pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Abhinav and Jason,

> The underlying C-object for a measurement does not support
> iterate/alter. This is rather silly; PyMOL should be able to tell you
> what's in the object.

As an ad-hoc hack, I wrote a Python script to access internal C-object
of distance representation and convert it to atom name.

Save the script to somewhere and

  run script_name.py
  list_dist

will do the job.

Takanori Nakane

=== Script start ===

from pymol import cmd

def parseDistObj(obj):
     if (obj[5][0][3][10] != 1): # 'show dashed' flag
         return ""
     points = obj[5][2][0][1]
     ret = []
     for i in range(len(points) / 6):
         ret.append([(points[i * 6], points[i * 6 + 1], points[i * 6 + 2]),
                     (points[i * 6 + 3], points[i * 6 + 4], points[i * 6 
+ 5])])
     return ret

def list_dist():
     names = cmd.get_session()['names']

     dist_pairs = []
     for obj in names:
         if (obj == None):
             continue
         if (obj[1] == 0 and obj[4] == 4):
             dist_pairs += parseDistObj(obj)

     namespace = {'dict': {}, 'a': 1}
     dict = {}
     cmd.iterate_state(1, 'all', 'dict[x,y,z] = 
chain+"/"+resn+resi+"/"+name' , space=namespace)

     dict = namespace['dict']
     for pair in dist_pairs:
         print dict.get(pair[0], '?') + " - " + dict.get(pair[1], '?')

cmd.extend('list_dist', list_dist)

Hi PyMOLers,
I noticed some strange behaviour when I do the following:
1) Load A.pdb into MacPyMOL via "pymol A.pdb"2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A"
3) Load a completely different structure (must have different number of atoms than A.pdb), B.pdb, into a separate/new instance/window of MacPyMOL via "pymol B.pdb"4) Load a CHARMM simulation trajectory into object "B" via "load B.dcd, B"
Loading of this second trajectory complains with the following error:
ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in the object (4551) did not equal the number of atoms in the 'dcd' (5889) file.

In this error, the number "5889" corresponds to the number of atoms in A.pdb while "4551" corresponds to the number of atoms in B.pdb.  Again, these are two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into the same window).  Somehow, the first instance of PyMOL sees what is happening in the other.
I should mention that in the real example, "A.pdb" and "B.pdb" actually have the same name but are located in different directories (in case it matters).
On a non-Mac machine, these commands are fine.  As an "experienced" PyMOL user, it was quite embarrassing when a set of commands/steps that worked on a Linux workstation does not work on a Mac (especially when I was trying to show the simulations to a VMD user).  I'm fairly new to Macs so maybe there's something that I need to do?
Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem to run "hide all" and "show cartoon" from my .pymolrc.
Any help/suggestions would be greatly appreciated!
Sean 		 	   		  

Gonzalo,

The cartoon representation is a stylized representation of the
structure using backbone atoms as guides. Setting stick_color or
line_color on a cartoon won't help -- you need to show lines or
sticks.  If you need sticks/lines back just type:

show lines, sele

or

show sticks, sele

where "sele" is your selected atoms.

Cheers,

-- Jason

On Tue, Jan 31, 2012 at 3:31 PM, Gonzalo Parra <gon...@ho...> wrote:
> Sorry guys, it's me again.
>
> It worked while I was seeing the structure in lines style, but when I change
> the style to cartoon, the bonds that I set dissapear.. How can I prevent it?
>
> Thanks again, and sorry for beeing that noob.
>
> Gonzalo
>
>> From: jas...@sc...
>> Date: Tue, 31 Jan 2012 15:07:51 -0500
>> Subject: Re: [PyMOL] drawing and formating bonds between atoms
>> To: gon...@ho...
>> CC: pym...@li...
>
>>
>> Gonzalo,
>>
>> Just pick a bond and issue the following setting command to make colored
>> lines:
>>
>> set_bond line_color, yourColor, sele
>>
>> You can also use
>>
>> set_bond stick_color, yourColor, sele
>>
>> for sticks.
>>
>> "sele" should be the two bound atoms.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Tue, Jan 31, 2012 at 1:51 PM, Gonzalo Parra <gon...@ho...>
>> wrote:
>> > Hello everyone,
>> >
>> > I was trying to make a pymol script. I have to draw different lines in
>> > my
>> > pdb structure with different colors.
>> >
>> > So, I find the way to draw a bond between to atoms, for example.
>> >
>> > "bond resi 234 and resn GLU and name CA, resi 259 and resn SER and name
>> > CA"
>> >
>> >
>> > But it always draw the bond with the same color. And I wasn't able to
>> > change
>> > a bond color without changing every bonds color.
>> >
>> >
>> > How can I color one specific bond color, for example just the bond that
>> > bonds resi 234 and resn GLU and name CA and resi 259 and resn SER and
>> > name
>> > CA?
>> >
>> >
>> > Thanks in advance
>> >
>> > Gonzalo
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Keep Your Developer Skills Current with LearnDevNow!
>> > The most comprehensive online learning library for Microsoft developers
>> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> > Metro Style Apps, more. Free future releases when you subscribe now!
>> > http://p.sf.net/sfu/learndevnow-d2d
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Sorry guys, it's me again.
It worked while I was seeing the structure in lines style, but when I change the style to cartoon, the bonds that I set dissapear.. How can I prevent it?
Thanks again, and sorry for beeing that noob.
Gonzalo

> From: jas...@sc...
> Date: Tue, 31 Jan 2012 15:07:51 -0500
> Subject: Re: [PyMOL] drawing and formating bonds between atoms
> To: gon...@ho...
> CC: pym...@li...
> 
> Gonzalo,
> 
> Just pick a bond and issue the following setting command to make colored lines:
> 
> set_bond line_color, yourColor, sele
> 
> You can also use
> 
> set_bond stick_color, yourColor, sele
> 
> for sticks.
> 
> "sele" should be the two bound atoms.
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Tue, Jan 31, 2012 at 1:51 PM, Gonzalo Parra <gon...@ho...> wrote:
> > Hello everyone,
> >
> > I was trying to make a pymol script. I have to draw different lines in my
> > pdb structure with different colors.
> >
> > So, I find the way to draw a bond between to atoms, for example.
> >
> > "bond resi 234 and resn GLU and name CA, resi 259 and resn SER and name CA"
> >
> >
> > But it always draw the bond with the same color. And I wasn't able to change
> > a bond color without changing every bonds color.
> >
> >
> > How can I color one specific bond color, for example just the bond that
> > bonds resi 234 and resn GLU and name CA and resi 259 and resn SER and name
> > CA?
> >
> >
> > Thanks in advance
> >
> > Gonzalo
> >
> >
> > ------------------------------------------------------------------------------
> > Keep Your Developer Skills Current with LearnDevNow!
> > The most comprehensive online learning library for Microsoft developers
> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> > Metro Style Apps, more. Free future releases when you subscribe now!
> > http://p.sf.net/sfu/learndevnow-d2d
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
 		 	   		  

Gonzalo,

Just pick a bond and issue the following setting command to make colored lines:

set_bond line_color, yourColor, sele

You can also use

set_bond stick_color, yourColor, sele

for sticks.

"sele" should be the two bound atoms.

Cheers,

-- Jason


On Tue, Jan 31, 2012 at 1:51 PM, Gonzalo Parra <gon...@ho...> wrote:
> Hello everyone,
>
> I was trying to make a pymol script. I have to draw different lines in my
> pdb structure with different colors.
>
> So, I find the way to draw a bond between to atoms, for example.
>
> "bond resi 234 and resn GLU and name CA, resi 259 and resn SER and name CA"
>
>
> But it always draw the bond with the same color. And I wasn't able to change
> a bond color without changing every bonds color.
>
>
> How can I color one specific bond color, for example just the bond that
> bonds resi 234 and resn GLU and name CA and resi 259 and resn SER and name
> CA?
>
>
> Thanks in advance
>
> Gonzalo
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hello everyone,I was trying to make a pymol script. I have to draw different lines in my pdb structure with different colors.So, I find the way to draw a bond between to atoms, for example."bond resi 234 and resn GLU and name CA, resi 259 and resn SER and name CA"
But it always draw the bond with the same color. And I wasn't able to change a bond color without changing every bonds color.
How can I color one specific bond color, for example just the bond that bonds resi 234 and resn GLU and name CA and resi 259 and resn SER and name CA?
Thanks in advanceGonzalo 		 	   		  

Hi Abhinav,

The underlying C-object for a measurement does not support
iterate/alter. This is rather silly; PyMOL should be able to tell you
what's in the object.

Please file a feature request on the open-source bug tracker and we'll
be sure to look at this ASAP.

Cheers,

-- Jason


On Tue, Jan 31, 2012 at 9:02 AM, Abhinav Verma <abh...@gm...> wrote:
> Hi thanks,
>
>  still it is not the same.. But thanks..
>  I wish Jason can reply if there is any way to get the list from the apply
> command.
>
> thanks,
> Abhi
>
> On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis <te...@gm...>
> wrote:
>>
>> I think you can reproduce the results from "apply->find->polar contacts"
>> option with the PyMOL built-in "distance" command. E.g.
>>
>> distance hbonds, all, all, 3.2, mode=2
>>
>>
>>
>> The problem is that you cannot set the A-H-D angle which is important for
>> the definition of the H-bond.
>>
>>
>>
>> On 30 January 2012 18:45, Abhinav Verma <abh...@gm...> wrote:
>>>
>>> Thanks Thomas,
>>>
>>>  I have been here and my problem is that I could not reproduce the
>>> results of default pymol behaviour. I just need to either reproduce 100% the
>>> pymol default behaviour or to just get a list of what is painted in the
>>> window. It should be possible I guess.
>>>
>>>  Do you have more ideas?
>>>
>>>
>>>
>>>
>>> On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis <te...@gm...>
>>> wrote:
>>>>
>>>> Probably because they set diffently the acceptor-donor cutoff and the
>>>> acceptor-hydrogen-donor angle. Use list_hbonds.py from:
>>>>
>>>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
>>>>
>>>> and set the cutoff and angle to the values you wish.
>>>>
>>>> Thomas
>>>>
>>>>
>>>>
>>>> On 30 January 2012 16:34, Abhinav Verma <abh...@gm...> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>  I am trying to get the list of hbonds formed using
>>>>> Apply-find-polarcontacts.
>>>>>
>>>>>  I searched and found some scripts, but they never give me the same
>>>>> result as the one by default pymol.
>>>>>
>>>>>  Any ideas how I can get the hbonds as a list.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Abhinav
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Try before you buy = See our experts in action!
>>>>> The most comprehensive online learning library for Microsoft developers
>>>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
>>>>> MVC3,
>>>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>>>> http://p.sf.net/sfu/learndevnow-dev2
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyM...@li...)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ======================================================================
>>>>
>>>> Thomas Evangelidis
>>>>
>>>> PhD student
>>>>
>>>> Biomedical Research Foundation, Academy of Athens
>>>>
>>>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>>>
>>>> email: te...@bi...
>>>>
>>>>           te...@gm...
>>>>
>>>>
>>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Try before you buy = See our experts in action!
>>>> The most comprehensive online learning library for Microsoft developers
>>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>>> http://p.sf.net/sfu/learndevnow-dev2
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>>
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: te...@bi...
>>
>>           te...@gm...
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi thanks,

 still it is not the same.. But thanks..
 I wish Jason can reply if there is any way to get the list from the apply
command.

thanks,
Abhi

On Mon, Jan 30, 2012 at 5:53 PM, Thomas Evangelidis <te...@gm...>wrote:

> I think you can reproduce the results from "apply->find->polar contacts"
> option with the PyMOL built-in "distance" command. E.g.
>
> distance hbonds, all, all, 3.2, mode=2
>
> The problem is that you cannot set the A-H-D angle which is important for
> the definition of the H-bond.
>
>
>
> On 30 January 2012 18:45, Abhinav Verma <abh...@gm...> wrote:
>
>> Thanks Thomas,
>>
>>  I have been here and my problem is that I could not reproduce the
>> results of default pymol behaviour. I just need to either reproduce 100%
>> the pymol default behaviour or to just get a list of what is painted in the
>> window. It should be possible I guess.
>>
>>  Do you have more ideas?
>>
>>
>>
>>
>> On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis <te...@gm...>wrote:
>>
>>> Probably because they set diffently the acceptor-donor cutoff and the
>>> acceptor-hydrogen-donor angle. Use list_hbonds.py from:
>>>
>>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
>>>
>>> and set the cutoff and angle to the values you wish.
>>>
>>> Thomas
>>>
>>>
>>>
>>> On 30 January 2012 16:34, Abhinav Verma <abh...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>>  I am trying to get the list of hbonds formed using
>>>> Apply-find-polarcontacts.
>>>>
>>>>  I searched and found some scripts, but they never give me the same
>>>> result as the one by default pymol.
>>>>
>>>>  Any ideas how I can get the hbonds as a list.
>>>>
>>>> Thanks,
>>>>
>>>> Abhinav
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Try before you buy = See our experts in action!
>>>> The most comprehensive online learning library for Microsoft developers
>>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>>> http://p.sf.net/sfu/learndevnow-dev2
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>
>>>
>>>
>>> --
>>>
>>> ======================================================================
>>>
>>> Thomas Evangelidis
>>>
>>> PhD student
>>>
>>> Biomedical Research Foundation, Academy of Athens
>>>
>>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>>
>>> email: te...@bi...
>>>
>>>           te...@gm...
>>>
>>>
>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Try before you buy = See our experts in action!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>> http://p.sf.net/sfu/learndevnow-dev2
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: te...@bi...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>

Thanks!

2012/1/31 Thomas Holder <sp...@us...>:
> I put a script on the PyMOLWiki that does renumbering based connectivity:
>
> http://pymolwiki.org/index.php/Renumber
>
> Cheers,
>  Thomas
>
>
> On 01/30/2012 02:52 PM, Thomas Holder wrote:
>>
>> On 01/30/2012 02:24 PM, gontchar andrey wrote:
>>>
>>> Thanks a lot!
>>> A very useful script, but not exactly that I need...
>>> In my pdb file residues are not numbered. I think that I have to
>>> determine amino acids only by atom sequence and connetcions... This
>>> problem is a little more complicated than assigning names to numbered
>>> residues, I think...
>>> Do you think, is it possible?
>>
>>
>> this is indeed more complicated. A simple heuristic would be to assume
>> that the first atom in a residue is always "N". I added a
>> "set_numbering" function to the script, maybe this works for you?
>>
>> Example:
>>
>> set_numbering myobj
>> set_sequence CDEFGHIKL, myobj
>>
>> Cheers,
>> Thomas
>>
>>> On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
>>>>
>>>> Hi Andrey,
>>>>
>>>> I have a script that updates the sequence based on residue numbering
>>>> (resi). See attachment.
>>>>
>>>> Usage: set_sequence sequence [, selection [, start ]]
>>>>
>>>> Example:
>>>>
>>>> # import script
>>>> run setseq.py
>>>>
>>>> # create a poly-ala peptide
>>>> fab AAAAAAAAA, myobj
>>>>
>>>> # set new sequence
>>>> set_sequence CDEFGHIKL, myobj
>>>>
>>>> # update sequence viewer
>>>> rebuild
>>>>
>>>> Cheers,
>>>> Thomas
>>>>
>>>> On 01/30/2012 01:38 PM, gontchar andrey wrote:
>>>>>
>>>>> Hi.
>>>>> We have a pdb-file of a small sequence of aminoacids. In this file
>>>>> there are atom names, atom coordinates, connects etc. except residue
>>>>> names records. Sure we can try to write them manually, but I'd like
>>>>> to know if there is some tool to do this automatically?
>>>>>
>>>>> --
>>>>>
>>>>> Andrey
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen



-- 

Андрей Гончар

I put a script on the PyMOLWiki that does renumbering based connectivity:

http://pymolwiki.org/index.php/Renumber

Cheers,
   Thomas

On 01/30/2012 02:52 PM, Thomas Holder wrote:
> On 01/30/2012 02:24 PM, gontchar andrey wrote:
>> Thanks a lot!
>> A very useful script, but not exactly that I need...
>> In my pdb file residues are not numbered. I think that I have to
>> determine amino acids only by atom sequence and connetcions... This
>> problem is a little more complicated than assigning names to numbered
>> residues, I think...
>> Do you think, is it possible?
>
> this is indeed more complicated. A simple heuristic would be to assume
> that the first atom in a residue is always "N". I added a
> "set_numbering" function to the script, maybe this works for you?
>
> Example:
>
> set_numbering myobj
> set_sequence CDEFGHIKL, myobj
>
> Cheers,
> Thomas
>
>> On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
>>> Hi Andrey,
>>>
>>> I have a script that updates the sequence based on residue numbering
>>> (resi). See attachment.
>>>
>>> Usage: set_sequence sequence [, selection [, start ]]
>>>
>>> Example:
>>>
>>> # import script
>>> run setseq.py
>>>
>>> # create a poly-ala peptide
>>> fab AAAAAAAAA, myobj
>>>
>>> # set new sequence
>>> set_sequence CDEFGHIKL, myobj
>>>
>>> # update sequence viewer
>>> rebuild
>>>
>>> Cheers,
>>> Thomas
>>>
>>> On 01/30/2012 01:38 PM, gontchar andrey wrote:
>>>> Hi.
>>>> We have a pdb-file of a small sequence of aminoacids. In this file
>>>> there are atom names, atom coordinates, connects etc. except residue
>>>> names records. Sure we can try to write them manually, but I'd like
>>>> to know if there is some tool to do this automatically?
>>>>
>>>> --
>>>>
>>>> Andrey

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

I think you got your answers from the AMBER and GROMACS mailing list :)

Just a comment about PRODRG server, it is not the best choice for geometry
optimization and charge calculation.

Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations
for Building GROMOS-Compatible Small Molecule Topologies. *J. Chem. Inf.
Model.* *50* (12): 2221-2235.

To our experience in the group it tends to define the "charge groups"
inaccurately and produce optimized geometries that have out of plane
hydrogens. There is a new online service for creating GROMOS compatible
topologies for organic compounds:

http://compbio.biosci.uq.edu.au/atb/

It uses a knowledge-based approach and higher level QM calculations for
geometry optimization and charge derivation. Yet the GROMOS ffs are united
atom thus you lose in resolution.

If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the
protein and GAFF for the organic compound (your chromophore). Unless you
have problems with the size of the organic molecule, you could optimize its
geometry and calculate RESP charges using the R.E.D. server:

http://q4md-forcefieldtools.org/REDS/

Also check out the option "Use RED IV for automatically generating amino
acid fragments " since your chromophore is covalently bonded to the protein
(I never used it so I am not sure if this will do your job).


Thomas



On 30 January 2012 14:16, James Starlight <jms...@gm...> wrote:

> Thomas,
>
> It's a big protein with the some non-standart functional group like GFP
>
> So the servers like PRORG are not good for that because of big size of the
> protein and subsiquent integration of both fragments.
>
> James
>
>
> 2012/1/30 Thomas Evangelidis <te...@gm...>
>
>> Is it a small organic molecule or a modified amino acid within the
>> context of a protein?
>>
>>
>>
>> 2012/1/29 Tim Schulte <tim...@ki...>
>>
>>>  Dear James,
>>> I agree with Joao, for fast and dirty minimisation you might try the
>>> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
>>> molecule the Prodrg server is the way to go.
>>> Cheers,
>>> Tim
>>>  ------------------------------
>>> *Von:* João Rodrigues [an...@gm...]
>>> *Gesendet:* Freitag, 27. Januar 2012 09:56
>>> *Bis:* James Starlight
>>> *Cc:* pym...@li...
>>> *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
>>> AMBERTOOLS or MODELLER, depending on what you want to model, or any other
>>> "real" simulation/modelling package otherwise your results are very weak...
>>>
>>>  My opinion only.
>>>
>>> João [...] Rodrigues
>>> http://nmr.chem.uu.nl/~joao
>>>
>>>
>>>
>>> No dia 27 de Janeiro de 2012 09:50, James Starlight <
>>> jms...@gm...> escreveu:
>>>
>>>> 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 benzol) because of long distance between adj atoms.
>>>>
>>>> How I could optimise geometry of the new mollecule? Have pymol some
>>>> built-in functions like conformational search be means of monte carlo or
>>>> energy minimisation ?
>>>>
>>>>
>>>> James
>>>>
>>>>
>>>> 2012/1/27 Thomas Holder <sp...@us...>
>>>>
>>>>>  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: " rel="nofollow">http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
>>>>> :-)
>>>>>
>>>>> The atoms must both be within the same object.
>>>>>
>>>>>
>>>>> Cheers,
>>>>>  Thomas
>>>>>
>>>>> --
>>>>> Thomas Holder
>>>>> MPI for Developmental Biology
>>>>> Spemannstr. 35
>>>>> D-72076 Tübingen
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Try before you buy = See our experts in action!
>>>> The most comprehensive online learning library for Microsoft developers
>>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
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>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Try before you buy = See our experts in action!
>>> The most comprehensive online learning library for Microsoft developers
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>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: te...@bi...
>>
>>           te...@gm...
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Try before you buy = See our experts in action!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
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>> _______________________________________________
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>> Archives: http://www.mail-archive.com/pym...@li...
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>
>


-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: te...@bi...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

I think you can reproduce the results from "apply->find->polar contacts"
option with the PyMOL built-in "distance" command. E.g.

distance hbonds, all, all, 3.2, mode=2

The problem is that you cannot set the A-H-D angle which is important for
the definition of the H-bond.


On 30 January 2012 18:45, Abhinav Verma <abh...@gm...> wrote:

> Thanks Thomas,
>
>  I have been here and my problem is that I could not reproduce the results
> of default pymol behaviour. I just need to either reproduce 100% the pymol
> default behaviour or to just get a list of what is painted in the window.
> It should be possible I guess.
>
>  Do you have more ideas?
>
>
>
>
> On Mon, Jan 30, 2012 at 5:38 PM, Thomas Evangelidis <te...@gm...>wrote:
>
>> Probably because they set diffently the acceptor-donor cutoff and the
>> acceptor-hydrogen-donor angle. Use list_hbonds.py from:
>>
>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
>>
>> and set the cutoff and angle to the values you wish.
>>
>> Thomas
>>
>>
>>
>> On 30 January 2012 16:34, Abhinav Verma <abh...@gm...> wrote:
>>
>>> Hi,
>>>
>>>  I am trying to get the list of hbonds formed using
>>> Apply-find-polarcontacts.
>>>
>>>  I searched and found some scripts, but they never give me the same
>>> result as the one by default pymol.
>>>
>>>  Any ideas how I can get the hbonds as a list.
>>>
>>> Thanks,
>>>
>>> Abhinav
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Try before you buy = See our experts in action!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
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>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: te...@bi...
>>
>>           te...@gm...
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Try before you buy = See our experts in action!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
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>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>


-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: te...@bi...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

Hi Nami,

You want http://www.pymolwiki.org/index.php/Ball_and_Stick

Katherine

On Mon, Jan 30, 2012 at 10:46 AM, nami sugiyama
<su...@ma...>wrote:

> Hi,
>
> We would like to visualize the protein structure at the atoms level,
> by visualizing atoms as "balls" and the bonds between them as
> "sticks". Is there a way??
>
> Nami
>
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

You can set something like this:

set sphere_scale, 0.2
set stick_radius, 0.15
show spheres
show sticks


I usually use lines for the bonds though.

Best,

João

Hi,

We would like to visualize the protein structure at the atoms level,  
by visualizing atoms as "balls" and the bonds between them as  
"sticks". Is there a way??

Nami

Probably because they set diffently the acceptor-donor cutoff and the
acceptor-hydrogen-donor angle. Use list_hbonds.py from:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

and set the cutoff and angle to the values you wish.

Thomas



On 30 January 2012 16:34, Abhinav Verma <abh...@gm...> wrote:

> Hi,
>
>  I am trying to get the list of hbonds formed using
> Apply-find-polarcontacts.
>
>  I searched and found some scripts, but they never give me the same result
> as the one by default pymol.
>
>  Any ideas how I can get the hbonds as a list.
>
> Thanks,
>
> Abhinav
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: te...@bi...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

On Mon, Jan 30, 2012 at 6:05 AM, Hong ZHAN <hz...@bi...> wrote:
> I am a new guy in this area.. And I just want to know how to build a structure model of my protein from homologues crystal structure and protein seq.???

You probably want to try using a homology modeling server for this
rather than PyMOL:

http://robetta.bakerlab.org/
https://modbase.compbio.ucsf.edu/scgi/modweb.cgi
http://swissmodel.expasy.org/

However, the "Mutagenesis Wizard" in PyMOL may be suitable for simple
editing if the only differences between your sequence and the crystal
structure is point mutations.

-Nat

Try MODELLER.

Hi everyone, 

I am a new guy in this area.. And I just want to know how to build a structure model of my protein from homologues crystal structure and protein seq.???

Thx

Hong
Sincerely, 

Hi,

 I am trying to get the list of hbonds formed using
Apply-find-polarcontacts.

 I searched and found some scripts, but they never give me the same result
as the one by default pymol.

 Any ideas how I can get the hbonds as a list.

Thanks,

Abhinav

Thanks! I'll try it!
On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
> Hi Andrey,
> 
> I have a script that updates the sequence based on residue numbering
> (resi). See attachment.
> 
> Usage: set_sequence sequence [, selection [, start ]]
> 
> Example:
> 
> # import script
> run setseq.py
> 
> # create a poly-ala peptide
> fab AAAAAAAAA, myobj
> 
> # set new sequence
> set_sequence CDEFGHIKL, myobj
> 
> # update sequence viewer
> rebuild
> 
> Cheers,
>   Thomas
> 
> On 01/30/2012 01:38 PM, gontchar andrey wrote:
> >Hi.
> >We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically?
> >
> >--
> >
> >Andrey
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen

On 01/30/2012 02:24 PM, gontchar andrey wrote:
> Thanks a lot!
> A very useful script, but not exactly that I need...
> In my pdb file residues are not numbered. I think that I have to determine amino acids only by atom sequence and connetcions... This problem is a little more complicated than assigning names to numbered residues, I think...
> Do you think, is it possible?

this is indeed more complicated. A simple heuristic would be to assume 
that the first atom in a residue is always "N". I added a 
"set_numbering" function to the script, maybe this works for you?

Example:

set_numbering myobj
set_sequence CDEFGHIKL, myobj

Cheers,
   Thomas

> On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
>> Hi Andrey,
>>
>> I have a script that updates the sequence based on residue numbering
>> (resi). See attachment.
>>
>> Usage: set_sequence sequence [, selection [, start ]]
>>
>> Example:
>>
>> # import script
>> run setseq.py
>>
>> # create a poly-ala peptide
>> fab AAAAAAAAA, myobj
>>
>> # set new sequence
>> set_sequence CDEFGHIKL, myobj
>>
>> # update sequence viewer
>> rebuild
>>
>> Cheers,
>>    Thomas
>>
>> On 01/30/2012 01:38 PM, gontchar andrey wrote:
>>> Hi.
>>> We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically?
>>>
>>> --
>>>
>>> Andrey

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

Thanks a lot! 
A very useful script, but not exactly that I need...
In my pdb file residues are not numbered. I think that I have to determine amino acids only by atom sequence and connetcions... This problem is a little more complicated than assigning names to numbered residues, I think... 
Do you think, is it possible?

On Mon, Jan 30, 2012 at 01:59:59PM +0100, Thomas Holder wrote:
> Hi Andrey,
> 
> I have a script that updates the sequence based on residue numbering
> (resi). See attachment.
> 
> Usage: set_sequence sequence [, selection [, start ]]
> 
> Example:
> 
> # import script
> run setseq.py
> 
> # create a poly-ala peptide
> fab AAAAAAAAA, myobj
> 
> # set new sequence
> set_sequence CDEFGHIKL, myobj
> 
> # update sequence viewer
> rebuild
> 
> Cheers,
>   Thomas
> 
> On 01/30/2012 01:38 PM, gontchar andrey wrote:
> >Hi.
> >We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically?
> >
> >--
> >
> >Andrey
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen

Hi Andrey,

I have a script that updates the sequence based on residue numbering 
(resi). See attachment.

Usage: set_sequence sequence [, selection [, start ]]

Example:

# import script
run setseq.py

# create a poly-ala peptide
fab AAAAAAAAA, myobj

# set new sequence
set_sequence CDEFGHIKL, myobj

# update sequence viewer
rebuild

Cheers,
   Thomas

On 01/30/2012 01:38 PM, gontchar andrey wrote:
> Hi.
> We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically?
>
> --
>
> Andrey

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

Hi.
We have a pdb-file of a small sequence of aminoacids. In this file there are atom names, atom coordinates, connects etc. except residue names records. Sure we can try to write them manually, but I'd like to know if there is some tool to do this automatically?

--

Andrey