[Mutinf-news] Re: Mutinf Query

[Dilraj LAMA]

Dear Chris,
            I am dropping by again. In addition to my previous queries  
in the mails before, I have some more questions. I am sure you are  
very busy with your work. So I am sorry to bother you with these emails.

I am currently trying to analyze the trajectories using the  
kullback-leiber divergence expansion. I have been able to successfully  
run the script. I used the following command for execution.

python2.6 $PATH/mutinf_2.1_with_new_kl_diverge_script/kl_diverge.py -a  
"no" -n 6 -o 6 -w 30 -f structure.pdb -b "phipsichi" $PATH1 $PATH2 -d/  
residue_apo.reslist residue_complex.reslist > temp

A set of out files are generated and I will be extremely grateful if  
you can kindly guide me forward. I have listed my queries below.

1) First of all, I used the script "kl_diverge.py" that you had  
attached in one of your previous mail since you mentioned that, this  
is the only change that you have made since mutinf ver 2.1. Is this  
correct?

2)  There is no specific description on the information content for  
the output files. So which of these output files should I concentrate  
on in order to get a quick idea of the analysis?

3)In the link  
"http://www.jacobsonlab.org/mutinf_manual/KLdiv_manual.htm", it is  
mentioned that we can generate pdb files using the  
"replace_res_bfac_mut.pl" script. For doing this an example is given  
as follows

replace_res_bfac_mut.pl <pdbfile> <*kldiv_res.txt or *jsdiv_res.txt  
file> <residue having mutation, if applicable É. GLY00 is the defult>

In the output files, I don't see any file which ends with the  
extension "kldiv_res.txt"

Is there anything I am missing here?

I am sure you are busy and occupied with you work. I will however be  
extremely great full if you can guide me with these queries.

Thank You,
Dilraj.

Quoting Chris McClendon <chris.lee.mc at gmail.com>:

> Hi Dilraj,
> Sorry I forgot to reply to your last message, I was at a workshop  
> last week and a conference for part of this week. I'll answer your  
> questions soon!
> --Chris
>
> Sent from my iPhone
>
> On Aug 10, 2012, at 5:03 AM, Dilraj LAMA <dilrajl at bii.a-star.edu.sg> wrote:
>
>> Dear Chris,
>>          I am not sure if you received my last email. Just in case  
>> you have not, I am appending the content below. In case you get  
>> sometime to go through this mail, I will be glad to hear from you.
>>
>> I wanted to get your opinion on a couple of more things.
>>
>> 1) I notice that in your paper, you have performed multiple short  
>> simulations of 10ns each. Whereas I am doing 3 long simulations of  
>> 100ns each and then dividing it into blocks. Which of the two  
>> options do you think will be more advisable for the current  
>> analysis? I know this is a subjective term but just would like to  
>> hear about it from you.
>>
>> 2)I am taking all possible Chi angles calculation using "g_chi". I  
>> was initially restricting it to 2. I suppose we need to take all  
>> the chi angles rather than just 2.
>>
>>
>> Will be looking forward to your response.
>>
>> Best Regards,
>> Dilraj.
>>
>> Quoting Dilraj LAMA <dilrajl at bii.a-star.edu.sg>:
>>
>>> Dear Chris,
>>>          I did the calculation on my simulation trajectories. Well  
>>> I have some queries and I will be glad if you give me your point  
>>> of view on the matter.
>>>
>>> 1) I have done 100ns simulation in triplicates and then divided  
>>> the simulation into blocks of 50ns each thereby having six blocks  
>>> for the analysis. Is that fine?
>>>
>>> 2) For the analysis I have used the following command:
>>>
>>> python2.6 $PATH dihedral_mutent.py -g gcc -x $PATH/mutinf_ver2.1/  
>>> -d/  -a yes -o 6 -w 30 -p 0 -n 6 -m 2 -c yes  
>>> $PATH/mutinf_ver2.1/residue.reslist > temp
>>>
>>> Are the parameters I have used fine? Especially the bin size (-w  
>>> 30). Are there any other parameters I need to consider?
>>>
>>> I see in the tutorial that some of the options are within  
>>> quotation like -a "yes". Is that critical or I can do away with  
>>> the quotations?
>>>
>>> 3) After the analysis, a set of output files are generated. I have  
>>> just used "residue.reslist-nsims6-structs50000  
>>> bin30_bootstrap_avg_mutinf_res_sum_0diag.txt" which gives the  
>>> mutual information between residues to plot the clustered and  
>>> unclustered heat map plots.
>>>
>>> However, besides these a number of other files are generated. I  
>>> got the description of some of these files from the tutorial. But  
>>> we don't have the description for all the files.
>>>
>>> Are many of them intermediate files and hence not critical for the  
>>> final output analysis?
>>>
>>> 4)I refereed to your JCTC paper where you have made plots like  
>>> that for Figure 4 and Figure 5. From the example that you have  
>>> mentioned in the tutorial on how to make such plots, I don't get  
>>> the file names that you have mentioned in the tutorial in the  
>>> output file from my analysis.
>>>
>>> For example I don't get the output file with the following extension
>>> "_quarter_kT_CA_dist_matrix_fixnames.txt". Has there been some  
>>> modifications in the file naming with the latest version or Am I  
>>> missing something?
>>>
>>> Sorry for this very long email. I hope you will have the patience  
>>> to go through it. will be glad to get your feedback.
>>>
>>> Best regards,
>>> Dilraj.
>>>
>>>
>>
>>
>>
>
>