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

[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
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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.
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>
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Re: [PyMOL] naming of chain id

[Spencer Bliven]

Are there plans to support 4-letter chain IDs, as defined by the current
xPDB/mmCIF specification?

-Spencer

On Tue, Sep 16, 2014 at 3:36 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Folmer and Yeping,
>
> to support upper and lower case letters, set this setting:
>
> PyMOL> set ignore_case, off
>
> Cheers,
>   Thomas
>
> On 16 Sep 2014, at 02:44, Folmer Fredslund  wrote:
> > Hi Yeping Sun,
> >
> > Did you solve your problem?
> >
> > According to http://www.wwpdb.org/procedure.html#toc_4
> > "
> > What is the maximum number of chain IDs in a file?
> >
> > Up to 62 chains can be included in the PDB entry. Upper case letters and
> numbers (0-9) should be used first for chain IDs. Lower case letters should
> be used only after all upper letters and numbers have been used. Symbols
> should never be used for chain IDs."
> >
> > you can use numbers and also small letters in the PDB file format.
> >
> >
> >
> > I don't know if PyMOL will let you do this, though.
> >
> > Regards,
> >
> > Folmer
> >
> >
> > 2014-09-02 10:41 GMT+02:00 sunyeping :
> > I have a protein which contains 32 chains. By using A-Z can only name 26
> chains. Can I use expression containing two character such as A1, AB, etc.
> to as chain id? Will this change the format of the pdb files?
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences
> >
> > --
> > Folmer Fredslund
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>
>
> --
> Want excitement?
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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
>>
>
>
--
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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]

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

[PyMOL] Pymol for iPad: is a custom URL scheme in use?

[Sula Armstrong]

Hello PyMol users

Is there a way to launch PyMol on the iPad [from another application] 
specifying additional parameters, e.g. a pdb code so that the app picks up the 
RCSB's PDB and takes you straight to the view?

E.g. .is there a custom URL scheme in use, like pymol://?PDB= that would 
permit this? 

Many thanks in advance for any advice.

Sula Armstrong
Business Analyst, Strategic Innovation Group
Royal Society of Chemistry
Thomas Graham House,
Science Park, Milton Road
Cambridge, CB4 0WF, UK

DISCLAIMER:

This communication (including any attachments) is intended for the use of the 
addressee only and may contain confidential, privileged or copyright material. 
It may not be relied upon or disclosed to any other person without the consent 
of the RSC. If you have received it in error, please contact us immediately. 
Any advice given by the RSC has been carefully formulated but is necessarily 
based on the information available, and the RSC cannot be held responsible for 
accuracy or completeness. In this respect, the RSC owes no duty of care and 
shall not be liable for any resulting damage or loss. The RSC acknowledges that 
a disclaimer cannot restrict liability at law for personal injury or death 
arising through a finding of negligence. The RSC does not warrant that its 
emails or attachments are Virus-free: Please rely on your own screening. The 
Royal Society of Chemistry is a charity, registered in England and Wales, 
number 207890 - Registered office: Thomas Graham House, Science Park, Mi
 lton Road, Cambridge CB4 0WF

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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]

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 

[PyMOL] List

[EVERLY FLEISCHER]

Could you please take my email off the PyMOL user list.

Thanks,

Everly FLEISCHER


Sent from my iPad

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Re: [PyMOL] naming of chain id

[Thomas Holder]

Hi Spencer,

multi-letter chain IDs of arbitrary length will be available in the next PyMOL 
version. It's in fact already available with the latest updates in our 
open-source SVN repository on sourceforge.

Cheers,
  Thomas

On 17 Sep 2014, at 06:36, Spencer Bliven  wrote:

> Are there plans to support 4-letter chain IDs, as defined by the current 
> xPDB/mmCIF specification? 
> 
> -Spencer
> 
> On Tue, Sep 16, 2014 at 3:36 PM, Thomas Holder 
>  wrote:
> Hi Folmer and Yeping,
> 
> to support upper and lower case letters, set this setting:
> 
> PyMOL> set ignore_case, off
> 
> Cheers,
>   Thomas
> 
> On 16 Sep 2014, at 02:44, Folmer Fredslund  wrote:
> > Hi Yeping Sun,
> >
> > Did you solve your problem?
> >
> > According to http://www.wwpdb.org/procedure.html#toc_4
> > "
> > What is the maximum number of chain IDs in a file?
> >
> > Up to 62 chains can be included in the PDB entry. Upper case letters and 
> > numbers (0-9) should be used first for chain IDs. Lower case letters should 
> > be used only after all upper letters and numbers have been used. Symbols 
> > should never be used for chain IDs."
> >
> > you can use numbers and also small letters in the PDB file format.
> >
> >
> >
> > I don't know if PyMOL will let you do this, though.
> >
> > Regards,
> >
> > Folmer
> >
> >
> > 2014-09-02 10:41 GMT+02:00 sunyeping :
> > I have a protein which contains 32 chains. By using A-Z can only name 26 
> > chains. Can I use expression containing two character such as A1, AB, etc. 
> > to as chain id? Will this change the format of the pdb files?
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences
> >
> > --
> > Folmer Fredslund
> 
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Re: [PyMOL] Pymol for iPad: is a custom URL scheme in use?

[Blaine Bell]

Currently right now Mobile PyMOL can be launched using file associations 
and URLs from any application that supports it (i.e., with file 
extensions pse, psw, sdf, mol2, mol, pdb)

We are in the process of releasing a new version of Mobile PyMOL with 
minor fixes and updates to support the newer versions of the PyMOL files.

The URL scheme "pymol://" will be supported in this next version (i.e., 
everything after "pymol://" is treated as a URL, so you need to replace 
a colon with "%3A").  We have not implemented fetch in mobile pymol yet, 
so you will need to supply the URL, not the PDB string.  We will put 
this on the list for the next version.

Blaine

On 9/17/14, 9:56 AM, Sula Armstrong wrote:
> Hello PyMol users
>
> Is there a way to launch PyMol on the iPad [from another application] 
> specifying additional parameters, e.g. a pdb code so that the app picks up 
> the RCSB's PDB and takes you straight to the view?
>
> E.g. .is there a custom URL scheme in use, like pymol://?PDB= that would 
> permit this?
>
> Many thanks in advance for any advice.
>
> Sula Armstrong
> Business Analyst, Strategic Innovation Group
> Royal Society of Chemistry
> Thomas Graham House,
> Science Park, Milton Road
> Cambridge, CB4 0WF, UK
>
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