Re: [ccp4bb] Charge vs. pH plot Isoelectric titration curve ascii plotter

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: David Garboczi dgarboczi {- at -} NIAID {- dot -} NIH {- dot -} GOV
Date: 2009-05-04

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Subject: Re: Charge vs. pH plot Isoelectric titration curve ascii plotter
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2009-05-04

Kewl :)

I have one online but its ability to graph has been switched off because of
the inanity of my hosting provider. The source for the script (which also
calculates m.w. and extinction/absorption theoretical values) is here
http://www.xtals.org/prop_calc_script.perl
and the data file it reads to do the calculations is here
http://www.xtals.org/residue.dat

Artem

---
When the Weasel comes to give New Year's greetings to the Chickens no good
intentions are in his mind.
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul
Smith
Sent: Monday, May 04, 2009 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Charge vs. pH plot Isoelectric titration curve ascii
plotter

Hello all,

I had the worst time the other day finding an online tool to calculate
charge versus pH values for an input protein sequence. There are many
programs for calculating the isoelectric point (pI), put not many that
output a complete titration curve.

Because such information is often useful in protein purification and
crystallization, I coded up a quick perl program I would like to share with
the CCP4 community.

The code is attached. It is pretty self-explanatory. Input a FASTA file as
a command line arguement and the program outputs charge vs. pH value pairs
(unsorted). The constants defined in the program header can be used to
alter the pKa values used, titration starting and ending points, and grid
sampling.

Please feel free to use, distribute, and modify freely.

Also attached is a ASCII plotting tool that takes paired values from a file
or STDIN and plots them to STDOUT in ascii using automatically determining
ranges and binning values. These two programs work well like so:

"./titrate.pl FASTA.seq
./plot.pl"

to produce a nice ascii plot of charge vs. pH.

I hope these are helpful to someone.

Best,

Paul Smith
Paladin Scientific
paladinscientific.com

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: reference manager software
From: David Garboczi dgarboczi {- at -} NIAID {- dot -} NIH {- dot -} GOV
Date: 2009-05-04

Next message:
Subject: Re: problem in transformation of pqe 30 clone
From: Ho-Leung Ng holeung {- at -} BERKELEY {- dot -} EDU
Date: 2009-05-04