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do_dssp manual
- xudongh
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11 years 5 months ago #1210
by xudongh
do_dssp manual was created by xudongh
Hello,
since i cannot use the dsspcmbi because i use a mac, I guess my only option is to generate the dssp on my own. I've been suggested to use do_dssp, but I looked into the parameters required for that function, and I don't think I have any of the files it requires as input since I'm following the tutorial on protein in water .
md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water
Let me know, thank you :)
since i cannot use the dsspcmbi because i use a mac, I guess my only option is to generate the dssp on my own. I've been suggested to use do_dssp, but I looked into the parameters required for that function, and I don't think I have any of the files it requires as input since I'm following the tutorial on protein in water .
md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water
Let me know, thank you :)
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- djurre
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11 years 5 months ago #1212
by djurre
DSSP does work, if you use the Mac binary: swift.cmbi.ru.nl/gv/dssp/HTML/distrib.html
Using the Mac binary martinize.py works perfectly on my Mac.
Replied by djurre on topic do_dssp manual
xudongh wrote: since i cannot use the dsspcmbi because i use a mac,
DSSP does work, if you use the Mac binary: swift.cmbi.ru.nl/gv/dssp/HTML/distrib.html
Using the Mac binary martinize.py works perfectly on my Mac.
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- xudongh
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11 years 5 months ago #1216
by xudongh
@djurre,
how do I replace that with what I have? do I execute it like how it was written in the tutorial? eventhough it calls it for dsspcmbi ?not dssp?
Replied by xudongh on topic do_dssp manual
djurre wrote:
xudongh wrote: since i cannot use the dsspcmbi because i use a mac,
DSSP does work, if you use the Mac binary: swift.cmbi.ru.nl/gv/dssp/HTML/distrib.html
Using the Mac binary martinize.py works perfectly on my Mac.
@djurre,
how do I replace that with what I have? do I execute it like how it was written in the tutorial? eventhough it calls it for dsspcmbi ?not dssp?
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- xudongh
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11 years 5 months ago #1217
by xudongh
Replied by xudongh on topic do_dssp manual
I tried re-install dsspcmbi replaced the binary with the one you showed me, this is the code i get:
In file included from DsspCMBI.c:341:
./p2c.h:51:13: warning: 'memcpy' macro redefined
# define memcpy my_memcpy
^
/usr/include/secure/_string.h:53:9: note: previous definition is here
#define memcpy(dest, src, len)
^
DsspCMBI.c:1198:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
fprintf(tapeout, gDSSP_Version);
^~~~~~~~~~~~~
2 warnings generated.
Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program...
xus-macbook-pro:dssp xudongh$ cd ..
xus-macbook-pro:Desktop xudongh$ sudo mv dssp /usr/local/src/
Password:
mv: rename dssp to /usr/local/src/dssp: Directory not empty
xus-macbook-pro:Desktop xudongh$ cd /usr/local/bin
xus-macbook-pro:bin xudongh$ sudo ln -s ../src/dssp/dsspcmbi
ln: ./dsspcmbi: File exists
xus-macbook-pro:bin xudongh$ dssp
-bash: /usr/local/bin/dssp: cannot execute binary file
xus-macbook-pro:bin xudongh$ dsspcmbi
-bash: /usr/local/bin/dsspcmbi: cannot execute binary file
xus-macbook-pro:bin xudongh$
In file included from DsspCMBI.c:341:
./p2c.h:51:13: warning: 'memcpy' macro redefined
# define memcpy my_memcpy
^
/usr/include/secure/_string.h:53:9: note: previous definition is here
#define memcpy(dest, src, len)
^
DsspCMBI.c:1198:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
fprintf(tapeout, gDSSP_Version);
^~~~~~~~~~~~~
2 warnings generated.
Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program...
xus-macbook-pro:dssp xudongh$ cd ..
xus-macbook-pro:Desktop xudongh$ sudo mv dssp /usr/local/src/
Password:
mv: rename dssp to /usr/local/src/dssp: Directory not empty
xus-macbook-pro:Desktop xudongh$ cd /usr/local/bin
xus-macbook-pro:bin xudongh$ sudo ln -s ../src/dssp/dsspcmbi
ln: ./dsspcmbi: File exists
xus-macbook-pro:bin xudongh$ dssp
-bash: /usr/local/bin/dssp: cannot execute binary file
xus-macbook-pro:bin xudongh$ dsspcmbi
-bash: /usr/local/bin/dsspcmbi: cannot execute binary file
xus-macbook-pro:bin xudongh$
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- djurre
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11 years 5 months ago #1219
by djurre
Replied by djurre on topic do_dssp manual
Did you get the mac binary from there? In my case it is called DSSP_MAC.EXE Download that, put it somewhere and test it by typing 'DSSP_MAC.EXE'
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- xudongh
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11 years 5 months ago #1257
by xudongh
Replied by xudongh on topic do_dssp manual
@ djurre,
I moved DSSP_MAC.EXE into a folder and I tried to run it while in that folder, doing DSSP_MAC.EXE, it says command not found. I tried -dssp DSSP_MAC.EXE, it says cannot be executed.
How do you use it? It doesn't seem to run on my mac.
I'd greatly appreciate it if you can help me get it working, because I am getting ready to run some CG work, and I can't without the dssp =(
Thanks.
I moved DSSP_MAC.EXE into a folder and I tried to run it while in that folder, doing DSSP_MAC.EXE, it says command not found. I tried -dssp DSSP_MAC.EXE, it says cannot be executed.
How do you use it? It doesn't seem to run on my mac.
I'd greatly appreciate it if you can help me get it working, because I am getting ready to run some CG work, and I can't without the dssp =(
Thanks.
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- xudongh
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11 years 5 months ago #1258
by xudongh
Replied by xudongh on topic do_dssp manual
*Update
I copied DSSP_MAC.EXE to /usr/local/bin and renamed it dssp, on command window, i type dssp, it says /usr/local/bin/dssp: Permission denied
How can I go around that?
I copied DSSP_MAC.EXE to /usr/local/bin and renamed it dssp, on command window, i type dssp, it says /usr/local/bin/dssp: Permission denied
How can I go around that?
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- djurre
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11 years 5 months ago #1261
by djurre
Replied by djurre on topic do_dssp manual
What is the mode of the DSSP_MAC.EXE file? If you type "ls -ltr DSSP_MAX.EXE" it will give you a list of all files. In front of each filename there will be a indication of the file-mode, something like: -rwxr--r--. The a number and then the name of the file-owner. The file-owner should be you and then the mode should have an x at position 4 (meaning it is executable for the owner).
If this is not the case you should change that:
"chmod 755 DSSP_MAC.EXE"
If this is not the case you should change that:
"chmod 755 DSSP_MAC.EXE"
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