Note Path:

1. Data / 02_note / 05_code / ci /

2.

delphi 5.1 vs Biskit

http://biskit.pasteur.fr/doc/wrappers/delphi

input model = PDBModel( 'mystructure.pdb' ) ;
D = Delphi( inputmodel ) ;
result = D.run() >>> result

http://biskit.pasteur.fr/use/workflows/delphi

計算 cavity cleft

Plos 好 paper

Cavities and Atomic Packing in Protein Structures and Interfaces

1. 新的？ 試用中
http://3vee.molmovdb.org/

2. McVol
- 有 source code 用過

- INSTALLATION:

1. Download the file
2. type tar -jxf McVol.tar
3. Go to the directory McVol/test: cd McVol/test
4. Type ../src/McVol all

3. SURFNET
- 要填寫同意書 所以沒用過

4. CAVER

5. dxTuber link1 link2
有 source code, 含 python code analysis
ps. 有另一套 Inflategro 用於 MD 的 -> inflategro.pl (only one)

6. MolSpace (SurfVol)
plugin 於 VMD

7. MetaPocket 2.0


LIGSITE^cs, PASS, Q-SiteFinder, SURFNET, Fpocket, GHECOM, ConCavity and POCASA

delphi 5.1

下載 delphi 5.1 準備在 mac 下 run

執行後缺少檔案？

mms-MacBook-Air:Desktop mm$ ./delphi5.1
dyld: Library not loaded: /usr/local/lib/libgfortran.3.dylib
Referenced from: /Users/mm/Desktop/./delphi5.1
Reason: image not found

爬文後到 http://hpc.sourceforge.net/ 下載這檔案
gcc-lion.tar.gz, gfortran-lion.tar.gz (gfortran only), updated Feb 2012 (10.7 Lion only).

解壓後 找到 libgfortran.3.dylib
用 sudo su 權限 cp 到 /usr/local/lib/

再執行又少了一個檔案

sh-3.2# ./delphi5.1
dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
Referenced from: /Users/mm/Desktop/./delphi5.1
Reason: image not found
Trace/BPT trap: 5

所以再找到這個檔案 cp 過去 即可





完成畫面

sh-3.2# ./delphi5.1

______ DelPhi V. 5 Release 1.0 __________
| |
| A program to solve the PB equation |
| in 3D, using non-linear form, incorporating |
| many dielectric regions, multisalt ionic |
| strength, different probe radii, periodic |
| and focussing boundary conditions, utilizing |
| stripped optimum successive over-relaxation |
| and an improved algorithm for mapping the |
| Mol. Surface to the finite-Difference grid |
| Recompiled on Linux and PC |
| August 2011, Maintained by Delphi |
| Development Team |
|____________ ____________|
DelPhi V. 5.1

Program started on 2012-03-08 at 23:50:02
parameter file fort.10 does not seem to exist.
Therefore stopping




網頁版 http://compbio.clemson.edu/sapp/delphi_webserver/userInput.html
好像比較方便

Plos one publish 格式

Plos one Link1 Link2

Export High Resolution Images from PyMol

To get a 300 ppi PNG file for a 4.92 inch by 9.25 inch image:

Ray-traced:

ray 3500,2500
png /Users/kevet/Desktop/ex.png, dpi=300

Enable the use of Arial in R

First, convert the Arial .ttf files to afm:

ttf2afm /usr/share/fonts/msttcorefonts/arial.ttf > ~/arial.afm
ttf2afm /usr/share/fonts/msttcorefonts/ariali.ttf > ~/ariali.afm
ttf2afm /usr/share/fonts/msttcorefonts/arialbd.ttf > ~/arialbd.afm
ttf2afm /usr/share/fonts/msttcorefonts/arialbi.ttf > ~/arialbi.afm

and then do the following in R:

postscript(file="try.ps", horizontal=F,
onefile=F,
width=4, height=4,
family=c("/home/stephen/arial.afm",
"/home/stephen/arialbd.afm",
"/home/stephen/ariali.afm",
"/home/stephen/arialbi.afm"),
pointsize=12)
hist(rnorm(100))
dev.off()

ps.

1. 若無 ttf2afm, 先至 http://www.tug.org/mactex/2011/ 安裝 MacTex

2. Mac 路徑
a. Lee-Kevinteki-MacBook:Fonts kevet$ ls Arial*
Arial Black.ttf Arial Rounded Bold.ttf
Arial Narrow Bold Italic.ttf Arial Unicode.ttf
Arial Narrow Bold.ttf ArialHB.ttf
Arial Narrow Italic.ttf ArialHBBold.ttf
Arial Narrow.ttf
b. /Library/Fonts/Microsoft/Arial.ttf

3. my commands:
ttf2afm /Library/Fonts/Microsoft/Arial.ttf > /Users/kevet/Library/Fonts/Arial.afm
ttf2afm /Library/Fonts/Microsoft/Arial.ttf > /Users/kevet/Library/Fonts/Ariali.afm
ttf2afm /Library/Fonts/Microsoft/Arial.ttf > /Users/kevet/Library/Fonts/Arialbd.afm
ttf2afm /Library/Fonts/Microsoft/Arial.ttf > /Users/kevet/Library/Fonts/Arialbi.afm



Macintosh OS X and PowerPoint 2008:

Step I: Convert PowerPoint File to PNG or PDF

1. Go to PowerPoint Preferences. Under the Save tab, at the bottom, set Advanced Resolution Settings to 1600 DPI.
2. File → Save As. In the Format pull-down menu, select either PNG or PDF. Save. Your PNG will be oversize at 72ppi, but will resize properly to 300ppi in Photoshop or GIMP. Your PDF will be the exact size of your PowerPoint slide at 300ppi. All other formats save as 72ppi no matter what you set in Preferences.

Step II: Convert Individual Files to TIFFs

In Photoshop:

1. File→Open the PNG or PDF.
2. Use the Crop Tool (fifth from the top of the toolbar) to select an area close to the borders of your image. Hit Enter to apply the crop.
3. Layer→Flatten Image
4. If you opened a PNG, go Image→Image Size. Uncheck the Resample Image checkbox. If the Width is over 17.35cm, type 17.35 in the Width box (17.35cm is our maximum allowable width for figures). The Resolution will go up automatically as the Width decreases. If the resolution does not hit 300 when you make the Width 17.35, type 300 in Resolution and as long as Width doesn't go below 8.3cm, everything is fine. Also, the height cannot be more than 23.35. If the Height and Width are within these prescribed limits, no adjustment to your figure size needs to be made.
5. If you opened a PDF, go Image→Image Size and check to make sure the PDF is within our dimension limits. Resize it down to fit within these limits if need be.
6. File→Save As. Save as TIFF, Image Compression set to LZW, Pixel Order set to Interleaved, Byte Order set to IBM PC.

SCRATCH

1. SSpro/ACCpro 4.03: Protein Secondary Structure and Solvent Accessibility Prediction

2. MUpro 1.1: Prediction of Stability Changes (ΔΔG) of Single Site Mutations from Protein Sequences

3. DOMpro 1.0: Protein Domain Prediction

4. DIpro 2.0: Protein Disulfide Bond Prediction ........

Lab website

Conservation

Lab website 9529901

WCN http://wcn.life.nctu.edu.tw/

SAS http://140.113.239.214/~weilun/


old link