How to generate an output about sequence similarity in PSI-BLAST?

When I do PSI-BLAST for a protein sequence against a non-redundant database (3 iterations) I get a PSSM matrix. Is it possible to generate any other output from PSI-BLAST for the above problem...

10 November 2012 3,187 2 View

How to generate ROC curve from svm-light output?

My svmlight output for binary classification (+1 for true and -1 for false classes) is like +1 0.001 -1 -0.34 +1 0.9 +1 055 -1 -0.2 I tried generating roc in R using ROCR package. But I...

09 October 2012 590 15 View

What is PROSET s/w and what is it used for?

Can anyone help me reg proset s/w. ALso I need help in installing it and using it.

09 October 2012 9,403 0 View

A doubt of ROC in R

I have installed R and ROC package in R. I need to generate ROC from my SVM output data . How to call my data in R to run ROCR?

09 October 2012 5,968 2 View

How to draw ROC curve and RI curve for prediction generation using SVM?

Will Rapidminer tool help me in drawing a ROC curve? Moreover, I tried installing it, but could not.

09 October 2012 205 5 View

How to run PSIBlast standalone and generate PSSM file?

I want to run PSIBlast stanalone in my machine and want to create PSSM file. I have blast standalone and it has psiblast too. I tried running command in it, but it is giving an error. I used the...

09 October 2012 391 5 View

How to increase heap size in weka3.6?

I tried increasing heap size by editing RunWeka.ini file and changed it to 1024m from 256m. I am using large dataset. After changing the file I saved it and ran WEKA again. But still I am getting...

09 October 2012 1,451 1 View

How to execute cross validation and generate ROC curve in SVMlight?

For doing cross validation is it the parameter x which has to be used? Or is it some other parameter? I am confused. For doing 10 cross validation -x 10 will be fine. Also in SVM light how to...

09 October 2012 7,187 9 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View