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pseudoatoms and bonds the
two pseudoatoms.
Cheers,
-- Jason
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rrors on VMD, however prefer Pymol for the ease of use and also the images
> are nice.
If you have Intel-based hardware you might try the following settings
upon startup:
set use_shaders, 0
set sphere_mode, 0
and then try your rendering plugin.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Direc
please be patient.
Cheers,
-- Jason
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, Rye Terrell wrote:
>
> Hi Jason,
>
> Thanks for the tip. I still couldn't get it to work. I'll google around some
> more, but here's the file. Thanks for any help.
>
> Cheers,
> Rye
>
>
> On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
> wrote:
&g
rge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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---
ata. We'll fix this
for the next release.
Cheers,
-- Jason
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Director of Core Modeling Product Management
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(e) jason.vertr...@schrodinger.com
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Keep yours
mware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
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-
w scripts the demonstrate their usage.
> In addition, is the pymol volume visualize (http://pymol.org/volume)
> available for educational use ?
Volume visualization is available in the Incentive version and
open-source builds, but not the free Educational version.
Cheers,
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i on the iPad browse to the www.pdb.org and find the
>> > structure you want.
>> > (2) Click "Download Files" from the upper right hand side of the
>> > structure's page and then select "PDB File (Text)".
>> > (3) Click "Open in PyMOL
el("caver1")
# print the list of coordinates for all atoms/pseudoatoms
# in the object/selection 'caver1'
print map(lambda a: a.coord, m.atom)
Cheers,
-- Jason
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Schröd
mer less than 2.0 Angstroms is:
dist smallHbonds, vis and organic, vis and polymer, mode=2, cutoff=2.0
Now the "smallHbonds" object will have only those h-bonds < 2.0 Angstroms.
Check out the PyMOLWiki (http://pymolwiki.org/index.php/Main_Page) for
more help.
Cheers,
-- Jason
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J
valuable resource in the community and I'm
glad we could work this out.
Cheers,
-- Jason
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windows8center.sourceforge.net/
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g
the PyMOL UI to make volumes easier to use.
Cheers,
-- Jason
> 26 okt 2012 kl. 06:15 skrev Jason Vertrees:
>
>> Hi Per,
>>
>>> I am wondering whether the open-source build of pymol for OS X (10.7) comes
>>> with the same volume-visualization capabilities as the
hesize maps from MTZ files.
Cheers,
-- Jason
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>
>
>
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> Make your we
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> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> _
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stops.
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Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New
Florian,
If you turn off stick_use_shader you will get slower and less pretty on
screen rendering. I suggest keeping that one enabled.
Cheers,
Jason
On Sunday, October 14, 2012, Florian Nachon wrote:
>
> On 14 oct. 2012, at 15:59, Jason Vertrees
> >
> wrote:
>
> > Fl
Florian,
This is a bug with OS X 10.8 and later. It also appears on some different
combinations of hardware. Anyhow, the fix is easy, and this will be
automatically fixed in our next release:
set cylinder_shader_ff_workaround, 1
Cheers,
Jason
Sent from my Android. Please excuse the concision a
the backbone atoms for tracing the cartoon?
>
> Thank you,
> Vitaly
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Don't let slo
t and returns SDF
output. Eg, if you symbolically linked a different binary to
'mengine.exe' PyMOL wouldn't be the wiser.
Cheers,
-- Jason
> On Fri, Oct 12, 2012 at 12:49 PM, Jason Vertrees
> wrote:
>>
>> Hi Osvaldo,
>>
>> > when I run t
ad time to look at this.
Please edit the file freemol/src/mengine/field.c, at line 7, and
change
charvdwtype[11]
to
charvdwtype[14]
Once you've done that, please remove all the .o files and rebuild
mengine. If this helped you, let me know and I can update freemol.
Cheer
e: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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g.
One last option is to divide the task into into N/M subtasks, where
N=num residues to mutate and M=num CPUs, and run that script from the
command line passing in residues ranges. This would require the least
amount of effort, maximize CPU usage, and be thread-safe as you'd be
running (N/M
at no cost today and get our sweet Data Nerd shirt too!
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-
to break anything?
Yes -- volumes won't render correctly and the high-performance and
-quality graphics won't be enabled. However, you should still have
basic rendering and functionality.
Cheers,
-- Jason
--
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PyMOL Product Manager
Schrödinger, Inc.
(e) jason.vertr...
ro hardware.
> Detected 24 CPU cores. Enabled multithreaded rendering.
The key seems to be,
> PyMOLShader_NewFromFile-Warning: default shader files not found, loading
> from memory.
We load shaders from disk, but when they're not found we just read in
some basic default sh
ays at 100 percent and no more menu's come up.
>> >> >>
>> >> >> The larger window says at the bottom that the version is supposed to
>> >> >> be licensed
>> >> >> but I just pulled it down from sourceforge and not sure that this
>>
urceforge.net/lists/listinfo/pymol-users
>> >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> >
>> > --
>> > Don't let slow site performance ruin your busin
ps://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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;y?
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est in malware
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olor \059message.
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t animate the change, remote ',animate=1' from the orient command.
Cheers,
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increases with the maturity
of the device. So, iPad3 will be better than iPad2 which will be
better than iPad1. Last, PyMOL was mainly designed for the iPad2 and
iPad3 -- for some reason Apple doesn't list this on the download page.
Cheers,
-- Jason
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eat time working at Schrödinger and know others do too.
Cheers,
-- Jason
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(e) jason.
e didn't make it available in version 1.0. If
something you want is missing, like this, please consider starting a
PyMOLWiki webpage detailing what you want.
Labels are important, so, I'm pretty sure it'll be in a future release.
Cheers,
-- Jason
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us at the Schrödinger booth #1501 in the expo.
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e
mset 1x60
# setup scene #1
scene 001, store
# do something different to setup scene #2
# store scene #2
scene 002, store
mview store, 1, scene=001
mview store, 60, scene=002
Now, the movie will not smoothly loop back to camera position 1.
Cheers,
-- Jason
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fo Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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uot;.
Cheers,
-- Jason
> On 23.07.12 18:19, Jason Vertrees wrote:
>> Hi Malai,
>>
>> Thanks for bringing this to our attention. The file you sent does have
>> a TER record (which separates chains) but it went ahead and
>> re-declared chain A. This confused PyMOL. You
; new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
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.
While not technically PyMOL's fault, we'll update the reader to handle
this more robustly in the future.
Cheers,
-- Jason
On Fri, Jul 20, 2012 at 5:44 PM, Jason Vertrees
wrote:
> Hi Malai,
>
> What structure? Can we see it? (Feel free to send it to me if you can share
test in malware
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; Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>
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ssions
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1, 2012 at 4:59 PM, Thomas Holder
> wrote:
>>
>> Or overload the cmd.load function:
>>
>> python
>> from pymol import cmd, preset
>> load_orig = cmd.load
>> def load_new(*args, **kwargs):
>> load_orig(*args, **kwargs)
>> preset.ligand
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chains". Click on the green colored word
"Selecting" in the lower right hand corner of PyMOL's visualization
window until it cycles to the method by which you'd like to select
(eg. atoms, residues, etc).
Cheers,
-- Jason
--
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PyMOL Product Ma
On Jul 5, 2012 3:38 PM, "H. Adam Steinberg" wrote:
>
> I just tried it again and it does indeed work. But over the last few weeks
> (on first attempts) it seems to return an error. Maybe it's just my satellite
> ISP...
>
> Thanks
>
> On Jul 5, 2012
t back "connection
> reset" in Firefox and "server dropped the connection" in Safari.
>
> I need the wiki! :)
>
>
> On Jun 12, 2012, at 8:42 AM, Jason Vertrees wrote:
>
>> Greetings,
>>
>> The PyMOLWiki recently went down due to a vulnerability
__
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y and the latest in malware
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ers offer powerful advances in
rendering as you have shown. Thanks for posting this -- great screen
shots. I hope others take some time to learn about shaders, too.
Cheers,
-- Jason
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PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603)
e Fab complex and optionally draw a representation of the
> vectors used to calculate it.
>
> It's under version control in the Pymol-scripts-repo, and any suggestions
> and/or fixes are welcome.
>
> Please note that elbow_angle requires transformations.py by Christoph Go
Greetings,
The PyMOLWiki is backup, safe and sound. The bug was not actually
related to the well-known MySQL vulnerability, but was due to an
update with php.
Cheers,
-- Jason
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PyMOL Product Manager
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374
n the meantime,
you should still be able to search and find what you need -- and dont'
forget you can always email this list.
Cheers,
-- Jason
--
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PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603
. In PyMOL, the underlying representations of molecules are
distances are completely different.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
---
rity and the latest in malware
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
y and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> PyMOL-us
and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
atest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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> Archives: htt
gt; Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Malai,
The PDB is corrupt. Please put an "ENDMDL" after your "TER" line.
Cheers,
-- Jason
On Fri, May 18, 2012 at 3:31 PM, Jason Vertrees
wrote:
> Hi Hendry,
>
> We're happy to help, but we need more information. Do you have a PDB
> which replicates this
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-arc
rs mailing list (PyMOL-users@lists.sourceforge.net)
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Jason Vertrees,
-
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and
> >> threat landscape has changed and how IT managers can respond.
> >> Discussions
> >> will include endpoint security, mobile securi
lusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
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