How do you submit private data to the morph server?

How do you submit private data to the morph server?

There is now a "Private" check box on the morph submission form. If checked, the submitter will still receive an email upon submission but the general public will have no way to find the morph. It will not appear when people use the search box on the front page, nor will it appear among the user-submitted morphs on the movies page. Search engines do not index morph pages since they are dynamically generated. The only way third parties could know of its existence is if they were somehow able to intercept the email sent from the server to the submitter. Thus it is highly unlikely that third parties would ever know of or find it. We trust this will provide sufficient privacy.

What is the Protein in the Logo at the Top of the Molmovdb Page?

I've been using your molecular movement database to find candidate proteins for a functionalization experiment that my group at Oregon State University is working on. The logo at the very top of the browsing page caught my attention (http://www.molmovdb.org/images/ProtMotDB.lrg-logo.gif). Would you happen to know what protein this is?

Lactoferrin. It's also part of Figure 4 in the original database publication from a very long time ago:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9722650

This has references to the specific structure publications.

What are the datasetsfor Hinge Atlas and Hinge Gold?

I found the database of your lab is very useful at http://www.molmovdb.org/cgi-bin/browse.cgi, which include many data sets of conformations. My current program can read the pdb files.

Could you send me with the database?




You might find the Hinge Atlas and Hinge Atlas Gold datasets the best curated and easiest to download. You can find the download links and instructions at: http://molmovdb.org/cgi-bin/sets.cgi.

Please cite our Hinge Atlas and/or FlexOracle papers if you use these datasets:

http://papers.gersteinlab.org/e-print/HingeAtlas/preprint.pdf
http://papers.gersteinlab.org/e-print/flexoracle/preprint.pdf

How to Cite Morph Server and CNS Script

I have found your Morph Server and CNS script very useful, particularly for providing a good visual aid for presentations and such. I am currently preparing some manuscripts for several protein crystal structures, which have two different conformational states. I was considering using your script to generate a morph of the two states, and creating an animated video of the conformational change to be included in the supplementary material of the paper. I was wondering if you had any requirements or wishes regarding the citation of your script. Obviously we would cite your work in the paper itself, but I was wondering if you had any other preferences for the inclusion of a citation in the supplementary material, such as putting a citation at the end of the animation. Any recommendation you could provide would be much appreciated.

Best to just cite
http://papers.gersteinlab.org/papers/molmovdb-update-nar/
http://papers.gersteinlab.org/papers/morphs-nar/
in the paper and end of suppl. material (if possible).

How to input parameters in NuProt Calculator

I would like to use the NucProt Calculator for an RNA/protein mix, more exactly the genome of a virus plus several copies of its viral enzymes. I am not sure how I should input things in the program. Shall I introduce the sequence of the viral genome followed by those of the viral proteins?

The NucProt Packing-Eff calculator works on PDB structures NOT sequences, so they cannot mean that:
http://www.molmovdb.org/cgi-bin/voronoi.cgi

The NucProt PSV and Volume Calculator:
http://www.molmovdb.org/cgi-bin/psv.cgi
is not the best written CGI code that can take several sequences at once, but since I didn't understand HTTP GET and POST very well, I had it put all in the information in the GET rather than the POST, so there is a browser limit. I don't think I have write access anymore to this file.

Technically it can take several sequence in FASTA format though.

Turning morph to a movie

I have a morph I created some time ago that illustrates an essential motion in the protein I study. I'd like to have the morph as part of my thesis talk. Can I turn it into a movie that I can store on my computer and have as a part of my power point presentation (in other words, can I have a copy of it so that I don't have to access the webpage?). How do I do this? Are there obvious directions on teh webpage that I"m just missing?


On the jmol morph page you will see a link that says:

Orient the molecule to your liking and then:
Generate high-res gif

Unfortunately it is just a wireframe animation. I had it set to do cartoons but for some reason it's back to wireframe now.

Alternatively, you can download the interpolated trajectory, then animate using vmd or jmol.

Look for an NMR-formatted PDB file called movie.pdb here:

http://www.molmovdb.org/uploads/b061676-11139

Deciding which Fragment is Flexible or not on MolmovDB

We want to know which fragment is flexible or not according to the information from “the molmovdb” database.

If your protein has been crystallized in two conformations you can submit a job to our "morph server." Visual inspection may then give you the information you seek. If you have only one structure, you can submit it to our HingeMaster server, and several different flexibility analysis programs will be used to find the hinge location. Note that this is designed for use with domain hinge bending proteins. It will not be very helpful if your protein moves by shear or order-disorder transition mechanisms.

We also have a motion prediction program, the Conformation Explorer, which predicts conformational change for hinge bending proteins, either induced by ligand or otherwise. It's still under development, and use would require further discussion.

MolMovDB Data Dump

You offer to provide the MolMovDB as a complete data set upon request. Where can we get a copy of it, preferably as a MySQL database?

The Hinge Atlas dataset, described in our recently accepted BMC Bioinformatics paper, is available for download here:

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

Just scroll down to the Hinge Atlas section. You probably want the coordinate set data, more than the mysql dump. The rest of the database is not yet available for download.

How to Create a Movie of Motions if there's DNA Lesion

We would like to create a movie of these motions for our publication and would not like to use the public morphing server if possible. The morphing of our structures might not possible at all, due to the cisplatin containing DNA lesion. We could send you also the CNS parameter and topology files we used for refinements.

If you submit the protein and DNA separately this should work. You would then have the problem, though, of putting the two back together. What I would suggest is submitting the two jobs and emailing me when they are done. I would then remove them from the public part of the database, but you could still download the structural interpolations. I would suggest using a small number of interpolated frames, at least for a first try, to minimize compute time.

Packing Software on Mac OS X

The packing software on molvovdb geometry site working on Mac OS X? If not, can you help with porting it to work on Mac OS X?

There has been problems compiling the program and making it work on Mac OS X. The program was written by a lab member who no longer is available for this. Please continue using the web interface.

Sieve-Fit Program

Regarding the availability of the "sieve-fit". Do you have the program (source, script or whatever) or know who could provide it to me?

see http://geometry.molmovdb.org/
then
http://bioinfo.mbb.yale.edu/geometry/screw-axis/

http://geometry.molmovdb.org/files/geometry/readme.html
then
http://geometry.molmovdb.org/files/geometry/src-prog3/sieve-fit.main.c

Complicated question regarding a protocol to decrease the transition

We are trying to calculate the energetic cost of the transition of two structures of TFIIB protein. I am using the CNS script available on the molmovdb to obtain multiples states along the transition between both structures. I am doing this from the xray to nmr structure on both ways. My problem is the following, after a few attempts I found a protocol to decrease the hysteresis of the transition. I begin with 500 frames and every frame energy minimizated with 500 powell steps. I tried to decreased even more the hysteresis and increase to 1000 steps with the same 500 powell steps. My problem began when in other attempt to decrease the hysterisis and I made 1500 frames with the same 500 powell steps, as you can see on the graph that I attached, It appears that the hysteresis increased with the 1500 steps. When I repeated the 1500 frames and minimizated with 1000 powell steps, the hysteresis decrease.

Do you think that this behavior is correct? Does it look strange that I have any energetic barrier of the transition?

I would be very cautious about assuming that a linear interpolation between two structures represents the thermodynamically most probable trajectory of motion. I don't know why using more frames would increase hysteresis -- presumably you mean that an energy difference resulted when the protein nearly finished its morph trajectory. Maybe the coarser interpolation jumped over a barrier and found a more favorable path. If you clarify what you are doing I may be able to provide a hint, though I think most likely I do not have a rigorous answer for you.