Re: [PyMOL] Protein Parameters?

[Joel Tyndall]

Hi Shane,

I think I meant weblogo which shows frequency of amino acids

e.g. http://weblogo.berkeley.edu/

Sorry for the confusion
J

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: Shane Neeley [mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 10:18 a.m.
To: Joel Tyndall
Subject: Re: [PyMOL] Protein Parameters?

Hi Thanks for the tip Joel.

I checked a few of the sequences for protein motifs but because they are so 
sort and because there really is no known function, i think it is unlikely to 
have any hits.


On Tue, Apr 3, 2012 at 2:58 PM, Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:
Hi Shane,

Whilst I am no expert, I would think possible a sequence motif (based on amino 
acid composition) may help. It may show up certain amino acids at specific 
points. Given the short length of the peptides, the question is what are they 
used for?

Hope this helps
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: Shane Neeley 
[mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Protein Parameters?

Hi,

This is unrelated to PyMol, but I just wanted to spam the community to see what 
they think about different protein parameters. Let me know if this sort of 
question is inappropriate for the forum.

I have thousands of randomly generated 7 amino acid peptide sequences that are 
within a virus. As we subject this virus to reproduction selective pressure in 
cell lines, we get back functional viruses with certain 7 amino acid sequences, 
while most random sequences are null mutations. So I am now testing the the 
positive sequences to see what they have in common, or what is most important.

I am doing this with a likely structural sequence and a likely surface sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be testing? 
Maybe something like Phi-value analysis?



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[PyMOL] Application deadline approaching: CCP4 summer school at APS, in USA

[Sanishvili, Ruslan]

Dear Colleagues,
We would like to point out that the application deadline for the 5th annual 
CCP4 Summer School "From data collection to structure refinement and beyond" is 
April 17, 2012. The school will take place from June 19 through June 26, 2012 
at the Advanced Photon Source (APS) near Chicago.
There is no registration fee for the school. The students will be responsible 
for their own travel and lodging expenses. These and other details (The 
program, the list of speakers, the application process, accommodations, site 
access, contacts etc) can be found at the workshop website at 
http://www.ccp4.ac.uk/schools/APS-2012/index.php
The school will cover all aspects of macromolecular structure determination and 
validation.

Some of the world's leading experts will be providing instruction and hand-on 
help.
We are looking forward to another productive school this summer.

Garib, Ronan and Nukri




Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667


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Re: [PyMOL] Protein Parameters?

[Joel Tyndall]

Hi Shane,

Whilst I am no expert, I would think possible a sequence motif (based on amino 
acid composition) may help. It may show up certain amino acids at specific 
points. Given the short length of the peptides, the question is what are they 
used for?

Hope this helps
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: Shane Neeley [mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Protein Parameters?

Hi,

This is unrelated to PyMol, but I just wanted to spam the community to see what 
they think about different protein parameters. Let me know if this sort of 
question is inappropriate for the forum.

I have thousands of randomly generated 7 amino acid peptide sequences that are 
within a virus. As we subject this virus to reproduction selective pressure in 
cell lines, we get back functional viruses with certain 7 amino acid sequences, 
while most random sequences are null mutations. So I am now testing the the 
positive sequences to see what they have in common, or what is most important.

I am doing this with a likely structural sequence and a likely surface sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be testing? 
Maybe something like Phi-value analysis?


--
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monitoring Big Data applications. Try Boundary one-second 
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[PyMOL] Protein Parameters?

[Shane Neeley]

Hi,

This is unrelated to PyMol, but I just wanted to spam the community to see
what they think about different protein parameters. Let me know if this
sort of question is inappropriate for the forum.

I have thousands of randomly generated 7 amino acid peptide sequences that
are within a virus. As we subject this virus to reproduction selective
pressure in cell lines, we get back functional viruses with certain 7 amino
acid sequences, while most random sequences are null mutations. So I am now
testing the the positive sequences to see what they have in common, or what
is most important.

I am doing this with a likely structural sequence and a likely surface
sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be
testing? Maybe something like Phi-value analysis?
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
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Re: [PyMOL] problem installing pymol plugin

[Thomas Holder]

Hi Vaibhav,

First: I assume you did NOT copy the "PocketPickerScript" to "C:\Program 
Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup", otherwise there 
would not be a "No such file" error.

Second: The plugin does not use the best coding style, it has hard coded 
file paths. So I would not be surprised if you will encounter more 
errors when using it. However, the plugin works for me on my Linux box 
after some modifications.

Also, there is no "version" command in PyMOL, but a "get_version" command.

Hope that helps.

Cheers,
   Thomas

On 04/03/2012 05:50 AM, vaibhav dixit wrote:
> Dear Pymol users,
> I am using pymol for modeling purposes. I wanted to display active site
> shape in my report.
> So I cam across your programm pocketpicker.
>
> I followed the procedure given on page
> http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/PocketPicker_Readme.pdf
>
> But unfortunately the plugin is not getting installed. I am using
> windows vista OS.
> Please suggest on how to install it correctly?
> Thank you.
>
> Following is the message displayed.
>
> 
> PyMOL>version
> Traceback (most recent call last):
>File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parser.py", line 455, in parse
>  exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>File "", line 1, in ?
> NameError: name 'version' is not defined
> PyMOL>run C:\Program Files\DeLano
> Scientific\Pymol\modules\pmg_tk\startup\PocketPickerScript\LigandKicker_1.0.py
> 
> Traceback (most recent call last):
>File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parser.py", line 332, in parse
>
> parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parsing.py", line 455, in run_file
>  execfile(file,global_ns,local_ns)
> IOError: [Errno 2] No such file or directory: 'C:\\Program Files\\DeLano
> Scientific\\Pymol\\modules\\pmg_tk\\startup\\PocketPickerScript\\LigandKicker_1.0.py
> '
> 
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X,  S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadi...@gmail.com 
> www.niper.nic.in 

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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Re: [PyMOL] hide tube / show only filled nucleic acid rings

[Troels Emtekær Linnet]

Have you tried this:

http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons

Best
Troels Emtekær Linnet

2012/4/2 Francis E Reyes 

>
> Tricky one I tried hide cartoon, name P but no go..
>
> instead cartoon skip will do it.
>
>
>
> On Apr 2, 2012, at 2:50 PM, Eike Schulz wrote:
>
> > Hello everybody,
> >
> > I am looking for a way to display nucleic acids in cartoon mode but
> > without showing the backbone trace. Unfortunately set
> > cartoon_tube_radius=0 leaves a thin line behind.
> >
> > Thanks a lot in advance
> >
> >   Best
> >
> >   Eike
> >
> >
> >
> >
> --
> > Better than sec? Nothing is better than sec when it comes to
> > monitoring Big Data applications. Try Boundary one-second
> > resolution app monitoring today. Free.
> > http://p.sf.net/sfu/Boundary-dev2dev
> > ___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
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Re: [PyMOL] Finding distances along molecular tunnels

[Thomas Holder]

Hi Sajeewa,

> [...]
> If I follow wizard --> measurements --> distance it asks for atoms to
> click on, but as the tunnels are empty space when I click on the
> starting points of the tunnels nothing is recognized.
> What would be the most accurate way of measuring the above two distances?

The tunnel is not really empty space, it's actually composed of 
pseudo-atoms and it's just a matter of visual representation. Hiding the 
surface and showing lines should be sufficient.

hide surface
show lines

Now try to use the measurement wizard.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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