The 3D stuff (Zalman, etc) is only if you're using 3D glasses. I typically
use the Tk + console option that opens two windows (the GUI and a
pythonesque console).
Jed
On Apr 21, 2017 2:16 PM, "AJ Vincelli" wrote:
> Hello all,
>
> I hate to ask a dumb question, but I need some seriously novice h
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Vincent,
You could use data2bfactor.py and then "spectrum b" to color residues in
cartoon settings.
https://pymolwiki.org/index.php/Color
(data2bfactor from Robert Campbell's script repository:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Jed
On 1/4/2017 11:05 AM, vincent Chaptal wrote
Vaheh,
You can modify the b-factor column, and color by b-factor. I have used
various value-to-bfactor scripts, with different measures of alignment
similarity.
The one problem I've had is extending the Ca color to the rest of the
residue in stick mode.
Jed
On Oct 28, 2015 3:34 PM, "Oganesyan, Vah
>>>> Hi Jason,
>>>>>>
>>>>>> Now what will come first? Pymol viewer for Android, for Mobile Windows
>>>>>> or for iPhone? Would be so cool to show off at a conference, and use
>>>>>> multi-tou
You could extract the flexible residues into one multistate object and use
show all_states. So, you'd only be dealing with 2 objects - Ca and residues.
Jed
On Sep 21, 2014 3:23 AM, "James Starlight" wrote:
> Dear Pymol users!
>
>
> In this topic I've decide to put all questions regarding visuali
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Jed Goldstone, PhD
Research Specialist
W
ombined_models", x, 1, -1)
python end
Cheers,
-- Jason
On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone <mailto:jgoldst...@whoi.edu>> wrote:
I know this seems silly, but I can't figure out how to combine
multiple
separate objects into one multistate object. I have a se
s like
it should do this, but all the objects end up in the first state (and
the cartoon representation is a subset of what it should be (other
representations are fine).
I'm using incentive v1.6.0.0 on Windows 7.
Jed
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Research Specialist
W
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Jed Goldstone, PhD
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Woods Hole Ocean
t;C:\Program
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py", line 638, in
loadFileContent
handler = open(file)
: [Errno 2] No such file or directory:
'C:/Users/Jed/modeling/caver/caver_output/2/warnings.txt'
--
Jed Goldstone, PhD
Research
ral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
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>
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> Master SQL Server Development, Adminis
James-
I think you need to seriously consider using software that's actually
designed to compute and refine protein models, such as Modeller. There
are forcefield and structural constraints that PyMol is just not
designed to do, and your results may not have the scientific validity
you require
age: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/
You might want to try using Modeller instead.
http://www.salilab.org/modeller/wiki/Mutate%20model
It does higher level modelling.
Jed
Martin Hediger wrote:
> Dear List
> I'm trying to automate the following sequence of steps in a PyMOL python
> script:
> 1. Start the mutagenesis wizard
> 2. Muta
gt;> I have pymol 1.3 (windows7 64bit)
>>
>> and I got:
>>
>> ImportError: Bad magic number in C:\Program Files
>> (x86)\PyMOL\PyMOL/modules\pmg_tk\startup\CASTpyMOL_v2.pyc
>> Error: unable to initialize plugin 'CASTpyMOL_v2'.
>>
>>
etely unfamiliar with this, and do not know how to implement it
(my desktop runs PyMol 1.2r1 on Windows XP). Would this be an
appropriate solution? Would it work to call remote plugins?
Jed
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Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
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> Ar
e of pymol.
Apologies to the list,
Jed
Robert Campbell wrote:
> Hi Jed,
>
> On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone wrote:
>
>
>> Of course, you could just use the .pdb file as a text file:
>>
>> grep CA .pdb | cut -f 2,4,7,8,9
>>
>> will
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>> Try the new software tools for yourself. Speed compiling, find bugs
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>> See why Inte
all__
return apply(self.func, args)
File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", line
1800, in select_flexible_residues
receptor_object = self.receptor_dic[rec]
: ''
Jed
--
Jed Gold
: No module named Numeric
Error: unable to initialize plugin 'autodock'.
Any help would be greatly appreciated.
Jed
------
Jed Goldstone
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-
?
--
Jed Goldstone
Visting Investigator
Woods Hole Oceanographic Institution
Redfield 3-52 MS #32
Woods Hole, MA 02543
http://www.mit.edu/people/jedgold/home.html
(508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI)
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