Q:

I like your paper about 3V tool and I try to apply it on my proteins. However there seems to be a problem with online version – I cannot get to results through the link provided, e.g. http://geometry.molmovdb.org/3v/tempfiles/nchan8269.pdb.gz

I tried both module for cavities and channels with similar failure.

Could you solve it for me please?

A:
I’ve set up a newer server that provides more feedback at http://3vee.molmovdb.org, I keep the old one around since people still prefer it.

All I can tell from looking at the server is that the file you are looking to download does not exist. So, maybe the program crashed. Try the new site and it might be more informative.

I would try Channel Finder instead of Channel Extraction. Channel Extraction is very particular about finding the exact coordinate of the channel — in fact I may change the algorithm to accommodate for this.

Q:
I download Voss Volume Voxelator from website
http://3vee.molmovdb.org/sourcecode.php. When I open the source of 3v, and
then use "make" to compile all the source. but the err happen as below:

####################################################################
cpuflags: cpuflags : unknown Intel Pentium3 model "42"
g++ -Wall -O3 -fomit-frame-pointer -ffast-math -funroll-loops -march=i686
-fopenmp -c -o utils-main.o utils-main.cpp
utils-main.cpp:1:0: error: CPU you selected does not support x86-64
instruction set
make: *** [utils-main.o] Error 1
####################################################################

I use "uame -a", and the specify information:
**********************************************************************************
Linux localhost.localdomain 2.6.35.6-45.fc14.x86_64
#1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
**********************************************************************************

What’s wrong with the compile of 3v program? Could you give me some
suggestion?

A:
Could you download the the latest subversion it should fix your problem:

svn checkout http://vossvolvox.svn.sourceforge.net/svnroot/vossvolvox/ vossvolvox/

Q:

I run into a problem using your 3v tool for the shell. I am using Mac OS X 10.6 with Xcode installed. During compiling I get the following warnings: cpuflags: CPU "core" not supported by compiler "gcc-2335.9" on Darwin g++ -Wall -O3 -fomit-frame-pointer -ffast-math -funroll-loops -fopenmp -o AllChannel.exe utils-main.o utils-output.o utils-mrc.o allchannel.cpp allchannel.cpp: In function ‘int main(int, char**)’: allchannel.cpp:57: warning: format not a string literal and no format arguments allchannel.cpp:67: warning: format not a string literal and no format arguments allchannel.cpp:73: warning: format not a string literal and no format arguments chmod 755 AllChannel.exe mv AllChannel.exe ../bin for all tools in the package. I was trying using the volume tool and I compared it with your web service. Both generated the same result without any error message. Then I moved on and tried screening for channels. This time however the script crashes with the message segmentation fault (command used ../bin/AllChannel.exe -b 12.000 -s 1.400 -t 1.500 -g 0.500 -v 700 -i 2RH2_WT67_model1-noions.xyzr 2> output.log). I compared it with the console output from the web service. Until the segmentation fault both outputs (local and web) are exactly the same. Do you have any idea what might cause the problem.

A:
I compiled it on a mac once, but it has been a while. My guess is that you do not have openMP installed on your mac (a simple library that allows multiprocessor support).

Go into the Makefile (it is a text file) and change the FLAGS line at the top to just:

FLAGS = -Wall

then try it again. Let me know if it works or not.

From what I can tell you are not using openmp, library named libgomp. If you use ‘top -s3
-ocpu’, can you tell if it is using more than 100%.

Ok, back to the seg fault. I have no idea, like you said it is the exact same command. I can see that it dies somewhere between line 180 and 300, but it does not run lines 202-266.

Can you go into utils.h and change the DEBUG flag to 1

#define DEBUG 1

then compile and run it again.

Also – Did you do a ‘make clean’ before compiling after changing the DEBUG flag? Because there should be a lot more output.

Another thing to try is slightly adjusting the grid size (go from 0.5 to 0.51), to see if it is trying to access memory outside the bounds of the array.