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Questions and answers > General discussions (Q&As)
find_pair and HETATM
xiangjun:
Hi Pascal,
What OS do you use? I will compile a version of 'find_pair' that works for you. As with v1.5, I will keep the currently distributed v2.0 as is, unless I notice some significant issues.
Xiang-Jun
auffinger:
Hi Xiang-Jun,
We use Linux Ubuntu 8.04 LTS. Thanks for your help,
Pascal
xiangjun:
Hi Pascal,
I have finally found time to update "find_pair" to fulfill your requests:
* I have added an option "-attach=STRING": where STRING is case-insensitive, and if it is "off", "no" or "0", then the attached HETATM groups will not be added to the output coordinate file.
* With the "-p" option, I have added an output file named "allpairs.ana" that can be fed into "analyze".
See my email for detailed instructions to update. Please post back here to confirm that my modifications work as advertised, or if you have further questions.
Xiang-Jun
auffinger:
Hi Xiang-Jun,
Finally we tested your option -attach that works really fine. A lot easier for us. now! The .ana output looks less interesting to us than our workaround since it s lacking some info that we get by rewriting the find_pair output with -pz to a new output readable by analyze. At a later stage, it would be nice to have a complete output for analyze comming out from "find_pair -pz".
Was just also looking at the RN9-YN1 and RC8-YC6 info you provide in the analyze output. The labeling of this columns seems not appropriate since you do not consider the YY and RR base pairs occurrences, do you ?. The YN1-YN1 and RN9-RN9 columns are missing apparently. From my point of view, the C1'-C1' and the two lambdas provide all the needed info.
Best wishes and thanks again for your help,
Pascal
xiangjun:
Hi Pascal,
--- Quote from: "Pascal" ---Finally we tested your option -attach that works really fine. A lot easier for us. now!
--- End quote ---
Glad to hear.
--- Quote from: "Pascal" ---The .ana output looks less interesting to us than our workaround since it s lacking some info that we get by rewriting the find_pair output with -pz to a new output readable by analyze. At a later stage, it would be nice to have a complete output for analyze comming out from "find_pair -pz".
--- End quote ---
Could you be more specific so I (or others who are interested in) can see what exactly you want to achieve? As mentioned before, the "-p" option of "find_pair" was incompatible with "analyze" by design for a valid reason. I understand that 3DNA serves also as a tool kit, being used in "unexpected" ways. I am open and I'd be more than willing to be convinced to new ideas. As a design principle, though, I change 3DNA only in ways that make sense to me. When adding a new feature (excluding experimental and undocumented one, of course), I have always asked myself this question: will I be able to give user a concrete explanation or quickly acknowledge (and possibly fix) a bug? As a supplement and complement, users are always welcome to share their tricks and scripts with the community in the Users' contributions section.
--- Quote from: "Pascal" ---Was just also looking at the RN9-YN1 and RC8-YC6 info you provide in the analyze output. The labeling of this columns seems not appropriate since you do not consider the YY and RR base pairs occurrences, do you ?. The YN1-YN1 and RN9-RN9 columns are missing apparently. From my point of view, the C1'-C1' and the two lambdas provide all the needed info.
--- End quote ---
Again, be specific (using a concrete example) to show where (you think) is wrong. As fas as I could tell, even though the column headers are always labeled RN9-YN1 and RC8-YC6 (intentionally), 3DNA should handle YY and RR pairs properly. Please verify.
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
