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Ramon Crehuet | 1 Aug 2005 17:32
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[BioPython] Superimposing CA atoms of a chain

       I'd like to superimpose two chains (all atoms from all residues) but 
    calculating the RMS only from CA atoms. That is, I'd like to calculate 
    the transformation matrix for the CA atoms and apply it to all atoms. (A 
    common operation, I guess...)
        Can I do that with the PDB.superimpose module? Otherwise, if I need 
    to use the SVDSuperimpose, can I manipule atom instances or it only 
    works with numeric arrays?
    Thanks,
    Ramon

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Thomas Hamelryck | 1 Aug 2005 17:26
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Re: [BioPython] Superimposing CA atoms of a chain

On Monday 01 August 2005 17:32, Ramon Crehuet wrote:
>        I'd like to superimpose two chains (all atoms from all residues) but
>     calculating the RMS only from CA atoms. That is, I'd like to calculate
>     the transformation matrix for the CA atoms and apply it to all atoms.
> (A common operation, I guess...)
>         Can I do that with the PDB.superimpose module? 

Yes.
Use the PDB.superimpose module to calculate the rotation/translation
for the CA atoms only and then apply these to the atoms you want using the
transform(rotation, translation) method of the atom object.

-Thomas

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Alexander A. Morgan | 2 Aug 2005 22:07
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Re: [BioPython] Changes in NCBI BLAST output format !!??

Hello:
    I've just run into the same problem, and I haven't seen a suggested 
fix go by, so I apologize if this is redundant information, but it seems 
that the files I've been getting from NCBI have a <p> removed from the 
header between the "RID: " line and the "<p>Query" line, and it is just 
a blank line now.  If you edit Bio.Blast.NCBIWWW to not look for the 
"<p>", it seems to work okay.

class _Scanner:
....
   def _scan_header(self, uhandle, consumer):
....

    change:
        attempt_read_and_call(uhandle, consumer.noevent, start='<p>')
    to: 
        attempt_read_and_call(uhandle, consumer.noevent)

aurelie.bornot <at> free.fr wrote:

>Thank you very much Jessica !!!
>
>Unfortunately, I need a lot of thing in the BLAST reports.....
>It will be difficult to do the same thing as you did....
>
>I will try to do something in the code of parser of Python.
>But it will be difficult for me..
>so if you or someone has advices !!!
>
>Thanks a lot again for your answer Jessica !
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Michiel De Hoon | 3 Aug 2005 20:37
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RE: [BioPython] Changes in NCBI BLAST output format !!??

Do you happen to know if this change can break anything else in the Blast
parser? From running Biopython's tests for Blast, it seems that this change
is OK. On the other hand, I don't use Blast much myself, so I don't trust my
own judgement in this matter.
If making this change does not cause any new bugs, I'd be happy to include it
in CVS.

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

-----Original Message-----
From: biopython-bounces <at> portal.open-bio.org on behalf of Alexander A. Morgan
Sent: Tue 8/2/2005 4:07 PM
To: aurelie.bornot <at> free.fr
Cc: biopython <at> biopython.org
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??

Hello:
    I've just run into the same problem, and I haven't seen a suggested 
fix go by, so I apologize if this is redundant information, but it seems 
that the files I've been getting from NCBI have a <p> removed from the 
header between the "RID: " line and the "<p>Query" line, and it is just 
a blank line now.  If you edit Bio.Blast.NCBIWWW to not look for the 
"<p>", it seems to work okay.
(Continue reading)

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Aurélie Bornot | 3 Aug 2005 20:54
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Re: [BioPython] Changes in NCBI BLAST output format !!??

Thank you very much Alexander !!
I didn't dare to change the code in the Bio.Blast.NCBIWWW on my own because
I didn't have time to make tests...
So I simply automatiquely added the <p> in the Blast file... not very nice..
I know !
I will try your method instead !

Thanks !
Aurélie

--------------
Aurelie BORNOT
MNHN
Paris

----- Original Message ----- 
From: "Alexander A. Morgan" <amorgan <at> mitre.org>
To: <aurelie.bornot <at> free.fr>
Cc: <biopython <at> biopython.org>
Sent: Tuesday, August 02, 2005 10:07 PM
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??

> Hello:
>    I've just run into the same problem, and I haven't seen a suggested fix 
> go by, so I apologize if this is redundant information, but it seems that 
> the files I've been getting from NCBI have a <p> removed from the header 
> between the "RID: " line and the "<p>Query" line, and it is just a blank 
> line now.  If you edit Bio.Blast.NCBIWWW to not look for the "<p>", it 
> seems to work okay.
>
(Continue reading)

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Daniel Tomso | 4 Aug 2005 22:40

[BioPython] Blast and multiple processors

Hello, all.

I'm working on improving my BLAST throughput, and I have some questions
about how the program handles multiple processors and multiple
processes.

Specifically, I've been experimenting with using BioPython's
NCBIStandalone to handle 3 or 4 simultaneous blast requests, since my
system has 4 processors.  I spin out the requests via
NCBIStandalone.blastall(blah, blah), then grab the blast_out and
blast_err file handles in a list.  Afterwards, I use blast_out.read() to
collect the reports from each of the 4 processes.

Is this wise and/or efficient?  My execution times do drop off when I
do, say, 4 jobs at a time instead of 1 at a time, so it is helping.  Do
the processor flags for blastall accomplish this more efficiently?

Sorry if this is not specific enough, but any insight would be
welcome!!!!

Dan T.

Daniel J. Tomso

Senior Scientist, Bioinformatics
Athenix Corporation

2202 Ellis Road

Suite B
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Michiel De Hoon | 8 Aug 2005 02:08
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RE: [BioPython] Changes in NCBI BLAST output format !!??

I've updated Biopython in CVS with this fix. See Bio/Blast/NCBIWWW.py
revision 1.41. Please let me know if you find any problems. Thanks for
finding this solution.

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

-----Original Message-----
From: Alexander A. Morgan [mailto:amorgan <at> mitre.org]
Sent: Wed 8/3/2005 2:48 PM
To: Michiel De Hoon
Subject: Re: [BioPython] Changes in NCBI BLAST output format !!??

Michiel:

I couldn't find anything wrong with it.  The Blast record objects seem 
to be correct and have the right alignments.  However, I don't know of a 
thorough way to test it.  In general the parser is pretty fragile though 
and will break for even the most minor changes in NCBI format, but it 
would be very challenging to try to make it more robust.

Thanks,

-Alex
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Greg Wilson | 9 Aug 2005 15:13
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[BioPython] re: software skills course

Hi,

I'm working with support from the Python Software Foundation to develop
an open source course on basic software development skills for people
with backgrounds in science and engineering.  I have a beta version of
the course notes ready for review, and would like to pull in people
in sci&eng to look it over and give me feedback.  If you know anyone
who fits this bill (particularly people who might be interested in
following along with a trial run of the course this fall), I'd be
grateful for pointers.

Thanks,
Greg Wilson

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xuying | 10 Aug 2005 07:55
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[BioPython] where to find an updated cookbook?

Can anyone tell me where to find an updated biopython tutorial?
Examples in the online tutorial are full of errors. Thanks!

　　　　　　　　xuying
　　　　　　　　xuying <at> sibs.ac.cn
　　　　　　　　　　2005-08-10

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Ann Loraine | 10 Aug 2005 22:11

Re: [BioPython] re: software skills course

Hello,

I would appreciate the chance to see the notes.  It would be helpful to 
the postdocs and students I supervise who would like to learn python.

Yours,

Ann Loraine

On Aug 9, 2005, at 6:13 AM, Greg Wilson wrote:

> Hi,
>
> I'm working with support from the Python Software Foundation to develop
> an open source course on basic software development skills for people
> with backgrounds in science and engineering.  I have a beta version of
> the course notes ready for review, and would like to pull in people
> in sci&eng to look it over and give me feedback.  If you know anyone
> who fits this bill (particularly people who might be interested in
> following along with a trial run of the course this fall), I'd be
> grateful for pointers.
>
> Thanks,
> Greg Wilson
>
> _______________________________________________
> BioPython mailing list  -  BioPython <at> biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
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