PyMOL Molecular Graphics System

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

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! 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

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

Thanks!

2012/1/31 Thomas Holder <speleo3@...>:
> 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 found a solution!
With openbabel a pdb without residue names and numbers can be easily fixed:
1. babel file.pdb file.mol
2. babel file.mol file.pdb

Et voila! Now you have a pdb with repaired residue names!

2012/1/31 Андрей Гончар <gontchar@...>:
> Thanks!
>
> 2012/1/31 Thomas Holder <speleo3@...>:
>> 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



-- 

Андрей Гончар