: 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
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
Dear PyMol users!
I have some structure.pdb from the md simulation wich consist of 1 chain
not defined in the pdb file explicitly ( missing chain id in the pdb file).
So the pymol recognise that chain as the ' ' . I need to rename this
chain to the desired name ( e.g to chain A ).
How I could
Hi James,
use the alter command:
alter chain , chain=A
See also http://pymolwiki.org/index.php/Alter
Cheers,
Thomas
James Starlight wrote, On 04/26/12 09:18:
Dear PyMol users!
I have some structure.pdb from the md simulation wich consist of 1 chain
not defined in the pdb file
Thanks Thomas!
Another question-
I have my protein.pdb with some inserted crystall waters within protein
interiour as well as water surrounded of my protein. I want to remove only
sorrounding water but prevent internal water ( wich could be functional
relevant ).
How I could to select such
Hi all :)
Recently I've been needed to parametrise my short protein mollecule by ATB
server for futher MD simulation.
The input pdb file for that server must consist of CONNECT records at the
bottom of such pdb.
How I could add such missing CONNECT records for my pdb ?
I've tried
set
Hi James,
connect_mode is for loading. I think pdb_conect_all is what you are
looking for:
set pdb_conect_all
http://www.pymolwiki.org/index.php/Pdb_Conect_All
http://www.pymolwiki.org/index.php/Connect_mode
Cheers,
Thomas
James Starlight wrote, On 03/30/12 11:53:
Hi all :)
Recently
Hi James,
Pymol adds a TER statement at the end of each continuous piece of the protein.
Cheers,
Tsjerk
2012/3/21 James Starlight jmsstarli...@gmail.com:
Hi Tsjerk,
I'm not quite understood if pymol adds TER enty after residues wich consist
of missing atoms or in the place with the missing
Hi James,
set pdb_use_ter_records, 0
This will not use TER records at all.
Cheers,
Thomas
On 03/20/2012 08:07 AM, James Starlight wrote:
Dear PyMol users!
After editing of my pdb files by means of PyMol I've noticed that some
of my structures contain of wrong TER enties in the body of
Hi James,
In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong. Yeah, they might be
the same chain, but
On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote:
In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong.
Hi Thomas,
'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument is,
that the answer given (with TER statements) is not wrong, but from a
chemical
Shucks! So much for trying to keep the developer out of the wind. But
he's a wrongdoer by PDB definitions anyway! So it would be best to
modify the behaviour concerning writing of TER records. Feel free to
file it as suggestion.
Gotta love polemics! -- Next time I'll manage, David. Next time...
On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Thomas,
'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument
molecule the Prodrg server is the way to go.
Cheers,
Tim
--
*Von:* João Rodrigues [anar...@gmail.com]
*Gesendet:* Freitag, 27. Januar 2012 09:56
*Bis:* James Starlight
*Cc:* pymol-users@lists.sourceforge.net
*Betreff:* Re: [PyMOL] Editing of the pdb structure
Dear
--
*Von:* João Rodrigues [anar...@gmail.com]
*Gesendet:* Freitag, 27. Januar 2012 09:56
*Bis:* James Starlight
*Cc:* pymol-users@lists.sourceforge.net
*Betreff:* Re: [PyMOL] Editing of the pdb structure
Dear James,
As someone has told you already, Pymol is a visualization tool
: Freitag, 27. Januar 2012 09:56
Bis: James Starlight
Cc: pymol-users@lists.sourceforge.net
Betreff: Re: [PyMOL] Editing of the pdb structure
Dear James,
As someone has told you already, Pymol is a visualization tool, not a modelling
suite. I guess you would be better off using something like
Dear PyMol users!
I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?
James
--
Try before you buy = See our experts in action!
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On 01/27/2012 09:11 AM, James Starlight wrote:
Dear PyMol users!
I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?
you could have guessed it: http://pymolwiki.org/index.php/Bond
:-)
The atoms must both be within the same object.
Cheers,
Arne, Thomas
Thanks alot. Bond works finw
I'd like just to ask what about geometry optimisation of the new structure
E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from
1.5 A from each other.
When I've create new bond by bond command new ring look like 6memb ( like
Dear James,
As someone has told you already, Pymol is a visualization tool, not a
modelling suite. I guess you would be better off using something like
AMBERTOOLS or MODELLER, depending on what you want to model, or any other
real simulation/modelling package otherwise your results are very
[mailto:jmsstarli...@gmail.com]
Sent: Monday, 14 November 2011 8:44 p.m.
To: Joel Tyndall
Subject: Re: [PyMOL] Editing of the pdb structure
Dear all, thank you for the advises :)
Thomas,
when I've tried to add ACE cap to the N-tem of the first residue
of
my
On Tuesday 10,January,2012 09:43 PM, James Starlight wrote:
Deal all!
I'm intresting about representation of the polarr contacts between
ligand and protein
1) Usually I'm ussing Present- Ligand sites option for that purposes
but in my current case I'm working with GFP where tree residues
November 2011 7:52 a.m.
To: Joel Tyndall
Subject: Re: [PyMOL] Editing of the pdb structure
Another question about working with the structure.
I have structure of the fulerene molecule wich consist of 60 carbon atoms
I switch to the Sequence mode- Atoms and try to select individual carbon
) at the bottom right of the viewer.
** **
Joel
** **
*From:* James Starlight [mailto:jmsstarli...@gmail.com]
*Sent:* Thursday, 17 November 2011 7:52 a.m.
*To:* Joel Tyndall
*Subject:* Re: [PyMOL] Editing of the pdb structure
** **
Another question about working
Hi James,
Recently I've opened such topic but I didnt obtain answer on this
question so I try to paraphrase my task. Also I want to specify this
topic on questions lincked with the processing of pdbs.
1) I need to remove some elements fron my structure described as the
individual
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