Re: [PyMOL] print hydrogen bonds involved residues

2011-09-11 Thread lina 
On Sun, Sep 11, 2011 at 3:59 AM, Thomas Holder 
spel...@users.sourceforge.net wrote:

 Hi Lina,

 have a look at:
 http://pymolwiki.org/index.**php/Polarpairshttp://pymolwiki.org/index.php/Polarpairs

 it takes two selections and has a state argument.


Thanks for the link.

I still have a question:

1]  save the script as polar_pairs.py
2] in pymol run polar_pairs.py
3] For

pairs = polarpairs('chain A', 'chain B')for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)

I don't know how to proceed this part, do I need to put those code in
another .py file?

sorry and thanks for your patience,


 Cheers,
  Thomas

 lina wrote, On 09/10/11 15:21:

  Hi,

 After dist hb, proA, proB, mode=2

 I can get the hydrogen bonds formation between protein A and protein B.

 But I don't know how to get the detailed involved residues very quickly,
 suppose I have had 10 models in this structure.

 I googled before,
 http://www.mail-archive.com/**pymol-users@lists.sourceforge.**
 net/msg06211.htmlhttp://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html
 is helpful for the single one selections,
 here I got two.

 Thanks for any suggestions,

 --
 Best Regards,

 lina


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




-- 
Best Regards,

lina
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[PyMOL] compare crystal packing of two different Space Groups

2011-09-11 Thread shukunluo 
Dear Pymol users,

I want to compare the crystal packing and contacts of two different space
groups of the same protein using pymol. Here's what I did: (1)loaded two
structures; (2) aligned two structures; (3) generated symmetry-related
objects of two structures. However, the symmetry-related molecules didn't
move with the source structure. I tried in coot to superimposed two
structures then save the moved molecules, but the space group changed to the
target structures. I also tried the matrix_copy command with failure.

Does anyone know how to do this? Thanks in advance.

Best,
Shukun
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Re: [PyMOL] compare crystal packing of two different Space Groups

2011-09-11 Thread Nat Echols 
I've never found a clean way to do this - what I do is to save a PDB file
with the original model and the relevant symmetry mates, which I then use
for the alignments.  There may be a way to do is with object groups,
however.  (FYI, you'll probably also need to rename the chain IDs for the
symmetry mates so you can still use a unique atom selection for the original
chain(s).)

-Nat


On Sunday, September 11, 2011, shukunluo shukun...@gmail.com wrote:
 Dear Pymol users,

 I want to compare the crystal packing and contacts of two different space
groups of the same protein using pymol. Here's what I did: (1)loaded two
structures; (2) aligned two structures; (3) generated symmetry-related
objects of two structures. However, the symmetry-related molecules didn't
move with the source structure. I tried in coot to superimposed two
structures then save the moved molecules, but the space group changed to the
target structures. I also tried the matrix_copy command with failure.

 Does anyone know how to do this? Thanks in advance.

 Best,
 Shukun
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Re: [PyMOL] print hydrogen bonds involved residues

2011-09-11 Thread Troels Emtekær Linnet 
You have to make .pml file and put the python commands inside pymol blocks.

Try look here for an example.

http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/9/11 lina lina.lastn...@gmail.com



 On Sun, Sep 11, 2011 at 3:59 AM, Thomas Holder 
 spel...@users.sourceforge.net wrote:

 Hi Lina,

 have a look at:
 http://pymolwiki.org/index.**php/Polarpairshttp://pymolwiki.org/index.php/Polarpairs

 it takes two selections and has a state argument.


 Thanks for the link.

 I still have a question:

 1]  save the script as polar_pairs.py
 2] in pymol run polar_pairs.py
 3] For

 pairs = polarpairs('chain A', 'chain B')for p in pairs:
 dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
 print p, 'Distance: %.2f' % (dist)

 I don't know how to proceed this part, do I need to put those code in
 another .py file?

 sorry and thanks for your patience,


 Cheers,
  Thomas

 lina wrote, On 09/10/11 15:21:

  Hi,

 After dist hb, proA, proB, mode=2

 I can get the hydrogen bonds formation between protein A and protein B.

 But I don't know how to get the detailed involved residues very quickly,
 suppose I have had 10 models in this structure.

 I googled before,
 http://www.mail-archive.com/**pymol-users@lists.sourceforge.**
 net/msg06211.htmlhttp://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html
 is helpful for the single one selections,
 here I got two.

 Thanks for any suggestions,

 --
 Best Regards,

 lina


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




 --
 Best Regards,

 lina




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[PyMOL] Writing a script yo pymol

2011-09-11 Thread Yotam Avital 
Hi.

How hard it is to write a (python?) script that will rotate the figure and
color some atoms? Nothing fancy... I searched a little bit but couldn't find
a quick and dirty tutorial for script writing.

Thanks

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Re: [PyMOL] Writing a script yo pymol

2011-09-11 Thread Troels Emtekær Linnet 
Well, not hard.

I made a script that can rotate a molecule around a line.
And I made a large tutorial to take one through the available functions of
this script.
It is a pymol command file, .pml.

Check out:
http://www.pymolwiki.org/index.php/Rotkit


Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/9/11 Yotam Avital yota...@gmail.com

 Hi.

 How hard it is to write a (python?) script that will rotate the figure and
 color some atoms? Nothing fancy... I searched a little bit but couldn't find
 a quick and dirty tutorial for script writing.

 Thanks

 --
 My other email account has a professional signature.



 --
 Using storage to extend the benefits of virtualization and iSCSI
 Virtualization increases hardware utilization and delivers a new level of
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Re: [PyMOL] Show Sticks - Turns Molecule Blue

2011-09-11 Thread David Hall 
Assuming you're using a recent version of openSUSE (11.3, 11.4, or
Factory), feel free to grab the svn compiled version from
http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol

-David

2011/9/11 Troels Emtekær Linnet tlin...@gmail.com:
 This should get you on the way on compiling from svn.

 http://www.pymolwiki.org/index.php/Linux_Install#Mint11_Linux_.28Ubuntu.29_-_Tested_for_PyMOL_1.4.1

 Best
 Troels


 2011/9/9 Sean Law magic...@hotmail.com

 Hi PyMOLers,

 I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old
 Pentium 4) and am finding that when I load a molecule and click Show --
 Sticks that the entire molecular gets colored blue (originally the green
 default lines color).  After trying to change the color (Color --
 Elements), it doesn't alter the color at all.  However, hiding the sticks
 representation takes me back to the hidden green default lines color.  I'm
 not sure if this is because I'm using an old computer or if I'm missing
 something (i.e. libraries).

 Any suggestions would be greatly appreciated.

 Thanks

 Sean


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Re: [PyMOL] Writing a script yo pymol

2011-09-11 Thread Yotam Avital 
Thanks.

I'm sorry but this is too complected. Currently, I can't afford the time to
learn another scripting  languish. Consider gnuplot script files, which are
simply a list of gnuplot commands. Sure you can do some sophisticated stuff
but you don't have to. All my files will be simple atom list in xyz
format (name
\t x \t y \t z), and all I want to do is select all the atoms of a certain
name, color them and then rotate the system.

Once again, I thank you for any help.

2011/9/11 Troels Emtekær Linnet tlin...@gmail.com

 Well, not hard.

 I made a script that can rotate a molecule around a line.
 And I made a large tutorial to take one through the available functions of
 this script.
 It is a pymol command file, .pml.

 Check out:
 http://www.pymolwiki.org/index.php/Rotkit


 Troels Emtekær Linnet
 Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
 04107 Leipzig, Tyskland
 Mobil: +49 1577-8944752



 2011/9/11 Yotam Avital yota...@gmail.com

  Hi.

 How hard it is to write a (python?) script that will rotate the figure and
 color some atoms? Nothing fancy... I searched a little bit but couldn't find
 a quick and dirty tutorial for script writing.

 Thanks

 --
 My other email account has a professional signature.



 --
 Using storage to extend the benefits of virtualization and iSCSI
 Virtualization increases hardware utilization and delivers a new level of
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