank you very much. Have you tried to use it with a Mac ?
We have not tried it with a Mac. The only stereo I can currently get
on the Mac is Zalman.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (
;ve been able to push 3D from
the Quadro 570 and up. The new volumes look fantastic in 3D.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
load with multiplex=0.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
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A question and answer gu
; http://p.sf.net/sfu/internap-sfd2d
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-
on easier in PyMOL.
Cheers,
-- Jason
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--
Colocation vs. Managed Hosting
A question and answer guide to
determining the best fit
> for your organization - today and in the future.
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.org/library/curses.html) for this?
Cheers,
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A
> For example, .hkl file that is generated by CNS 1.3 and contains map
> coefficients/phases.
The code also supports CIF and CNS files, but those won't be fully
functional until a later update release.
> I'm very looking forward to PyMOL v1.4 release,
Awesome--so am I!
Cheers,
y MTZ reader on various MTZ files new and old. If you have an
MTZ file you'd like to share for testing, please email it directly to
me (jason.vertr...@schrodinger.com) and I'll be sure we run it through
our tests.
Cheers,
-- Jason
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PyMOL Product Manager
Schro
ll stay there during the animation...
>
> Could that be a bug in pymol? Or is there still something I'm missing?
>
> I hope the example code will help out.
>
> Thanks a lot!
>
> Nicolas
>
>
> On Mon, Mar 7, 2011 at 10:17 PM, Jason Vertrees
> wrote:
>>
age: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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-
s drawn for all later frames.
>
> Thus, how can I add an object only for a given state/frame? Should I delete
> the object at the next state/frame? What would be the command to delete a
> cgo object?
>
> Should I store what load_cgo() returns and issue a "delete" ov
effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
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e atom is clipped.
> The trick then is to turn m back into a selection.
>
> Hope it helps,
>
> Tsjerk
>
> On Feb 25, 2011 5:18 PM, "Johannes Wollbold" wrote:
>
> Jason Vertrees wrote: > Having said this, you can however, can get the
> clipping information
Hi all,
> That's cool enough to be it's own script. I'll add that to the
> PyMOLWiki if I find the time.
This is now a script on the PyMOLWiki
(http://www.pymolwiki.org/index.php/HighlightAlignedSS).
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
representation
as cartoon
# hide indicators
select none
That's cool enough to be it's own script. I'll add that to the
PyMOLWiki if I find the time.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, L
tried creating a pov file, and rendering with pov-ray, but
> pymol still crashed. What are my options for rendering out my scene, if
> any? Thank you.
Last, are you using 32-bit PyMOL or 64-bit PyMOL? I know your OS is
64-bit, but what about the PyMOL binary?
Cheers,
-- Jason
--
Jason V
physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
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uot;
mcache 50, "show surface, poly within 10 or org"
...
store scenes, plan movie, etc.
...
mCacheApply 50
I made something similar for making movie fades, just cache the string
an apply it when necessary.
Cheers,
-- Jason
--
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PyMOL Product Manager
Schrodinge
OL-users@lists.sourceforge.net)
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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/listinfo/pymol-users
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Index, S
;
>
> Best regards, Alex
>
> --
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security
Hi John,
> I'm running version Version 1.2r2.
This is probably why. I don't recall the exact version in which this
became doable, but it's now available in the latest version.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr.
nd parallel code that limit performance.
>>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>>> ___
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>>>>> Info Page: https://lists.sourcef
ng list (PyMOL-users@lists.sourceforge.net)
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P
errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
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fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
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> I
eb
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n 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
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cycle.
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--
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
>
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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--
The ultimate al
e. PyMOL places its plugins in modules/pmg_tk/startup/. Since
PyMOL does not read the script but once, upon initialization, any
changes you make will be recognized simply by restarting PyMOL, but
you don't need to reinstall.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Sc
mplementation.
Thanks for pointing this out. I like the representation. We'd have
to consider how best to utilize it from within PyMOL.
> Thanks for the great work developing PyMOL further.
I'm glad it's appreciated. Even though working on PyMOL can be
challenging, it is gre
to either use a different
stereo viewing mode (Zalman, anaglyph, etc) or acquire an NVidia
Quadro card. This is not our doing: we would love to see stereoscopic
3D supported more broadly.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.
.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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(o) +1 (603) 374-7120
---
n better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
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> Info Page: https://lists.s
1rx2_map
set grid_slot, 2, e_lvl_1_1
Now, you should be set and have an image like that I posted on the PyMOLWiki.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
talled.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally
/sfu/arcsight-sfd2d
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--
Ja
son
On Thu, Jan 27, 2011 at 7:59 PM, Jason Vertrees
wrote:
> Hi David,
>
> Can you please send me the PSE? If not, do you have multiple states?
> Are you using the save command or the GUI?
>
> Cheers,
>
> -- Jason
>
> On Thu, Jan 27, 2011 at 1:50 PM, David A. Hori
>> >> #print q_sel+":",
>> >> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>> >> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>> >> #print
>> >>
>> >> stored.qry_info[0],
ebruary 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
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e your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
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PyMOL Product Manag
0:47 AM
> Subject: all_states failure with 500 or more models
> To: Jason Vertrees
>
>
> Hi Jason,
>
> Another glitch with all_states it seems. When loading a pdb with 500
> frames or more, the OpenGL window starts displaying weird behaviour.
> It doesn't properly re
nd customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
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consumers' information secure
> and instills the confidence they need to proceed with transactions.
> http://p.sf.net/sfu/oracle-sfdevnl
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ions.
Very cool.
Cheers,
-- Jason
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Learn how Oracle Real Application Clusters (RAC) One Node allows
evnl
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me or disruption
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&g
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---
of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
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ctiveX:
* Consistent cross platform deployment would be my largest concern
Use whatever's best for your project. Hope this helps and good luck!
Cheers,
-- Jason
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PyMOL Product Manager
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(e)
e-d2d
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ect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
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-
12 2HG PRO A 1 52.313 -3.615 43.311 1.00 0.00 PROT
> H
> TER 13 PRO A 1
> ATOM 11 1HD PHE D 14 56.847 -4.922 34.497 1.00 0.00 PROT
> H
> TER 12 PHE D 14
> ATOM 13 1HD PRO A 1 54.110 -5.062 42.704 1.00 0.00
rsity
> School of Medicine
> 801-712-8799
>
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to those commonly used in the
data, "DA" "DT", etc.
Cheers,
-- Jason
On Fri, Dec 10, 2010 at 1:48 AM, Keitaro Yamashita
wrote:
> It's very useful.
> How about RNA/DNA sequence?
>
> Thanks in advance,
>
> Keitaro
>
> 2010/12/10 Jason Vertrees :
&g
DHDYVFDTFFK...
>
> Peptide:
>
> GKTQKV
Use the 'ps.' (peptide sequence) modifier:
select targetSeq, ps. GKTQKV
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jaso
ndividual objects into one??
> Hope for answer.
>
> kind regards
> Björn
>
>
> p.s. In this way:
> cmd.pseudoatom('grid', pos=[i,j,k], color='white')
> the calculation of 5670 gridpoints needs ca. 8hours
>
> Zitat von Jason Vertrees :
>
&g
the issue, we are working on a reasonable "end-of-life"
policy to balance the needs of our users with ease of software
maintenance. PyMOL's official end-of-life policy for builds will be
posted on our website (http://pymol.org/eol) soon.
Cheers,
-- Jason
--
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prizes are up for grabs.
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--
in for PyMOL, but this is quite
> expensive. Does anyone know of any cheaper option of how I can use PyMOL
> in a CAVE.
PyMOL can be used in the CAVE. Virtalis is the only resource that I
know of that offers this extension to PyMOL.
Cheers,
-- Jason
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2dev
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ck in with the load command
> just to be able to get access to the 'discrete' flag. That's where I thought
> I might be missing something if I explained the case further.
> Thanks,
> Seth
>
> On Tue, Nov 16, 2010 at 5:37 AM, Jason Vertrees
> wrote:
>>
>>
nformation.
In Seth's case, it looks like that difference was confusing PyMOL.
Cheers,
-- Jason
On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell
wrote:
> Hi Seth,
>
> On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
> wrote:
>
>> Hi Seth,
>>
>> I have
__
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PyMOL Prod
PyMOLers,
Work on bringing PyMOL's code up to a newer openGL standard has begun.
This will bring us access to new openGL features. We're taking a
poll of which openGL version your systems support.
To cast your vote please visit: http://pymol.org/poll
Cheers,
-- Jason
--
Jason Ver
ogy
> Purdue University
> 240 S. Martin Jischke Drive
> West Lafayette, IN 47907
>
>
>
> Quoting Jason Vertrees :
>
>> Hi Saif,
>>
>> Can you please show us the commands you used in PyMOL to load the data
>> and generate the map? (Also, can you send me a
ime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
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, Web Runtime, or Java and Publish to Ovi Store
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> The Netherlands
>
> --
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> $10 million total in pr
s
> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
> Spend less time writing and rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
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> _
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t; --
> Download new Adobe(R) Flash(R) Builder(TM) 4
> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
> Flex(R) Builder(TM)) enable the development of rich applications that run
> across multiple browser
tiple browsers and platforms. Download your free trials today!
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Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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eweb
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time creating great
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Jason Vertrees, PhD
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Schrodinger, LLC
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ng great
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Sch
horizon, will this address Radeon
> performance or should I go back to my old MacPro with it's nVidia 7300 video
> cards?
We wanted to release a 64-bit version for a while, but the Tcl/Tk
toolkit was not ready. I think it's still in alpha/beta. 64-bit
MacPyMOL will be released when
fy application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
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t;> 426d
>> nan
>> 1acb_2_again
>> nan
>>
>>
>> -David
>
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> Thomas Holder
> Group of Steffen Schmidt
> Department of Biochemistry
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
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