Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[James Starlight]

thank u very much again!

the problem is that the vina output is also stripped from the hydrogen ( i
don’t know why because I've made each ligand including hydrogens from the
initial.pdb where they were)

pythonsh ${tools}/prepare_ligand4.py -v -l ${mol2} -o
${ligands_out}/${filenamenoextention_lig}/${filenamenoextention_lig}.pdbqt
-A hydrogens_bonds

so antechamber will also send me error dealing with that stripped files :)

will the acpype available as some software not web server?

James

2014-09-17 16:27 GMT+02:00 Gianluca Santoni :

> Sorry, I didn't get this important point.
>
> Have you tried to run antechamber using your vina output as an input?
> You could do something like
>
> grep HETATM output.pdbqt | cut -c1-66 > output.pdb
>
> and use acpype to prepare the topology, with output.pdb as an input file.
> https://code.google.com/p/acpype/
>
> This should work fine later to start your md simulations as it should
> conserve your docked coordinates.
>
> Cheers,
> Gian
>
>
> On 9/17/14 3:56 PM, James Starlight wrote:
>
>> all manual and GUI operations are not accepted here!
>> I'm dealing with the a huge number of protein-ligand complexes (many
>> many different proteins but only 1 ligand- so the situation is not very
>> bad !). But what is bad that I need to dock each complex using vina and
>> make its parametrization by amber
>>
>> :)
>>
>> James
>>
>> 2014-09-17 15:32 GMT+02:00 Gianluca Santoni > >:
>>
>>
>> Hi James,
>> what usually worked for me was simply to do it manually, in editing
>> mode
>> with pymol.
>> Consider that you will perform an energy minimization after, so a few
>> 1/10 of angstroms of difference in your initial model are not a big
>> deal, in my opinion.
>>
>> Cheers,
>> Gian
>>
>> On 9/17/14 3:17 PM, James Starlight wrote:
>> > Hi Fotis,
>> >
>> > thank you very much for the suggestion!
>> >
>> > Indeed I have not had such problem with the preparation structure
>> for
>> > NAMD but in case of amber its really exist (the structure of the
>> ligand
>> > provided in the complex with the receptor.pdb must be EXACTLY the
>> same
>> > as it was previously parametrized using some amber program called
>> > antechamber).
>> > So I will be interesting in two options
>> > 1) to find some shell utility for superimposition of the 2 ligands
>> in
>> > one-style command (because here I'm dealing with some script and I
>> need
>> > to do it in loop many times)
>> > or (which is better!)
>> >
>> > 2) use pdb2pqr software (because I'm using it in the part of this
>> script
>> > to process complex and to add hydrogens to ligand as well)- here I
>> > noticed that ligand should be provided as the separate .mol2 file
>> (not
>> > pdb)- which is a bit not comfortable for me (because I obained all
>> > docking poses from VINA as the pdb). I guess I should here to put
>> ligand
>> > from complex, to convert it to mol2 and proceed 2 files (receptor
>> and
>> > ligand) to the pdb2pqr. But may be the better solution is exist?
>> >
>> > James
>> >
>> >
>> >
>> > 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas <
>> fotis.baltou...@gmail.com 
>>  > > >>:
>> >
>> > Hello James,
>> > You can use the Pair Fitting wizard (Menu: Wizards=>Pair
>> Fitting) or
>> > the pair_fit command to superimpose small molecules. It's not as
>> > straightforward as protein super/align, since you have to
>> define the
>> > atom pairs that will be superimposed, but it's fairly easy.
>> After
>> > that, just make a selection of your receptor and your new
>> ligand and
>> > save it as a molecule.
>> >
>> > However, I don't think you really have a problem here. Since the
>> > only issue you mention is the lack of hydrogen atoms, couldn't
>> you
>> > just reintroduce them through some function in the AmberTools? I
>> > have no experience with Amber parameterization tools but, if
>> they're
>> > even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then
>> they
>> > can add hydrogen atoms for you easily.
>> > Another option would be to create a PQR file, either through
>> PDB2PQR
>> > (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the
>> APBSTools
>> > GUI in PyMOL. Part of the PQR creation includes adding hydrogen
>> > atoms, and you can use AMBER parameters both for proteins and
>> for
>> > ligands (mol2 format). Your result would be the structure of
>> your
>> > complex, with hydrogens, in the AMBER format.
>> >
>> > Hope I helped,
>> > Fotis Baltoumas
>> >
>> > 2014-09-17 13:01 GMT+03:00 James Starlight <
>> jmsstarli...@gmail.com 

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[Gianluca Santoni]

Sorry, I didn't get this important point.

Have you tried to run antechamber using your vina output as an input?
You could do something like

grep HETATM output.pdbqt | cut -c1-66 > output.pdb

and use acpype to prepare the topology, with output.pdb as an input 
file. https://code.google.com/p/acpype/

This should work fine later to start your md simulations as it should 
conserve your docked coordinates.

Cheers,
Gian


On 9/17/14 3:56 PM, James Starlight wrote:
> all manual and GUI operations are not accepted here!
> I'm dealing with the a huge number of protein-ligand complexes (many
> many different proteins but only 1 ligand- so the situation is not very
> bad !). But what is bad that I need to dock each complex using vina and
> make its parametrization by amber
>
> :)
>
> James
>
> 2014-09-17 15:32 GMT+02:00 Gianluca Santoni  >:
>
> Hi James,
> what usually worked for me was simply to do it manually, in editing mode
> with pymol.
> Consider that you will perform an energy minimization after, so a few
> 1/10 of angstroms of difference in your initial model are not a big
> deal, in my opinion.
>
> Cheers,
> Gian
>
> On 9/17/14 3:17 PM, James Starlight wrote:
> > Hi Fotis,
> >
> > thank you very much for the suggestion!
> >
> > Indeed I have not had such problem with the preparation structure for
> > NAMD but in case of amber its really exist (the structure of the ligand
> > provided in the complex with the receptor.pdb must be EXACTLY the same
> > as it was previously parametrized using some amber program called
> > antechamber).
> > So I will be interesting in two options
> > 1) to find some shell utility for superimposition of the 2 ligands in
> > one-style command (because here I'm dealing with some script and I need
> > to do it in loop many times)
> > or (which is better!)
> >
> > 2) use pdb2pqr software (because I'm using it in the part of this script
> > to process complex and to add hydrogens to ligand as well)- here I
> > noticed that ligand should be provided as the separate .mol2 file (not
> > pdb)- which is a bit not comfortable for me (because I obained all
> > docking poses from VINA as the pdb). I guess I should here to put ligand
> > from complex, to convert it to mol2 and proceed 2 files (receptor and
> > ligand) to the pdb2pqr. But may be the better solution is exist?
> >
> > James
> >
> >
> >
> > 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas  
>  >  >>:
> >
> > Hello James,
> > You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or
> > the pair_fit command to superimpose small molecules. It's not as
> > straightforward as protein super/align, since you have to define the
> > atom pairs that will be superimposed, but it's fairly easy. After
> > that, just make a selection of your receptor and your new ligand and
> > save it as a molecule.
> >
> > However, I don't think you really have a problem here. Since the
> > only issue you mention is the lack of hydrogen atoms, couldn't you
> > just reintroduce them through some function in the AmberTools? I
> > have no experience with Amber parameterization tools but, if they're
> > even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they
> > can add hydrogen atoms for you easily.
> > Another option would be to create a PQR file, either through PDB2PQR
> > (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools
> > GUI in PyMOL. Part of the PQR creation includes adding hydrogen
> > atoms, and you can use AMBER parameters both for proteins and for
> > ligands (mol2 format). Your result would be the structure of your
> > complex, with hydrogens, in the AMBER format.
> >
> > Hope I helped,
> > Fotis Baltoumas
> >
> > 2014-09-17 13:01 GMT+03:00 James Starlight  
>  > >>:
>  >
>  > Dear Pymol users,
>  >
>  > I've decide to make a copy of this topic from the amber mail
>  > list because this problem could be solves by ones of the
> methods
>  > implemented in Pymol.
>  >
>  > Here I'm facing with the problem of the preparation of
>  > protein-ligand complexes for amber md simulation:
>  > Following amber's tutorial I've made parametrization of the
>  > ligand using antechamber obtaining ligand.frcmod and
> ligand.lib
>  > files consisted of the parameters for my ligand and its
>  > coordinates in mol2 assoc

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[James Starlight]

all manual and GUI operations are not accepted here!
I'm dealing with the a huge number of protein-ligand complexes (many many
different proteins but only 1 ligand- so the situation is not very bad !).
But what is bad that I need to dock each complex using vina and make its
parametrization by amber

:)

James

2014-09-17 15:32 GMT+02:00 Gianluca Santoni :

> Hi James,
> what usually worked for me was simply to do it manually, in editing mode
> with pymol.
> Consider that you will perform an energy minimization after, so a few
> 1/10 of angstroms of difference in your initial model are not a big
> deal, in my opinion.
>
> Cheers,
> Gian
>
> On 9/17/14 3:17 PM, James Starlight wrote:
> > Hi Fotis,
> >
> > thank you very much for the suggestion!
> >
> > Indeed I have not had such problem with the preparation structure for
> > NAMD but in case of amber its really exist (the structure of the ligand
> > provided in the complex with the receptor.pdb must be EXACTLY the same
> > as it was previously parametrized using some amber program called
> > antechamber).
> > So I will be interesting in two options
> > 1) to find some shell utility for superimposition of the 2 ligands in
> > one-style command (because here I'm dealing with some script and I need
> > to do it in loop many times)
> > or (which is better!)
> >
> > 2) use pdb2pqr software (because I'm using it in the part of this script
> > to process complex and to add hydrogens to ligand as well)- here I
> > noticed that ligand should be provided as the separate .mol2 file (not
> > pdb)- which is a bit not comfortable for me (because I obained all
> > docking poses from VINA as the pdb). I guess I should here to put ligand
> > from complex, to convert it to mol2 and proceed 2 files (receptor and
> > ligand) to the pdb2pqr. But may be the better solution is exist?
> >
> > James
> >
> >
> >
> > 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas  > >:
> >
> > Hello James,
> > You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or
> > the pair_fit command to superimpose small molecules. It's not as
> > straightforward as protein super/align, since you have to define the
> > atom pairs that will be superimposed, but it's fairly easy. After
> > that, just make a selection of your receptor and your new ligand and
> > save it as a molecule.
> >
> > However, I don't think you really have a problem here. Since the
> > only issue you mention is the lack of hydrogen atoms, couldn't you
> > just reintroduce them through some function in the AmberTools? I
> > have no experience with Amber parameterization tools but, if they're
> > even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they
> > can add hydrogen atoms for you easily.
> > Another option would be to create a PQR file, either through PDB2PQR
> > (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools
> > GUI in PyMOL. Part of the PQR creation includes adding hydrogen
> > atoms, and you can use AMBER parameters both for proteins and for
> > ligands (mol2 format). Your result would be the structure of your
> > complex, with hydrogens, in the AMBER format.
> >
> > Hope I helped,
> > Fotis Baltoumas
> >
> > 2014-09-17 13:01 GMT+03:00 James Starlight  > >:
> >
> > Dear Pymol users,
> >
> > I've decide to make a copy of this topic from the amber mail
> > list because this problem could be solves by ones of the methods
> > implemented in Pymol.
> >
> > Here I'm facing with the problem of the preparation of
> > protein-ligand complexes for amber md simulation:
> > Following amber's tutorial I've made parametrization of the
> > ligand using antechamber obtaining ligand.frcmod and ligand.lib
> > files consisted of the parameters for my ligand and its
> > coordinates in mol2 associated with those topologies. Now I'd
> > like to dock this ligand to the active site of the receptor
> > using autodock vina and make further tleap processing of
> > complex.pdb produced by autodock to obtain all input data for
> > simulation. Here some problems: because (superimposed to the
> > receptor cavity) ligand.pdb produced by autodock have been
> > stripped from all hydrogen’s so its coordinates not equal to
> > initial ligand.mol2 . How do you think will it possible to use
> > some method of the ligand superimposition to superimpose initial
> > ligand.mol2 (with correct corrdinates) agains docking pose
> > produced by vina and use superimposed ligand.mol2 for the
> > preparation of my complex?
> >
> > Thanks for help,
> >
> > James
> >
> >
>  
> --
> > Want excitement?
> > Manually upgrad

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[Gianluca Santoni]

Hi James,
what usually worked for me was simply to do it manually, in editing mode 
with pymol.
Consider that you will perform an energy minimization after, so a few 
1/10 of angstroms of difference in your initial model are not a big 
deal, in my opinion.

Cheers,
Gian

On 9/17/14 3:17 PM, James Starlight wrote:
> Hi Fotis,
>
> thank you very much for the suggestion!
>
> Indeed I have not had such problem with the preparation structure for
> NAMD but in case of amber its really exist (the structure of the ligand
> provided in the complex with the receptor.pdb must be EXACTLY the same
> as it was previously parametrized using some amber program called
> antechamber).
> So I will be interesting in two options
> 1) to find some shell utility for superimposition of the 2 ligands in
> one-style command (because here I'm dealing with some script and I need
> to do it in loop many times)
> or (which is better!)
>
> 2) use pdb2pqr software (because I'm using it in the part of this script
> to process complex and to add hydrogens to ligand as well)- here I
> noticed that ligand should be provided as the separate .mol2 file (not
> pdb)- which is a bit not comfortable for me (because I obained all
> docking poses from VINA as the pdb). I guess I should here to put ligand
> from complex, to convert it to mol2 and proceed 2 files (receptor and
> ligand) to the pdb2pqr. But may be the better solution is exist?
>
> James
>
>
>
> 2014-09-17 12:32 GMT+02:00 Fotis Baltoumas  >:
>
> Hello James,
> You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or
> the pair_fit command to superimpose small molecules. It's not as
> straightforward as protein super/align, since you have to define the
> atom pairs that will be superimposed, but it's fairly easy. After
> that, just make a selection of your receptor and your new ligand and
> save it as a molecule.
>
> However, I don't think you really have a problem here. Since the
> only issue you mention is the lack of hydrogen atoms, couldn't you
> just reintroduce them through some function in the AmberTools? I
> have no experience with Amber parameterization tools but, if they're
> even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they
> can add hydrogen atoms for you easily.
> Another option would be to create a PQR file, either through PDB2PQR
> (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools
> GUI in PyMOL. Part of the PQR creation includes adding hydrogen
> atoms, and you can use AMBER parameters both for proteins and for
> ligands (mol2 format). Your result would be the structure of your
> complex, with hydrogens, in the AMBER format.
>
> Hope I helped,
> Fotis Baltoumas
>
> 2014-09-17 13:01 GMT+03:00 James Starlight  >:
>
> Dear Pymol users,
>
> I've decide to make a copy of this topic from the amber mail
> list because this problem could be solves by ones of the methods
> implemented in Pymol.
>
> Here I'm facing with the problem of the preparation of
> protein-ligand complexes for amber md simulation:
> Following amber's tutorial I've made parametrization of the
> ligand using antechamber obtaining ligand.frcmod and ligand.lib
> files consisted of the parameters for my ligand and its
> coordinates in mol2 associated with those topologies. Now I'd
> like to dock this ligand to the active site of the receptor
> using autodock vina and make further tleap processing of
> complex.pdb produced by autodock to obtain all input data for
> simulation. Here some problems: because (superimposed to the
> receptor cavity) ligand.pdb produced by autodock have been
> stripped from all hydrogen’s so its coordinates not equal to
> initial ligand.mol2 . How do you think will it possible to use
> some method of the ligand superimposition to superimpose initial
> ligand.mol2 (with correct corrdinates) agains docking pose
> produced by vina and use superimposed ligand.mol2 for the
> preparation of my complex?
>
> Thanks for help,
>
> James
>
> 
> --
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> 
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> ___
> 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/

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[James Starlight]

Hi Fotis,

thank you very much for the suggestion!

Indeed I have not had such problem with the preparation structure for NAMD
but in case of amber its really exist (the structure of the ligand provided
in the complex with the receptor.pdb must be EXACTLY the same as it was
previously parametrized using some amber program called antechamber).
So I will be interesting in two options
1) to find some shell utility for superimposition of the 2 ligands in
one-style command (because here I'm dealing with some script and I need to
do it in loop many times)
or (which is better!)

2) use pdb2pqr software (because I'm using it in the part of this script to
process complex and to add hydrogens to ligand as well)- here I noticed
that ligand should be provided as the separate .mol2 file (not pdb)- which
is a bit not comfortable for me (because I obained all docking poses from
VINA as the pdb). I guess I should here to put ligand from complex, to
convert it to mol2 and proceed 2 files (receptor and ligand) to the
pdb2pqr. But may be the better solution is exist?

James



2014-09-17 12:32 GMT+02:00 Fotis Baltoumas :

> Hello James,
> You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or the
> pair_fit command to superimpose small molecules. It's not as
> straightforward as protein super/align, since you have to define the atom
> pairs that will be superimposed, but it's fairly easy. After that, just
> make a selection of your receptor and your new ligand and save it as a
> molecule.
>
> However, I don't think you really have a problem here. Since the only
> issue you mention is the lack of hydrogen atoms, couldn't you just
> reintroduce them through some function in the AmberTools? I have no
> experience with Amber parameterization tools but, if they're even remotely
> like the PSF makers for CHARMM/X-PLOR/NAMD, then they can add hydrogen
> atoms for you easily.
> Another option would be to create a PQR file, either through PDB2PQR (
> http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools GUI in
> PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can
> use AMBER parameters both for proteins and for ligands (mol2 format). Your
> result would be the structure of your complex, with hydrogens, in the AMBER
> format.
>
> Hope I helped,
> Fotis Baltoumas
>
> 2014-09-17 13:01 GMT+03:00 James Starlight :
>
>> Dear Pymol users,
>>
>> I've decide to make a copy of this topic from the amber mail list because
>> this problem could be solves by ones of the methods implemented in Pymol.
>>
>> Here I'm facing with the problem of the preparation of protein-ligand
>> complexes for amber md simulation:
>> Following amber's tutorial I've made parametrization of the ligand using
>> antechamber obtaining ligand.frcmod and ligand.lib files consisted of the
>> parameters for my ligand and its coordinates in mol2 associated with those
>> topologies. Now I'd like to dock this ligand to the active site of the
>> receptor using autodock vina and make further tleap processing  of
>> complex.pdb produced by autodock to obtain all input data for simulation.
>> Here some problems: because (superimposed to the receptor cavity)
>> ligand.pdb produced by autodock have been stripped from all hydrogen’s so
>> its coordinates not equal to initial ligand.mol2 . How do you think will it
>> possible to use some method of the ligand superimposition to superimpose
>> initial ligand.mol2 (with correct corrdinates) agains docking pose produced
>> by vina and use superimposed ligand.mol2 for the preparation of my complex?
>>
>> Thanks for help,
>>
>> James
>>
>>
>> --
>> Want excitement?
>> Manually upgrade your production database.
>> When you want reliability, choose Perforce
>> Perforce version control. Predictably reliable.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>> ___
>> 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
>>
>
>
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk___
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

Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

[Fotis Baltoumas]

Hello James,
You can use the Pair Fitting wizard (Menu: Wizards=>Pair Fitting) or the
pair_fit command to superimpose small molecules. It's not as
straightforward as protein super/align, since you have to define the atom
pairs that will be superimposed, but it's fairly easy. After that, just
make a selection of your receptor and your new ligand and save it as a
molecule.

However, I don't think you really have a problem here. Since the only issue
you mention is the lack of hydrogen atoms, couldn't you just reintroduce
them through some function in the AmberTools? I have no experience with
Amber parameterization tools but, if they're even remotely like the PSF
makers for CHARMM/X-PLOR/NAMD, then they can add hydrogen atoms for you
easily.
Another option would be to create a PQR file, either through PDB2PQR (
http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools GUI in
PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can
use AMBER parameters both for proteins and for ligands (mol2 format). Your
result would be the structure of your complex, with hydrogens, in the AMBER
format.

Hope I helped,
Fotis Baltoumas

2014-09-17 13:01 GMT+03:00 James Starlight :

> Dear Pymol users,
>
> I've decide to make a copy of this topic from the amber mail list because
> this problem could be solves by ones of the methods implemented in Pymol.
>
> Here I'm facing with the problem of the preparation of protein-ligand
> complexes for amber md simulation:
> Following amber's tutorial I've made parametrization of the ligand using
> antechamber obtaining ligand.frcmod and ligand.lib files consisted of the
> parameters for my ligand and its coordinates in mol2 associated with those
> topologies. Now I'd like to dock this ligand to the active site of the
> receptor using autodock vina and make further tleap processing  of
> complex.pdb produced by autodock to obtain all input data for simulation.
> Here some problems: because (superimposed to the receptor cavity)
> ligand.pdb produced by autodock have been stripped from all hydrogen’s so
> its coordinates not equal to initial ligand.mol2 . How do you think will it
> possible to use some method of the ligand superimposition to superimpose
> initial ligand.mol2 (with correct corrdinates) agains docking pose produced
> by vina and use superimposed ligand.mol2 for the preparation of my complex?
>
> Thanks for help,
>
> James
>
>
> --
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> ___
> 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
>
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk___
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