Re: [ccp4bb] adding gaussian noise to an mtz data column
Dear Bernhard,
Thank you, but I didn't mean it.
I'd like to use the package cRy made by James since I'm an R user!
Thanks,
Keitaro
2011/2/7 Bernhard Rupp (Hofkristallrat a.D.) :
> R is a well-documented statistics package.
> http://www.r-project.org/
>
> BR
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Keitaro Yamashita
> Sent: Sunday, February 06, 2011 2:10 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] adding gaussian noise to an mtz data column
>
> Dear James,
>
> I'm very interested in your crystallographic R package.
> Is it available to the public?
>
> Thanks in advance,
>
> Keitaro
>
> 2011/2/4 James Foadi :
>> If you fancy using R (and its endless ways of generating random
>> deviates), then you could use part of the crystallographic package we
>> are developing here (cRy).
>>
>> Then you would carry out the following in R:
>>
>>> source("cRy/all_load.R")
>>> mtz <-
>>>readMTZ("test.mtz")
>>> # Load data from mtz file
>>> newF <-
>>>mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H)) #
>>>Add gaussian deviates with mean 0 and standard dev 1
>>>mtz$reflections$Fnew <- newF # Replace new column
>>>writeMTZ(mtz,"new_test.mtz")
>>> # Write modified file with a different name
>>
>>
>> If you are interested I can provide you with my R code for doing this.
>>
>>
>>
>> J
>>
>> Dr James Foadi PhD
>> Membrane Protein Laboratory
>> Diamond Light Source Ltd.
>> Diamond House
>> Harwell Science and Innovation Campus
>> Didcot
>> Oxfordshire
>> OX11 0DE
>> United Kingdom
>>
>>
>> office email: james.fo...@diamond.ac.uk alternative email:
>> j.fo...@imperial.ac.uk
>>
>>
>>
>> - Original Message
>> From: Vellieux Frederic
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Fri, 4 February, 2011 12:40:35
>> Subject: [ccp4bb] adding gaussian noise to an mtz data column
>>
>> Before re-inventing the wheel...
>>
>> Is there anywhere some software (freely available software, I mean)
>> that can add some Gaussian noise to data. The data is currently stored
>> in a data column in an mtz (not phase data, but "amplitudes", "sigma
>> values"...) but can be exported to another format if required.
>>
>> Before writing a computer program to do this, does anyone know if this
>> can be done without writing any code. If it can then obviously I won't
> write new code.
>>
>> Thanks,
>>
>> Fred.
>>
>>
>>
>>
>>
>
>
Re: [ccp4bb] adding gaussian noise to an mtz data column
R is a well-documented statistics package.
http://www.r-project.org/
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keitaro Yamashita
Sent: Sunday, February 06, 2011 2:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] adding gaussian noise to an mtz data column
Dear James,
I'm very interested in your crystallographic R package.
Is it available to the public?
Thanks in advance,
Keitaro
2011/2/4 James Foadi :
> If you fancy using R (and its endless ways of generating random
> deviates), then you could use part of the crystallographic package we
> are developing here (cRy).
>
> Then you would carry out the following in R:
>
>> source("cRy/all_load.R")
>> mtz <-
>>readMTZ("test.mtz")
>> # Load data from mtz file
>> newF <-
>>mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H)) #
>>Add gaussian deviates with mean 0 and standard dev 1
>>mtz$reflections$Fnew <- newF # Replace new column
>>writeMTZ(mtz,"new_test.mtz")
>> # Write modified file with a different name
>
>
> If you are interested I can provide you with my R code for doing this.
>
>
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science and Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> United Kingdom
>
>
> office email: james.fo...@diamond.ac.uk alternative email:
> j.fo...@imperial.ac.uk
>
>
>
> - Original Message
> From: Vellieux Frederic
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Fri, 4 February, 2011 12:40:35
> Subject: [ccp4bb] adding gaussian noise to an mtz data column
>
> Before re-inventing the wheel...
>
> Is there anywhere some software (freely available software, I mean)
> that can add some Gaussian noise to data. The data is currently stored
> in a data column in an mtz (not phase data, but "amplitudes", "sigma
> values"...) but can be exported to another format if required.
>
> Before writing a computer program to do this, does anyone know if this
> can be done without writing any code. If it can then obviously I won't
write new code.
>
> Thanks,
>
> Fred.
>
>
>
>
>
Re: [ccp4bb] adding gaussian noise to an mtz data column
Dear James,
I'm very interested in your crystallographic R package.
Is it available to the public?
Thanks in advance,
Keitaro
2011/2/4 James Foadi :
> If you fancy using R (and its endless ways of generating random deviates),
> then you could use part of the crystallographic package we are developing here
> (cRy).
>
> Then you would carry out the following in R:
>
>> source("cRy/all_load.R")
>> mtz <-
>>readMTZ("test.mtz")
>> # Load data from mtz file
>> newF <- mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H))
>> #
>>Add gaussian deviates with mean 0 and standard dev 1
>> mtz$reflections$Fnew <-
>>newF
>># Replace new column
>>writeMTZ(mtz,"new_test.mtz")
>> # Write modified file with a different name
>
>
> If you are interested I can provide you with my R code for doing this.
>
>
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science and Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> United Kingdom
>
>
> office email: james.fo...@diamond.ac.uk
> alternative email: j.fo...@imperial.ac.uk
>
>
>
> - Original Message
> From: Vellieux Frederic
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Fri, 4 February, 2011 12:40:35
> Subject: [ccp4bb] adding gaussian noise to an mtz data column
>
> Before re-inventing the wheel...
>
> Is there anywhere some software (freely available software, I mean) that can
> add
> some Gaussian noise to data. The data is currently stored in a data column in
> an
> mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported
> to
> another format if required.
>
> Before writing a computer program to do this, does anyone know if this can be
> done without writing any code. If it can then obviously I won't write new
> code.
>
> Thanks,
>
> Fred.
>
>
>
>
>
Re: [ccp4bb] adding gaussian noise to an mtz data column
On 04/02/11 12:40, Vellieux Frederic wrote: > Before re-inventing the wheel... > > Is there anywhere some software (freely available software, I mean) that > can add some Gaussian noise to data. The data is currently stored in a > data column in an mtz (not phase data, but "amplitudes", "sigma > values"...) but can be exported to another format if required. > > Before writing a computer program to do this, does anyone know if this > can be done without writing any code. If it can then obviously I won't > write new code. > There's also the RAN_G function in SFTOOLS's CALC command (works on your MTZ directly, of course).
Re: [ccp4bb] adding gaussian noise to an mtz data column
Thanks Ian, I think this is good enough for what I have in mind. So I did not have to reinvent the wheel after all... Fred. Ian Tickle wrote: Hi Fred Doesn't sftools do this - from 'man sftools': CALC F COL Fsimulated = COL Fcalc ran_g 10 * + Create a column with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic wrote: Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
Re: [ccp4bb] adding gaussian noise to an mtz data column
Hi Fred Doesn't sftools do this - from 'man sftools': CALC F COL Fsimulated = COL Fcalc ran_g 10 * + Create a column with label Fsimulated which contains the value of column Fcalc plus 10 times a random number from a Gaussian distribution with average = 0 and variance = 1 Cheers -- Ian On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic wrote: > Before re-inventing the wheel... > > Is there anywhere some software (freely available software, I mean) that can > add some Gaussian noise to data. The data is currently stored in a data > column in an mtz (not phase data, but "amplitudes", "sigma values"...) but > can be exported to another format if required. > > Before writing a computer program to do this, does anyone know if this can > be done without writing any code. If it can then obviously I won't write new > code. > > Thanks, > > Fred. >
Re: [ccp4bb] adding gaussian noise to an mtz data column
If you fancy using R (and its endless ways of generating random deviates),
then you could use part of the crystallographic package we are developing here
(cRy).
Then you would carry out the following in R:
> source("cRy/all_load.R")
> mtz <-
>readMTZ("test.mtz")
>
> # Load data from mtz file
> newF <- mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H))
> #
>Add gaussian deviates with mean 0 and standard dev 1
> mtz$reflections$Fnew <-
>newF
>
># Replace new column
>writeMTZ(mtz,"new_test.mtz")
>
> # Write modified file with a different name
If you are interested I can provide you with my R code for doing this.
J
Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom
office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
- Original Message
From: Vellieux Frederic
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 4 February, 2011 12:40:35
Subject: [ccp4bb] adding gaussian noise to an mtz data column
Before re-inventing the wheel...
Is there anywhere some software (freely available software, I mean) that can
add
some Gaussian noise to data. The data is currently stored in a data column in
an
mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported
to
another format if required.
Before writing a computer program to do this, does anyone know if this can be
done without writing any code. If it can then obviously I won't write new code.
Thanks,
Fred.
[ccp4bb] adding gaussian noise to an mtz data column
Before re-inventing the wheel... Is there anywhere some software (freely available software, I mean) that can add some Gaussian noise to data. The data is currently stored in a data column in an mtz (not phase data, but "amplitudes", "sigma values"...) but can be exported to another format if required. Before writing a computer program to do this, does anyone know if this can be done without writing any code. If it can then obviously I won't write new code. Thanks, Fred.
