Morphing TRAP1

Q1:
in the past months I tried several times to us the multi-chain morph server for creating a movie of the heterodimeric protein TRAP1. I never got an e-mail back and when I used the old version of the server it does not seem to come to a result since more than 24 hours. It always gives the message not completed yet. I am wondering what the problem is.

A1:
Thank you for your query regarding the server. We’ll look into this, but may I ask why you are using the old version of our server specifically? I only ask because I ran tests on our newer multi-chain server on Sunday, and things worked very well there:

http://molmovdb.org/cgi-bin/beta.cgi

Having said that, we’ll check on things. Would you mind providing us with your Job ID (if you still have it), as well as the PBD files which you’d like to morph?

Q2:
I used the old server because I had used the new one before several times with the same job and never got an e-mail that it was finished. the job number is m716893-2511.

A2:
I was unable to find the directory corresponding to your morph, so our apologies for that. There are two possibilities I can think of:

1) We recently did some minor work on the server. Things were down for a short time, but when I checked over the weekend, things were back to normal. It is possible that your issue was a temporary one.

2) The second possibility is that your PDB files have formatting irregularities or some type of heteroatom which is not being processed or recognized by our server.

The best way to address the 1st possibility is for you to just re-submit your jobs on the newer server [ http://molmovdb.org/cgi-bin/beta.cgi ], and see if everything works. The easiest way to address the 2nd possible issue may be if you just send us your PDB files, and we can have a closer look at them.

Q3:
I tried the morph again in ran through this time but the movie file was empty and the pdb-files I could download just had "end" written in them. I also tried pdb-files of single chains. I also removed heteroatoms and made sure the number of amino acids is identical in both files. The message I get from the server is that it is not yet complete. The latest jog has the number 018936-29130. I do not understand what is wrong with these pdb-files. Please find enclosed the template pdbs that I have tried last. It would be great, if you would find out what is wrong with this.

A3:
Your PDB files look very good. It is not clear why your previous submission failed, but we were able to successfully generate your morph. You may view it here:

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=032929-30641

You may or may not find the attached image useful, but we have also produced a structure alignment for you (blue corresponds to low-RMSD regions of the alignment, and red corresponds to regions with higher RMSD between your two structures).

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