Re: [PyMOL] 60-mer virus capsid (need computing power!)

[Shane Neeley]

Hi Jason,

Thanks a lot for the performance info. I think that a full capsid would be
around 300,000 atoms, so your info is very helpful.

We will probably invest in the newest version of pymol when we purchase the
computer.



On Fri, Jun 15, 2012 at 12:19 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Shane,
>
> With PyMOL v1.5 and later, and a reasonable machine you should be able
> to use large systems (>250,000, and upward of 1,000,000+ atoms)
> without much of a problem. Using the following simple test script:
>
> fetch 2xpj, type=pdb1, async=0
> split_states 2xpj
> delete 2xpj
> orient
>
> For these 240,000 atoms on a Dell T5500 with a very nice video card, I get:
>  * 30 FPS as lines
>  * 28 FPS using cartoons
>  * 30 FPS a ribbons
>  * 30 FPS as surface
>
> For these 240,000 atoms on a (1 year old) MacBookPro (with ATI Radeon
> HD 6770) I get
>  * 60 FPS as lines
>  * 33 FPS as cartoon
>  * 36 FPS as ribbon
>  * 27 FPS as surface
>
> 30--60 FPS is surely in the realm of "interactive". Earlier versions
> of PyMOL would have a tough time with these data. (Plus the new
> versions of PyMOL have nicer rendering in real time.)
>
> Next, you wrote:
>
> > Is a 12-core mac like this overkill?
> > http://store.apple.com/us_smb_78313/configure/MD771LL/A
>
> With Moore's Law still in effect, nothing is overkill. However,
> consider value for money: the recent announcements from Apple centered
> around the MacBookPro -- not the MacPro.
>
> It should be clear that those who financially support PyMOL are
> responsible for this level progress. The diff from v1.4 to v1.5 was in
> the range of 50,000+ lines -- and we couldn't have done that work
> without our supporters. So, a special thanks goes out to them!
>
> Cheers,
>
> -- Jason
>
>
> On Wed, Jun 13, 2012 at 2:32 PM, Shane Neeley 
> wrote:
> > Hi,
> >
> > Does anyone use pymol for very large structures, such as a full virus
> 60-mer
> > capsid? If so, what processing power, memory, graphics card, etc. do you
> > need to render these large files and manipulate them without any slowing?
> > PyMol takes about 1 minute to think after trying to spin one of these
> full
> > capsids, and that is on a dual-core 8gb ram laptop.
> >
> > Is a 12-core mac like this overkill?
> > http://store.apple.com/us_smb_78313/configure/MD771LL/A
> >
> > Has anyone built other machines to do this sort of work?
> >
> > Appreciate your input,
> >
> > Shane Neeleu
> >
> >
> >
> --
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> > ___
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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[PyMOL] 60-mer virus capsid (need computing power!)

[Shane Neeley]

Hi,

Does anyone use pymol for very large structures, such as a full virus
60-mer capsid? If so, what processing power, memory, graphics card, etc. do
you need to render these large files and manipulate them without any
slowing? PyMol takes about 1 minute to think after trying to spin one of
these full capsids, and that is on a dual-core 8gb ram laptop.

Is a 12-core mac like this overkill?
http://store.apple.com/us_smb_78313/configure/MD771LL/A

Has anyone built other machines to do this sort of work?

Appreciate your input,

Shane Neeleu
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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?
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[PyMOL] color_by_mutation needs identical atom counts?

[Shane Neeley]

Hi, I am using color_by_mutations on PyMol 1.3.

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

I get this error:

PyMOL>run color_by_mutation.py
PyMOL>color_by_mutation aav2, aav8
ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs
30227)
 Executive: Error -- no atoms left after refinement!
ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs
30227)
 Executive: Error -- no atoms left after refinement!
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--


How could there every be an exact atom count between two unidentical
structures anyways?
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Re: [PyMOL] fink install pymol help

[Shane Neeley]

I've installed all of the packages for pymol-py27 with fink. And my
terminal went back to normal. Now what? How do I make PyMol an application?

On Thu, Mar 15, 2012 at 5:28 PM, Shane Neeley wrote:

> Thanks Guys I just had to self update fink.
>
>
> On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley wrote:
>
>> Hi, S.S. Thanks for your help. It says,
>>
>> Failed: no package found for specification 'pymol-py27'!
>>
>> null-b88d121ba616:~ chimpsarehungry$ fink list pymol
>> Information about 312 packages read in 1 seconds.
>> null-b88d121ba616:~ chimpsarehungry$
>>
>> It doesn't appear to be a package available to me.
>>
>> On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj > > wrote:
>>
>>>
>>> Try  fink install pymol-py27
>>>
>>>   --
>>> *From:* Shane Neeley 
>>> *To:* pymol-users@lists.sourceforge.net
>>> *Sent:* Thursday, March 15, 2012 4:53 PM
>>> *Subject:* [PyMOL] fink install pymol help
>>>
>>> I installed Fink on my mac because apparently it has pymol as a port so
>>> that I can download a newer version.
>>> According to this:
>>> http://pymol.sourceforge.net/newman/user/S0120install.html
>>>
>>> In terminal I type
>>>
>>> sudo -s
>>> apt-get *pymol install*
>>> *
>>> *
>>> But it did not work. Do you know how I could install it with fink?
>>>
>>>
>>> --
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>>>
>>>
>>
>
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Re: [PyMOL] fink install pymol help

[Shane Neeley]

Thanks Guys I just had to self update fink.

On Thu, Mar 15, 2012 at 4:46 PM, Shane Neeley wrote:

> Hi, S.S. Thanks for your help. It says,
>
> Failed: no package found for specification 'pymol-py27'!
>
> null-b88d121ba616:~ chimpsarehungry$ fink list pymol
> Information about 312 packages read in 1 seconds.
> null-b88d121ba616:~ chimpsarehungry$
>
> It doesn't appear to be a package available to me.
>
> On Thu, Mar 15, 2012 at 4:27 PM, S. Shunmugasundararaj 
> wrote:
>
>>
>> Try  fink install pymol-py27
>>
>>   --
>> *From:* Shane Neeley 
>> *To:* pymol-users@lists.sourceforge.net
>> *Sent:* Thursday, March 15, 2012 4:53 PM
>> *Subject:* [PyMOL] fink install pymol help
>>
>> I installed Fink on my mac because apparently it has pymol as a port so
>> that I can download a newer version.
>> According to this:
>> http://pymol.sourceforge.net/newman/user/S0120install.html
>>
>> In terminal I type
>>
>> sudo -s
>> apt-get *pymol install*
>> *
>> *
>> But it did not work. Do you know how I could install it with fink?
>>
>>
>> --
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>>
>>
>
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[PyMOL] fink install pymol help

[Shane Neeley]

I installed Fink on my mac because apparently it has pymol as a port so
that I can download a newer version.
According to this:
http://pymol.sourceforge.net/newman/user/S0120install.html

In terminal I type

sudo -s
apt-get *pymol install*
*
*
But it did not work. Do you know how I could install it with fink?
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[PyMOL] AttributeError: 'module' object has no attribute 'super'

[Shane Neeley]

AttributeError: 'module' object has no attribute 'super'

I am trying to run color_by_mutation

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

But I get that error. Maybe my version of Mac PyMol from 2006 doesn't have
that superimpose command? How do I fix this?

Thank you.

Shane
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[PyMOL] How to tell what amino acids are in view?

[Shane Neeley]

Hi,

Does anyone know of a way to tell which amino acids are currently in view?
I am imagining something that highlights the the parts of the sequence that
are visible as you rotate the molecule around. It may be much more complex
than I am describing.

Shane
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Re: [PyMOL] New to PyMol. Want to extract sequence from .pse file w/ colors.

[Shane Neeley]

Hi Pymol Network,
>
> I would appreciate someones help in extracting the sequence in the viewer
> above the protein. I have gone through the sequence and changed AAs to
> different colors based on their position. I would ideally like to be able
> to copy that sequence with the colors that they are coded so that I could
> export it to an excel file. Is this possible?
>
> Thanks very much.
>
> Shane
>
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