[PyMOL] Coordinates of ligand-binding site
Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sites ( e.g if i visualize ligand binding site by means of Pymol itself ). Thx for help James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
I'm thinking a good work around is simply this. Select the binding site of the amino acids and ligand in pymol. Then copy those selected aa's and atoms to another object: save -> model -> copied_object as output.pdb output.pdb will then contain all the x,y,z coordinates of only what was selected. Then just get those columns and upload them to swiss dock. Jordan On Jul 18, 2012, at 2:23 AM, James Starlight wrote: > Dear PyMol users! > > > Some of docking servers (e.g swiss dock) which I'm using need in > explicit definition of the coordinates (in XYZ) of the docking region > as well as coordinates of its COM. How I could obtain such coordinates > of intrested pdb file based on the knowing protein-ligand interaction > sites ( e.g if i visualize ligand binding site by means of Pymol > itself ). > > > Thx for help > > > James > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
Jordan, Thank you for advise. I've tried to do the same already but 1- In Resulted pbd file ( with ligand and surrounded residues only) the coordinates of ligand and residues have been changed in comparison to the initial pdb/ How to prevent it? 2- The resulted pdb consist of coordinates of each atoms but how to define the proper coordinates of ligand-binding BOX based on that point coordinates? James 2012/7/18 Jordan Willis : > I'm thinking a good work around is simply this. > > > Select the binding site of the amino acids and ligand in pymol. > > Then copy those selected aa's and atoms to another object: > save -> model -> copied_object as output.pdb > > output.pdb will then contain all the x,y,z coordinates of only what was > selected. > > Then just get those columns and upload them to swiss dock. > > Jordan > > > > > > > > On Jul 18, 2012, at 2:23 AM, James Starlight wrote: > >> Dear PyMol users! >> >> >> Some of docking servers (e.g swiss dock) which I'm using need in >> explicit definition of the coordinates (in XYZ) of the docking region >> as well as coordinates of its COM. How I could obtain such coordinates >> of intrested pdb file based on the knowing protein-ligand interaction >> sites ( e.g if i visualize ligand binding site by means of Pymol >> itself ). >> >> >> Thx for help >> >> >> James >> >> -- >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> ___ >> 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 > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
Hi James,
the "get_extent" command in PyMOL will give you the corners of the
selected region, from which you easily can calculate center and edge
lengths.
http://pymolwiki.org/index.php/Get_extent
Example:
box = cmd.get_extent('sele')
print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)]
print 'Size:', [(b-a) for (a,b) in zip(*box)]
Regarding your issue (1-): Coordinates should not change unless you
align to some other molecule.
Cheers,
Thomas
On 07/18/2012 09:37 AM, James Starlight wrote:
> Jordan,
>
> Thank you for advise.
>
> I've tried to do the same already but
>
> 1- In Resulted pbd file ( with ligand and surrounded residues only)
> the coordinates of ligand and residues have been changed in
> comparison to the initial pdb/ How to prevent it?
>
> 2- The resulted pdb consist of coordinates of each atoms but how to
> define the proper coordinates of ligand-binding BOX based on that
> point coordinates?
>
> James
>
> 2012/7/18 Jordan Willis :
>> I'm thinking a good work around is simply this.
>>
>>
>> Select the binding site of the amino acids and ligand in pymol.
>>
>> Then copy those selected aa's and atoms to another object:
>> save -> model -> copied_object as output.pdb
>>
>> output.pdb will then contain all the x,y,z coordinates of only what was
>> selected.
>>
>> Then just get those columns and upload them to swiss dock.
>>
>> Jordan
>>
>>
>> On Jul 18, 2012, at 2:23 AM, James Starlight wrote:
>>
>>> Dear PyMol users!
>>>
>>>
>>> Some of docking servers (e.g swiss dock) which I'm using need in
>>> explicit definition of the coordinates (in XYZ) of the docking region
>>> as well as coordinates of its COM. How I could obtain such coordinates
>>> of intrested pdb file based on the knowing protein-ligand interaction
>>> sites ( e.g if i visualize ligand binding site by means of Pymol
>>> itself ).
>>>
>>>
>>> Thx for help
>>>
>>>
>>> James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Re: [PyMOL] Editing of the pdb structure
Dear all! I have input multi state structure consisted of protein in one state and ligand in the second state generated by Chimera. I want to merge both of that objects in one common object. How I could do it? James 2012/7/18 James Starlight : > Dear all! > > > I have input multi state structure consisted of protein in one state > and ligand in the second state generated by Chimera. I want to merge > both of that objects in one common object. How I could do it? > > > James > > 2012/4/30 Thomas Holder : >> Hi James and Joel, >> >> I would use a homology modeling tool to add missing atoms (basically rebuild >> the structure, given the incomplete structure as template). >> >> Examples for web servers: >> * http://toolkit.tuebingen.mpg.de/modeller >> * http://swissmodel.expasy.org/ >> >> pdb2pqr can also add a limited number of missing atoms, see >> http://www.poissonboltzmann.org/pdb2pqr/d/web-servers >> >> >> Hope that helps. >> >> Cheers, >> Thomas >> >> Joel Tyndall wrote, On 04/30/12 00:07: >> >>> Surely you could use pymol mutagenesis wizard to do tis. >>> >>> Also James, It is a good practice to start a new thread (new email with >>> new subject for each set of questions you have >>> >>> Regards >>> >>> Joel >>> >>> From: James Starlight [mailto:jmsstarli...@gmail.com] >>> Sent: Friday, 27 April 2012 8:25 p.m. >>> To: pymol-users >>> Subject: Re: [PyMOL] Editing of the pdb structure >>> >>> Dear all! >>> >>> I want to prepare my pdb structure for MD simulation. I've done all >>> required things but my protein consist of some missing heavy atoms the list >>> of which I've obtained from my pdb hedader >>> >>> REMARK 470 M RES CSSEQI ATOMS >>> REMARK 470 ARG A 220CG CD NE CZ NH1 NH2 >>> REMARK 470 ARG A 222CG CD NE CZ NH1 NH2 >>> REMARK 470 ASN B 212OCG OD1 ND2 >>> REMARK 470 LYS C 43CG CD CE NZ >>> REMARK 470 GLY C 225O >>> I've heard that there are some web servers wich could be usefull to build >>> such missing atoms. >>> In particular in my structure there are lack not only side chain atoms but >>> also two backbone Oxygens in the Gly and Asn wich could be the main problem >>> of such task. >>> >>> In any case I'll be very thankfull if you provide me with such server >>> James >> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
