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Problems with the new martinize.py script
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12 years 5 months ago #805
by OJA_DK
Problems with the new martinize.py script was created by OJA_DK
Hi.
I am currently doing a research project in which I would like to use elastic network dynamics. I have had some problems getting it to work (I might start another topic about this later on). Therefore, it was with great joy that I found out that you have made the new martinize.py script. However, for some reason, I can not get it to run without errors.
Here is what I have done so far. I have downloaded the "protein_tutorial.tar.gz" from the "Protein in water" tutorial and untarred it. When running the following command within the "proteins" folder, I get the errors written below the command.
Command
./martinize.py -f 1UBQ/1UBQ.pdb -o system.top -x cg 1UBQ/1UBQ.pdb -dssp /usr/local/bin/dssp -p backbone
Error message
Traceback (most recent call last):
File "./martinize.py", line 669, in ?
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '1UBQ/1UBQ.pdb'
I get the same error message if I copy 1UBQ.pdb into the proteins folder and use that as input. The command is copied directly from the "Protein in water" tutorial, where the only thing that has been edited is the path to the dssp binary. I have also tried to run the command using the "-ss 1UBQ/1UBQ.ssd" flag, again with the same error, so it should not be a dssp problem. I have tried updating the python installation using "yum install python", but this did not solve the problem.
Whether I am doing something wrong, or it is an error with the script, I do not know, but I hope that you are able to help.
Best regards
Ole Juul Andersen
I am currently doing a research project in which I would like to use elastic network dynamics. I have had some problems getting it to work (I might start another topic about this later on). Therefore, it was with great joy that I found out that you have made the new martinize.py script. However, for some reason, I can not get it to run without errors.
Here is what I have done so far. I have downloaded the "protein_tutorial.tar.gz" from the "Protein in water" tutorial and untarred it. When running the following command within the "proteins" folder, I get the errors written below the command.
Command
./martinize.py -f 1UBQ/1UBQ.pdb -o system.top -x cg 1UBQ/1UBQ.pdb -dssp /usr/local/bin/dssp -p backbone
Error message
Traceback (most recent call last):
File "./martinize.py", line 669, in ?
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '1UBQ/1UBQ.pdb'
I get the same error message if I copy 1UBQ.pdb into the proteins folder and use that as input. The command is copied directly from the "Protein in water" tutorial, where the only thing that has been edited is the path to the dssp binary. I have also tried to run the command using the "-ss 1UBQ/1UBQ.ssd" flag, again with the same error, so it should not be a dssp problem. I have tried updating the python installation using "yum install python", but this did not solve the problem.
Whether I am doing something wrong, or it is an error with the script, I do not know, but I hope that you are able to help.
Best regards
Ole Juul Andersen
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12 years 5 months ago #806
by djurre
Replied by djurre on topic Problems with the new martinize.py script
Dear Ole,
The '1UBQ/1UBQ.pdb' argument comes in twice in the commandline. I would say the second is wrong (or that is an copy/past error in your forum post):
-x cg 1UBQ/1UBQ.pdb
Maybe that should be:
-x cg_1UBQ/1UBQ.pdb
If that does not solve the problem, could you try to move the pdbfile to the current directory? Or execute the martinize.py script while you are in the '1UBQ' directory?
If that actually solves the problem, I would be really happy to know, as it could be considered a bug...
Hope that solves the problem.
Groetnis,
Djurre
The '1UBQ/1UBQ.pdb' argument comes in twice in the commandline. I would say the second is wrong (or that is an copy/past error in your forum post):
-x cg 1UBQ/1UBQ.pdb
Maybe that should be:
-x cg_1UBQ/1UBQ.pdb
If that does not solve the problem, could you try to move the pdbfile to the current directory? Or execute the martinize.py script while you are in the '1UBQ' directory?
If that actually solves the problem, I would be really happy to know, as it could be considered a bug...
Hope that solves the problem.
Groetnis,
Djurre
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12 years 5 months ago #807
by OJA_DK
Replied by OJA_DK on topic Problems with the new martinize.py script
Hi Djurre.
Thank you for your reply.
Unfortunately, I have allready tried all your suggestions without any luck. All I get is new (different) error messages.
/Ole
Thank you for your reply.
Unfortunately, I have allready tried all your suggestions without any luck. All I get is new (different) error messages.
/Ole
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12 years 5 months ago #808
by djurre
Replied by djurre on topic Problems with the new martinize.py script
Dear Ole,
The different errors could indicate that the original problem was solved and a new, different error came up. Could you post the other errors? (or did you mean they were just different in the argument? (1UBQ/1UBQ.pdb))
Also could you check which version of python you have? We have seen problem with older versions of python (I believe 2.4 and older). Probably 3.0 and newer will not work either.
What you could also try is not giving the -x and -o options. The files will get defaullt names then.
The different errors could indicate that the original problem was solved and a new, different error came up. Could you post the other errors? (or did you mean they were just different in the argument? (1UBQ/1UBQ.pdb))
Also could you check which version of python you have? We have seen problem with older versions of python (I believe 2.4 and older). Probably 3.0 and newer will not work either.
What you could also try is not giving the -x and -o options. The files will get defaullt names then.
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12 years 5 months ago #809
by OJA_DK
Replied by OJA_DK on topic Problems with the new martinize.py script
I am running python 2.4.3. When you write that you have had problems with python 2.4 and older, do you mean all versions of 2.4, or is the 2.4.3 new enough? I am running CentOS 5.7, and it seems that installing newer versions of Python is a difficult task on CentOS 5, as it requires 2.4.x to run proberly (according to various search results on google). Therefore, I hope that I can use python 2.4.3. If not, what version would you advise me to install?
I would like to have resolved this issue before sending you all the other error messages, there is no reason for doing that if the errors are caused by the python version :).
/Ole
I would like to have resolved this issue before sending you all the other error messages, there is no reason for doing that if the errors are caused by the python version :).
/Ole
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12 years 5 months ago #810
by djurre
Replied by djurre on topic Problems with the new martinize.py script
I'm not sure if it was version 2.4.3 or other with which we had the problems. I do not have 2.4.3 installed here, so I'm not able to check. I think you can have multiple copies of python installed. Just make sure the operating system finds the right one. If you want to try that, I'm using 2.6.5, working very wel.
But then, the error does not seem such that it is caused by the python version. Not sure though. Also, since the error changes, it would be strange if all the different errors are being caused by having the wrong python version.
Groetnis,
Djurre
But then, the error does not seem such that it is caused by the python version. Not sure though. Also, since the error changes, it would be strange if all the different errors are being caused by having the wrong python version.
Groetnis,
Djurre
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12 years 5 months ago #811
by OJA_DK
Replied by OJA_DK on topic Problems with the new martinize.py script
Okay.
I have an Ubuntu installation at home. I think I will go home and see if I can get the script to work on that, and try with different versions of python. I do not want to risk messing up my workstation at the office =).
If I can not get it to work, I will return with the other error messages tomorrow.
FYI: I tried running the script without using the -x and -o options, but that also resulted in an error message.
Thank you for your help so far.
I have an Ubuntu installation at home. I think I will go home and see if I can get the script to work on that, and try with different versions of python. I do not want to risk messing up my workstation at the office =).
If I can not get it to work, I will return with the other error messages tomorrow.
FYI: I tried running the script without using the -x and -o options, but that also resulted in an error message.
Thank you for your help so far.
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12 years 5 months ago #812
by OJA_DK
Replied by OJA_DK on topic Problems with the new martinize.py script
Dear Djurre.
The python version on my Ubuntu installation is the same as yours, 2.6.5. I am happy to announce that the script is now working =).
However, it only works when changing "cg 1UBQ.pdb" to "cg_1UBQ.pdb". Could you please make sure that this is corrected in the tutorial? And perhaps also leave a note about which python version to run? Furthermore, in point 2 & 3 in the tutorial, it says "topology le" where it should say "topology file" (or is that just in my web browser?).
Thank you very much for your help, it is always nice when your problems can be resolved =).
Best regards
Ole
The python version on my Ubuntu installation is the same as yours, 2.6.5. I am happy to announce that the script is now working =).
However, it only works when changing "cg 1UBQ.pdb" to "cg_1UBQ.pdb". Could you please make sure that this is corrected in the tutorial? And perhaps also leave a note about which python version to run? Furthermore, in point 2 & 3 in the tutorial, it says "topology le" where it should say "topology file" (or is that just in my web browser?).
Thank you very much for your help, it is always nice when your problems can be resolved =).
Best regards
Ole
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12 years 5 months ago #814
by djurre
Replied by djurre on topic Problems with the new martinize.py script
Dear Ole,
I've added the note about python versions and repaired the missing 'fi' and '_'.
Thanks a lot for pointing it out!
Groetnis,
Djurre
I've added the note about python versions and repaired the missing 'fi' and '_'.
Thanks a lot for pointing it out!
Groetnis,
Djurre
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12 years 5 months ago #815
by OJA_DK
Replied by OJA_DK on topic Problems with the new martinize.py script
Hi Djurre.
I read your note in the tutorial regarding the python version. I would like to add that I have tested the script on my Mac, which has version 2.7.1, and there it also seems to work fine. And also, in the note it should say "to hear from you", not "to here from you" (not trying to be annoying, just wanted to let you know ;) ).
/Ole
I read your note in the tutorial regarding the python version. I would like to add that I have tested the script on my Mac, which has version 2.7.1, and there it also seems to work fine. And also, in the note it should say "to hear from you", not "to here from you" (not trying to be annoying, just wanted to let you know ;) ).
/Ole
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