pymol-users

[PyMOL] alignment by residue

[sasi k. <sbk...@gm...>]

dear pymol users,

i have a homodimer, with two identical monomers. i would like to know the
rmsd of each residue in the first monomer with respect to each residue in
the second monomer.

i guess pair_fit should give the rmsd.

is there a better command to look at the per residue rmsd.

thank you.

sasi

Re: [PyMOL] alignment by residue

[Thomas H. <sp...@us...>]

Hi Sasi,

for "pair_fit" you have to match all atom pairs manually. I guess what 
you want is "align" on the full monomers and then "rms_cur" (or just 
distance measure) on each CA pair.

Have a look at the "rmsd_b.py" script from
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

It writes per residue deviation to the b-factor column.

Example:

fetch 2hv1, async=0
extract mono2, chain B
align mono2, 2hv1, cycles=0, object=aln
rmsd_b mono2 & aln, 2hv1 & aln
iterate mono2 and name CA, print (resi,b)

Hope that helps.

Cheers,
   Thomas

sasi kodathala wrote, On 12/27/11 01:37:
> dear pymol users,
> 
> i have a homodimer, with two identical monomers. i would like to know 
> the rmsd of each residue in the first monomer with respect to each 
> residue in the second monomer.
> 
> i guess pair_fit should give the rmsd.
> 
> is there a better command to look at the per residue rmsd.
> 
> thank you.
> 
> sasi

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

[PyMOL] sequence file extraction

[Oganesyan, V. <Oga...@Me...>]

I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
=========================
Traceback (most recent call last):
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
    self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
    st = _self.get_fastastr(selection)
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
    if seq.has_key(obj):
AttributeError: 'str' object has no attribute 'has_key'
=========================

Is there now a different way of extracting sequence info in PyMOL?

Thank you.

     Vaheh
To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Re: [PyMOL] sequence file extraction

[Jason V. <jas...@sc...>]

Hi Vaheh,

Thanks for pointing this out. I just fixed this, am testing, and will
push the changes shortly.

Cheers,

-- Jason


On Tue, Dec 27, 2011 at 11:15 AM, Oganesyan, Vaheh
<Oga...@me...> wrote:
> I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
> I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
> =========================
> Traceback (most recent call last):
>   File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
>     self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
>     st = _self.get_fastastr(selection)
>   File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
>     if seq.has_key(obj):
> AttributeError: 'str' object has no attribute 'has_key'
> =========================
>
> Is there now a different way of extracting sequence info in PyMOL?
>
> Thank you.
>
>      Vaheh
> To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
>
> ------------------------------------------------------------------------------
> Write once. Port to many.
> Get the SDK and tools to simplify cross-platform app development. Create
> new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

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

Re: [PyMOL] sequence file extraction

[Oganesyan, V. <Oga...@Me...>]

Never mind. After restarting the computer fasta file is being written.

     Vaheh




-----Original Message-----
From: Oganesyan, Vaheh [mailto:Oga...@Me...]
Sent: Tuesday, December 27, 2011 11:16 AM
To: pym...@li...
Subject: [PyMOL] sequence file extraction

I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
=========================
Traceback (most recent call last):
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
    self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
    st = _self.get_fastastr(selection)
  File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
    if seq.has_key(obj):
AttributeError: 'str' object has no attribute 'has_key'
=========================

Is there now a different way of extracting sequence info in PyMOL?

Thank you.

     Vaheh
To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

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To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Re: [PyMOL] sequence file extraction

[Stefano M. <s....@un...>]

I have got the same problem with pymol 1.5.0.4 and restarting the 
computer is not fixing it.

Any help please?

Thanks

Stefano

Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit :
> Never mind. After restarting the computer fasta file is being written.
>
>       Vaheh
>
>
>
>
> -----Original Message-----
> From: Oganesyan, Vaheh [mailto:Oga...@Me...]
> Sent: Tuesday, December 27, 2011 11:16 AM
> To: pym...@li...
> Subject: [PyMOL] sequence file extraction
>
> I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
> I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
> =========================
> Traceback (most recent call last):
>    File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
>      self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>    File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
>      st = _self.get_fastastr(selection)
>    File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
>      if seq.has_key(obj):
> AttributeError: 'str' object has no attribute 'has_key'
> =========================
>
> Is there now a different way of extracting sequence info in PyMOL?
>
> Thank you.
>
>       Vaheh
> To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
>
> ------------------------------------------------------------------------------
> Write once. Port to many.
> Get the SDK and tools to simplify cross-platform app development. Create
> new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
>
> ------------------------------------------------------------------------------
> Write once. Port to many.
> Get the SDK and tools to simplify cross-platform app development. Create
> new or port existing apps to sell to consumers worldwide. Explore the
> Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
> http://p.sf.net/sfu/intel-appdev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

-- 
Dr. Stefano MARZI
UPR 9002 CNRS-ARN
Université De Strasbourg
IBMC
15 Rue René Descartes
67084 Strasbourg-France
Phone +33 (0)3 88417051
Fax: +33 (0)3 88602218
E-mail: s....@ib...
http://www-ibmc.u-strasbg.fr/arn/Romby/

Re: [PyMOL] sequence file extraction

[Thomas H. <sp...@us...>]

Hi Stefano,

this is a known bug and it has not been fixed yet. A workaround is to 
only save one object at a time to fasta format.

See bug report:
http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546

Cheers,
   Thomas

On 07/24/2012 12:08 PM, Stefano Marzi wrote:
> I have got the same problem with pymol 1.5.0.4 and restarting the
> computer is not fixing it.
>
> Any help please?
>
> Thanks
>
> Stefano
>
> Le 27/12/2011 20:19, Oganesyan, Vaheh a écrit :
>> Never mind. After restarting the computer fasta file is being written.
>>
>>        Vaheh
>>
>>
>> -----Original Message-----
>> From: Oganesyan, Vaheh [mailto:Oga...@Me...]
>> Sent: Tuesday, December 27, 2011 11:16 AM
>> To: pym...@li...
>> Subject: [PyMOL] sequence file extraction
>>
>> I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to extract the sequence info.
>> I'm typing "save objectname.fasta" in old version and get the fasta file. In 1.4.1 it complains
>> =========================
>> Traceback (most recent call last):
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py", line 254, in parse
>>       self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 535, in save
>>       st = _self.get_fastastr(selection)
>>     File "C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py", line 178, in get_fastastr
>>       if seq.has_key(obj):
>> AttributeError: 'str' object has no attribute 'has_key'
>> =========================
>>
>> Is there now a different way of extracting sequence info in PyMOL?
>>
>> Thank you.
>>
>>        Vaheh

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

Re: [PyMOL] sequence file extraction

[Robert C. <rob...@qu...>]

Hi Thomas,

On Tue, 2012-07-24 12:57  EDT,  Thomas Holder
<sp...@us...> wrote:

> Hi Stefano,
> 
> this is a known bug and it has not been fixed yet. A workaround is to 
> only save one object at a time to fasta format.
> 
> See bug report:
> http://sourceforge.net/tracker/?func=detail&aid=3466472&group_id=4546&atid=104546

Another bug (I guess I should report it via the bug tracker) is that if a
structure has multiple conformations (at least at the CA atom), then the
residue appears twice in the sequence.

Cheers,
Rob


-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc