Q1:
I needed to use the Hinge Atlas Gold for my research. I tried using http://www.molmovdb.org/tarballs/hinge_atlas_gold/hinge_atlas_gold.txt link as mentioned in the paper and on the link but it doesn’t have any data but just the metadata.

Can you please help me with this?

A1:
does
http://www.molmovdb.org/tarballs/hinge_atlas_gold/
have what you need?

Q2:
I needed to know annotated hinge residue numbers and their corresponding PDB IDs/ Morph IDs from Hinge Atlas Gold

The link: http://www.molmovdb.org/tarballs/hinge_atlas_gold/hinge_atlas_gold.txt
Has information about the data but not the actual data.
Paper and the link mentions that It is supposed to have tab-delimited data as it says:
This is a tab-delimited database of hinge predictor results and gold standard hinge annotation for the Hinge Atlas Gold dataset used in our submitted HingeMaster manuscript, also used in our BMC Bioinformatics paper, ‘FlexOracle: predicting flexible hinges by identification of stable domains’ by Flores et al.
However, the data is not present over there. Please let me know where I can find it.

A2:
There was a script on the server to refres/regenerate the mysql dump ever so many years ago. It is possible this was run in some way that led to an empty result.

I looked at the Hinge Atlas Gold gallery

There was a script on the server to refres/regenerate the mysql dump ever so many years ago. It is possible this was run in some way that led to an empty result. I looked at the Hinge Atlas Gold gallery (http://molmovdb.org/cgi-bin/movie.cgi?set=HingeAtlasGold ) but it seems to not work either, at least I cannot follow it to pull up the individual morphs. This was all years ago, I don’t have access now which is just as well since I probably don’t have time to debug.

Maybe someone in Mark’s lab can get the gallery back up?

Q3:
Thank you for the response. I read your reply and based on that, I have a suggestion:

‘Hinge Atlas’ (Not Hinge Atlas Gold) link seems to work (http://www.molmovdb.org/tarballs/hingeatlas/hingeatlas.txt) so maybe the shell script in hinge atlas (following):

echo "drop table temp; create table temp select distinct(stats.mid_) from sequence, stats where stats.mid_=sequence.mid_ and stats.nonredundant=1 and (sam_hinge or leslie_hinge); select sequence.mid_,resnum,restype,(sam_hinge or leslie_hinge) from sequence,temp where sequence.mid_=temp.mid_ order by mid_,resnum;" | mysql -u root -p molmovdb > hingeatlas.txt

will possibly work if everything stored in the same table just by replacing stats.nonredundant=1 to stats. (Something representing Hinge Atlas Gold field)

Again, this is just a suggestion.

A3:
The numbering does not seem to quite match up with 1dv2 or 1bnc.pdb . I think maybe it has to do with some renumbering of the PDB file. Probably ff1.pdb would settle this.

Q:
I am interested in using some of the data stored in molmovdb, but I am unable to access the data. For example, from the page:

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

Once I click on automated set 2 the page returns “Sorry, no values in this range ( to ). Please try again!”

This happens on many (if not all) of the links. Is this data still available, or has the site been effectively decommissioned?

A:
this is something that is selected in lib/select.pm. Look at the explanation of the %selectors at the top of that file.

For example, for ‘auto’, the non-redundant automatic set, the selector uses the getNR function, which ultimately looks at this file to get the morph ID’s:

/usr/local/server/htdocs/tmp/auto.txt

You can similarly obtain the automatic set, which is not from a text file but rather an sql query.. you’ll see what I mean.