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y application deployment and
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hanks in advance.
>
> Regards
>
> Renuka
>
>
>
> --
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate you
ge.net/lists/listinfo/pymol-users
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lection, e.g. the site picked to mutate?
>
> Thanks for any advise on this.
>
> Martin
>
>
>
>
>
>
>
>
>
>
> Am 20.09.10 16:59, schrieb Jason Vertrees:
>>
>> Hi Martin,
>>
>>> atoms within less than VdW distance. Is there a
now I did
> :-) ).
>
> fetch 2kqt
> pseudoatom pseudo, pos=[0,0,-12]
> show spheres, pseudo
> zoom pseudo
> set sphere_quality, 2, pseudo
>
> Vitaly
>
> - Original Message -
> From: Vitaly Vostrikov
> Date: Sunday, September 19, 2010 1:16 am
> Subje
favourable, i.e.
> atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
> way of fixing this? Can the sculpting wizard be used for this?
>
> Thanks a lot for any suggestions.
>
> Martin
>
>
>
>
>
>
>
> Am 19.09.10 19:00, schrieb Jason
is great. Thanks a lot.
> I am wondering, are there any scripts/ plugins for PyMOL out there that
> facilitate the generation of a large amount of rotamers for different
> mutants? I might take the effort and start building this into a plugin.
>
> Martin
>
>
>
>
>
>
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gt;>
>>> pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
>>> from pymol import stored
>>> from pymol import cmd
>>> stored.r = ''
>>>
>>> # What are we doing h
PyMOL), choose to
support PyMOL yourself, or register to access the educational version
of PyMOL.
Good luck to all in your coursework, research, and teaching.
Cheers,
-- Jason
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uld help me a lot.
>
> As I said, all I want is a PDB file for every rotamer itself. If there is a
> simpler way to achieve this, that is fine with me. The number of rotamers is
> only important to me, since I need to know how many times i should issue
> 'cmd.forward()' an
useful for many.
The PyMOLWik page is http://www.pymolwiki.org/index.php/AngleBetweenHelices.
Great job, Thomas.
Cheers,
-- Jason
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> kind of hash by just adding a matching list, and zipping.
>
> Then to extract a sequence, I tend to go for a construction like:
>
> sequence = [ aa321[i.resn] for i in cmd.get_model(selection + " and n.
> ca").atom ]
>
> Cheers,
>
> Tsjerk
>
> On Mon
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ere no braces or quotation marks needed? Its not
> perfectly clear to me if 'first' and 'my_res' are selections (indicated by
> braces) or objects (name without braces in the main window).
> I understand 'resn' is something like 'GLU', if I want to kno
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Start uncovering the many advantages
, Michael can be
reached at michaelgler...@gmail.com.
Fellows are listed on our website (http://pymol.org/fellowship).
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-- Jason
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computer. If you are a current
AxPyMOL subscriber, you do not need AxPyMOL Reader, as the full
version of AxPyMOL includes Reader capabilities.
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-- Jason
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a cinch to
cite PyMOL. If you spot errors or can improve upon what's there,
please feel free to comment.
Cheers,
-- Jason
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>
and how does it differ from the full
> version?
>
> Thanks.
>
> On 8/19/2010 3:30 PM, Jason Vertrees wrote:
>
> Greetings,
>
> I'd like to pass on a few notes to let you know some of what's going
> on in the world of PyMOL.
>
> First, the PyMOL website has
I will fix this.
Cheers,
-- Jason
>
>> Second,
>
> Yes...?
>
>
> Well, keep up the good work (and make it yet that bit better)!
>
> Cheers,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular
enge
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s and also for that podium computer where we all present
from. I'll announce this when it's ready.
Cheers,
-- Jason
On Thu, Aug 19, 2010 at 3:30 PM, Jason Vertrees
wrote:
> Greetings,
>
> I'd like to pass on a few notes to let you know some of what's going
&
#x27;t look too stodgy corporate-like.
Anyhow, it's up and I like it alot, actually.
Second,
--
Jason Vertrees, PhD
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d by
>
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gt;>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Aug 16, 2010 at 6:49 AM, s dat wrote:
>> > Hi Jason
>> >
>> > Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP
>> > Professional 2002 SP3.
>> >
>> > Thanks f
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hardcodes only being able to get pdb1 right now.
>
> -David
>
> On Thu, Aug 5, 2010 at 5:47 PM, Jason Vertrees
> wrote:
>> Greetings,
>>
>> Fetch has been fixed and the code checked into SVN with some other
>> changes. I'm calling this v1.3r1 b
oblems.
Cheers,
-- Jason
On Wed, Aug 4, 2010 at 12:33 AM, Jason Vertrees
wrote:
> Hi Daphna,
>
> The PDB servers underwent some reorganization and moved the files on
> us! I will post a fix for this by tomorrow night.
>
> Thanks!
>
> -- Jason
>
> On Sun, Aug 1, 2010
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Bradley Hintze
wrote:
> I'm writing a manuscript and just need clarification.
>
> Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
> use pymol's DSS to assign secondary structure? If not, how is this
> command assigning secondary struc
icular object??)
> I tried looking at CGO but all I can find on the wiki is how to draw
> text and circles. Is there a page I'm not seeing that explaining
> cmd.load_cgo in detail??
>
> On Thu, Jul 22, 2010 at 12:22 PM, Jason Vertrees
> wrote:
>> Bradley,
>>
>&g
?
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for proteins only right?
>
> How does it work for methane? How does it recognize that is lacks 4 atoms?
> If you can point me to the file where that part is described, that would be
> amazing! I've lost two weeks trying to figure it out already and I can't...
>
>
, and then
h_adding them back. Remove/add them a few times to the lone carbon to
see the effect of the randomized placement.)
Cheers,
-- Jason
On Thu, Jul 1, 2010 at 10:40 AM, Jason Vertrees
wrote:
> João,
>
> Thanks for being patient on this. I just moved to a big city and am
> s
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hon version 2.5 and 2.6 , both of
>> them dont do the right thing i.e allow the property to be set only for
>> the object and instead propagate the property to all objects.
>>
>> I must admit that both of ubuntu builds were compiled by me , but
>> everything is working just f
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8 ip 7f00abd88626 sp 7f009444be30
>> error 4 in libX11.so.6.3.0[7f00abd36000+134000]
>>
>> Cheers,
>>
>> Edward
>>
>
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en a humbling experience to step into the shoes of
my mentor and get a glimpse of what he had been shouldering for the
past decade. He was a genius who worked and gave incessantly. While
it was easier for us when Warren was here, we still need to learn and
move forward.
PyMOL v1.3 is us, movi
the
> lucky parental unit. See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
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Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel: +49 (0)40 42838-3626 (-3484)
> mail: krug...@chemie.uni-hamburg.de
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
>
--
Jason Vertrees, PhD
PyMOL Product Manager
ther programs stopped
> working etc. Now everything is ok. The pymol version that I have has come
> with ubuntu package, it's Version 1.1r2pre. Works fine.
>
> Maia
>
>
>
> Jason Vertrees wrote:
>>
>> Maia and Robin,
>>
>> What version of Windows an
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-
>
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,
-- Jason
On Fri, May 28, 2010 at 11:37 AM, Jason Vertrees
wrote:
> Hi Bernhard,
>
> After re-reading Timothy's original email, this very much sounds like
> a driver issue. Timothy reports proper functionality using the same
> laptop, but in Windows. Regardless, here&
get an
ATI card to more testing.
"""
I cannot be more helpful at this time because my Linux boxes only run
NVidia cards. I will either find a machine or go buy an ATI card for
my Linux box and let you know the results.
Cheers,
>
>
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(e.g. using
> MODELLER).
You can load FASTA files into PyMOL. Good luck understanding the
results though. For example:
# fetch a protein and save its sequence
fetch 1cll, async=0
save 1cll.fasta, 1cll
# delete everything & load the FASTA file
dele *
load 1cll.fasta
Cheers,
-- Jason
--
y
>
>
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>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodin
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--
Jason Vertrees, Ph
tended only for the use of the individual(s) or
>> > entity named on the e-mail. If the reader of this e-mail is not the
>> > intended
>> > recipient, or the employee or agent responsible for delivering it to the
>> > intended recipient, you are hereby notified that reading it is strictly
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