Re: [PyMOL] Movie to export

2011-11-09 Thread Vitali Stanevich 
have a look at this link:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera

disregard morph part. you can modify script to contain "frames" instead of
"states". i installed ffmpeg from repositories on ubuntu and don't remember
any issues with kodecs.

vitali

On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte  wrote:

> **
> Hi,
> Quick time player 7 pro does a great job for me.
> Cheers
> Tim
>
> Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet:
>
> Hi.
>
>  I have made a nice little movie in Pymol.
> 1500 frames.
>
>  So now I am wondering what is the best method to export?
>
>  At the moment I do export to .png with ray tracing each image.
> set ray_trace_frames = 1
> That takes a long time.
>  And what program should I use to pack them together? The easy wasy?
>
>  Can it be done faster with the MPEG method?
>
>  Best
> Troels
>
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Re: [PyMOL] Movie to export

2011-11-09 Thread Vitali Stanevich 
one more thing: ffmpeg script at that link didn't work for me so i had to
modify it like that

ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg

On Wed, Nov 9, 2011 at 11:22 PM, Vitali Stanevich wrote:

> have a look at this link:
>
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera
>
> disregard morph part. you can modify script to contain "frames" instead of
> "states". i installed ffmpeg from repositories on ubuntu and don't remember
> any issues with kodecs.
>
> vitali
>
> On Wed, Nov 9, 2011 at 8:14 AM, Tim Schulte  wrote:
>
>> **
>> Hi,
>> Quick time player 7 pro does a great job for me.
>> Cheers
>> Tim
>>
>> Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet:
>>
>> Hi.
>>
>>  I have made a nice little movie in Pymol.
>> 1500 frames.
>>
>>  So now I am wondering what is the best method to export?
>>
>>  At the moment I do export to .png with ray tracing each image.
>> set ray_trace_frames = 1
>> That takes a long time.
>>  And what program should I use to pack them together? The easy wasy?
>>
>>  Can it be done faster with the MPEG method?
>>
>>  Best
>> Troels
>>
>> Troels Emtekær Linnet
>> Slotsvej 2
>> 4300 Holbæk
>> Mobil: +45 60210234
>>
>>
>> --
>> RSA(R) Conference 2012
>> Save $700 by Nov 18
>> Register nowhttp://p.sf.net/sfu/rsa-sfdev2dev1
>>
>>
>> ___
>> 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
>>
>>
>>
>>
>> --
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>> Save $700 by Nov 18
>> Register now
>> http://p.sf.net/sfu/rsa-sfdev2dev1
>>
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>>
>>
>
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Re: [PyMOL] query

2011-11-20 Thread Vitali Stanevich 
check this out:
http://www.pymolwiki.org/index.php/InterfaceResidues

if you want faster and easier, but less reliable (in my opinion) way, you
can analyze your .pdb with PISA:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

vitali

On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in <
rjayashree13-scie...@yahoo.co.in> wrote:

> I have a PDB file for a dimeric protein. Is it possible to depict the
> intersubunit contacts for any PDB file? Is Pymol alone sufficient for this
> purpose or will it only help visualization?
> Could you also tell me which commands in Pymol can I use for this purpose?
> I have tried a lot but could not get an answer to this. I will be very
> thankful for the favour.
>
> Dr. Jayashree Ramana
>
> 
>
>
> --
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Re: [PyMOL] query

2011-11-21 Thread Vitali Stanevich 
here it is:
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

vitali

On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-scie...@yahoo.co.in <
rjayashree13-scie...@yahoo.co.in> wrote:

> Thank you. It works, but it does not bring out the type of interaction
> responsible for interface contact-hydrogen bonding or electrostatic
> interaction etc.
>  I am using another tool called PSAP for analyzing inter-molecular
> interactions (iris.physics.iisc.ernet.in/psap)
> It gives me the residues involved in hydrogen bonding, now using Pymol I
> can label these residues, but is there any way to depict these hydrogen
> bonds also and the distances?
>
> Dr. Jayashree Ramana
>
>  <http://www.juit.ac.in/bio/jsr.php>
>
>   ------
> *From:* Vitali Stanevich 
> *To:* "rjayashree13-scie...@yahoo.co.in" 
>
> *Cc:* "pymol-users@lists.sourceforge.net" <
> pymol-users@lists.sourceforge.net>
> *Sent:* Sunday, 20 November 2011 1:57 PM
> *Subject:* Re: [PyMOL] query
>
> check this out:
> http://www.pymolwiki.org/index.php/InterfaceResidues
>
> if you want faster and easier, but less reliable (in my opinion) way, you
> can analyze your .pdb with PISA:
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
>
> vitali
>
> On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in <
> rjayashree13-scie...@yahoo.co.in> wrote:
>
> I have a PDB file for a dimeric protein. Is it possible to depict the
> intersubunit contacts for any PDB file? Is Pymol alone sufficient for this
> purpose or will it only help visualization?
> Could you also tell me which commands in Pymol can I use for this purpose?
> I have tried a lot but could not get an answer to this. I will be very
> thankful for the favour.
>
> Dr. Jayashree Ramana
>
>  <http://www.juit.ac.in/bio/jsr.php>
>
>
> --
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
>
--
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contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
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[PyMOL] 1.5 version runs slow with "large" objects

2012-02-14 Thread Vitali Stanevich 
Hi,

I recently installed a new version of licensed pymol 1.5. It works ok with
small molecules (<25 kDa). But, unfortunately, I found that after I load
relatively large molecules (>60 kDa) everything really slows down,
movements become somewhat abrupt and etc. At the same time, I can open this
molecule with coot, generate bunch of symmetry mates, add maps, but
everything runs really smooth. How can I make pymol run smooth again
(version 1.2 worked well before)?

Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same
result)
OS: Ubuntu 10.10
Video card: nVidia GeForce 7150M
CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits)

Thanks,
Vitali
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Re: [PyMOL] 1.5 version runs slow with "large" objects

2012-02-16 Thread Vitali Stanevich 
Jason,

I did install latest driver for a card (295.20) from nvidia site. The
problem still exists. Any other suggestions?

Thanks,
Vitali

On Wed, Feb 15, 2012 at 9:14 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Vitaly,
>
> Have you installed the latest graphics drivers for your card?
>
> Cheers,
>
> -- Jason
>
> On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich 
> wrote:
> > Hi,
> >
> > I recently installed a new version of licensed pymol 1.5. It works ok
> with
> > small molecules (<25 kDa). But, unfortunately, I found that after I load
> > relatively large molecules (>60 kDa) everything really slows down,
> movements
> > become somewhat abrupt and etc. At the same time, I can open this
> molecule
> > with coot, generate bunch of symmetry mates, add maps, but everything
> runs
> > really smooth. How can I make pymol run smooth again (version 1.2 worked
> > well before)?
> >
> > Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same
> > result)
> > OS: Ubuntu 10.10
> > Video card: nVidia GeForce 7150M
> > CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits)
> >
> > Thanks,
> > Vitali
> >
> >
> --
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>
>
>
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Re: [PyMOL] 1.5 version runs slow with "large" objects

2012-02-16 Thread Vitali Stanevich 
Jason,

I do not have .pymorc file.

But when I set "use_shaders" to 0, then everything becomes fast and nice. I
guess I just can turn on shaders only as the final step before ray_tracing.

Thanks for help,
Vitali

On Thu, Feb 16, 2012 at 1:22 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Vitaly,
>
> It looks like the 7150M has only 57 megs of dedicated memory. Once you
> exhaust that your performance will decrease dramatically. I'l contact
> NVidia and see if they have any suggestions.
>
> Also, do you have a ~/.pymolrc file? If so, what's in it? For the new
> graphics to perform, you need the "use_shaders" setting turned on.
>
> Cheers,
>
> -- Jason
>
> On Thu, Feb 16, 2012 at 2:09 PM, Vitali Stanevich 
> wrote:
> > Jason,
> >
> > I did install latest driver for a card (295.20) from nvidia site. The
> > problem still exists. Any other suggestions?
> >
> > Thanks,
> > Vitali
> >
> >
> > On Wed, Feb 15, 2012 at 9:14 AM, Jason Vertrees
> >  wrote:
> >>
> >> Hi Vitaly,
> >>
> >> Have you installed the latest graphics drivers for your card?
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Tue, Feb 14, 2012 at 5:27 PM, Vitali Stanevich 
> >> wrote:
> >> > Hi,
> >> >
> >> > I recently installed a new version of licensed pymol 1.5. It works ok
> >> > with
> >> > small molecules (<25 kDa). But, unfortunately, I found that after I
> load
> >> > relatively large molecules (>60 kDa) everything really slows down,
> >> > movements
> >> > become somewhat abrupt and etc. At the same time, I can open this
> >> > molecule
> >> > with coot, generate bunch of symmetry mates, add maps, but everything
> >> > runs
> >> > really smooth. How can I make pymol run smooth again (version 1.2
> worked
> >> > well before)?
> >> >
> >> > Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the
> same
> >> > result)
> >> > OS: Ubuntu 10.10
> >> > Video card: nVidia GeForce 7150M
> >> > CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits)
> >> >
> >> > Thanks,
> >> > Vitali
> >> >
> >> >
> >> >
> --
> >> > Keep Your Developer Skills Current with LearnDevNow!
> >> > The most comprehensive online learning library for Microsoft
> developers
> >> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
> MVC3,
> >> > Metro Style Apps, more. Free future releases when you subscribe now!
> >> > http://p.sf.net/sfu/learndevnow-d2d
> >> > ___
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> >> > 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
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
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[PyMOL] install Pymol 1.5 on Linux Mint 13

2013-09-12 Thread Vitali Stanevich 
Hi,

I'm trying to install PyMOL-v1.5.0.4-Linux-x86_64 on Linux Mint 13.

After successful unpacking, "sh"-ing and copying into /usr/local/bin/pymol
I tried to execute Pymol from the terminal, but error came out:

vitali@vs-Think ~/install/pymol $ pymol
/home/vitali/install/pymol/pymol.exe: 1:
/home/vitali/install/pymol/pymol.exe: Syntax error: ")" unexpected

What am I doing wrong? I tried to google, but nothing similar came up.

Thanks,
Vitali
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