Conflicting SEQRES records

Q:
I’m trying to visualize a morph between two structures. However, I’m prompted with the error message “Conflicting SEQRES records”. How may I resolve this?

A:
This is by far the most comment cause of failure. The server uses SEQRES data to determine the actual protein sequence. However, this frequently conflicts with the sequence intuited from ATOM records (including official PDB files from http://www.rcsb.org). If the server cannot automatically resolve these conflicts, it will fail. The easiest workaround to this is to submit files with SEQRES records deleted; if you supplied a PDB ID rather than a file you will need to download the proper file from the PDB, then modify and upload it. However, this may sometimes lead to other distortions, depending on the sequence numbering.

Preventing submissions on the morph server from becoming public

Q:
I understand that, by default, the structures I submit to your morph server become public on your database. However, I am submitting coordinates that have not yet been published, or which are commercial. Thus, I’d prefer that my submission not be made public. Can you help me?

A:
We strongly discourage private submissions because they go against the spirit of the database, which is not only intended to provide free morphing to individual users, but also to serve as a browseable and searchable repository of morphs which are useful to others. We understand, however, that some morphs may reveal confidential information and so beyond moral suasion nothing prevents you from using the “Private” check box on our single- and multi-chain morph submission forms. This sets a flag in our database that tells our movie gallery page not to display the morph. Also, the search tool on our front page will not return it. The only way a member of the public could possibly find your morph is if they were able to intercept the email you got from our server with the link to it. We consider the probability that this will happen to be very low. Generally we cannot handle specific requests for further security unless as part of an official collaboration.

probe radius

Q:


I would like to calculate the solvent accessible surface of certain
proteins. By using your method (online available on
http://helixweb.nih.gov/structbio/basic.html) one can set the probe radius
to maximal size of 1.6 Å. Because I would like to mimic methylene groups as
solvent, the probe radius should be ~1.9 Å (Johnson R.M. et al, Biochemistry
2006, 45, 8507-8515) .
Is there a possibility to increase the probe size radius to 1.9 Å and
calculate the accessible surface using your method?

Question goes here

A:

Your answer here

I think you can do this by downloading the software from
http://www2.molmovdb.org/wiki/info/index.php/Macromolecular_Geometry

morph server question

Q:

I am currently using your server to morph two actin structures (open nucleotide cleft and closed). Besides morphing the two actin chains, I would also like to morph the bound ATP molecules. Although I can the two actin structures to morph, I cannot seem to figure out how to morph the ATPs. So basically my question is: can bound nucleotides be morphed? How should they be defined in the PDB filem which server to use, and should the morphs be done separately (i.e. protein and ATP as separate morphs)?

A:

Thank you for your query, and for using MolMovDB. Specifically, which server is it that you have been using, and what error message(s) are returned? It is sometimes the case that the formatting of the PDB files must be manually changed in certain ways, and this in and of itself can be a little tricky. If you like (and if you don’t mind), you may send the PDB files to me, and I will spend some time on trying to format them for the server. If all else fails, it may indeed be necessary to morph things separately, but combining the resultant morphs may be an endeavor on its own.

Finally (and importantly), I should point out that the PDB formats may not be the issue at all; it may be the case that that there is an issue with ATP constituting ‘heteroatoms’. Dealing with heteroatoms in our server is extremely difficult, and this is sometimes a result of the way in which they’re numbered in your input files. In addition, parameterizing heteroatoms using our interpolation software is very difficult (to the point that, if you do indeed obtain a morph, the resultant interpolation may be very questionable, so it may be a use-at-your-own-risk practice if the parameterization is not done properly).