Category Archives: molmov

Server errors on molmovdb

Posted on by
Reply

Q:
I was trying a couple of tools: Morph Server and RigidFinder and in both cases I get a server error indicating that files could not be written. Specifically, RigidFinder complains: "Cann’t write to file ‘/tmp/rid74285/upfile1.pdb’." and Morph Server says "Can’t create morph directory!". If this site is still being maintained, please consider addressing these issues.

A:
Thank you for your interest in our servers and for letting us know of
problems you’ve encountered.

Rigidfinder’s disk filled up. I cleared some space and it should be
working again.

Molmovdb, however, is a more complicated issue. It needs an upgrade
since it is more than 15 years old. Occasionally, we simply roll back
to a previous version but then any submissions would be lost. We also
cannot guarantee when the next roll back would be.

We apologize for any inconvenience this may have caused. We provide
related software in our FAQs for those who are interested.
http://www2.molmovdb.org/wiki/info/index.php/Related_Resources

Question re. Yale Morph Server

Posted on by
Reply

Q:
I’m having trouble with the multi-chain morph server. My protein includes chains that are designated as an upper case “A” and lower case “a”. When I upload the PDB file and specify all chains including A and a, the resulting Morph PDB file does not contain the lower case chain a. Is there any way to fix this problem?

A:
Thank you for reaching out to us regarding the morph server. It is perhaps the case that the server is internally case-insensitive with regard to the chain. If possible, I would suggest changing chain "a" to a different letter in the PDB input file (ie, by changing "a" to "B" using a simple script). Then, once you get your output from the server, you can again change chain "B" to the original label chain "a".

Yale Morph Server job not being completed

Posted on by
Reply

Q:
I uploaded my PDB files on the multi-chain morph server, the job ID is b499364-832. It has been two days but the results page still says that the job is not yet complete. Is there any problem with my morph? I understand that my files are very large so it may take a long time to finish, but is it possible that it takes this long? I would really appreciate your assistance.

A:
Files generated by the multi-chain server can be found in
http://www.molmovdb.org/uploads/<job ID>/
Yours are in
http://www.molmovdb.org/uploads/b499364-832/

Looking at it, some files seem to be missing.
For e.g., a complete run would look like
http://www.molmovdb.org/uploads/b649592-16743/

There is a job running and it seems to be related to yours
"/usr/bin/perl ./multi.pl b499364-832 –chains=WCBAXHGFEDJLMNOPQRYAIS
–nframes=8 –email=seiga –engine=CNS –debug"

The short of it is that your job is probably stuck since you seem to
have submitted it 6 days ago judging from the submit time. Note that
we cannot guarantee the full functionality of this service as it is
from 2005 and has not been fully maintained since. Occasionally, we
may roll back but that would mean you will need to resubmit your job.

MorphServer job

Posted on by
Reply

Q:
I am trying to use Morph Server, my job ID: b198308-29491
It has been running for 5 days and is still not completed. Could you please check?

A:
The files in the folder of your jobs seems to indicate that it
finished successfully. You can find the files using

http://www.molmovdb.org/uploads/JobID

So yours would be in

http://www.molmovdb.org/uploads/b198308-29491/

Unfortunately, some of the other features of the web interface need
maintenance.

HingeAtlas (2007)

Posted on by
Reply

Q:
I am reading your Hinge Atlas (2007) paper.
I searched for your dataset to study the pdb structures you used and their
hinge residues, but I could not download it from the page:
http://molmovdb.org/cgi-bin/sets.cgi.
Could you please send a file if it is possible by email, or please check and
fix if there is a bug on the web page.

A:
Please try the Hinge Atlas Gold while we investigate the webpage. This may take time.

Tab delimited Hinge Atlas Gold

Posted on by
Reply

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.

MolmovDB job ID b956969-31750

Posted on by
Reply

Q:
Could you please have a look at my submission from yesterday and tell me what I did wrong that they job does not finish?

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b956969-31750

A:
The server is running fine. Please follow the tutorial vedio for input file preparations. We are not responsible for user’a input files that are not compatible with the original script of the server.

We do not run jobs for those users, given that the server runs fine as it is originally supposed to be. There’s FAQ and tutorial I made on the webpage that you should follow.

Questions About MolmovDB Database

Posted on by
Reply

Q:
I am working with conformational change in protein structure. I would like to do some
research using your molmovdb (Domain motion) database, however I check
the website and it doesn’t work. How could I get access to the Molmov
database?

I mean when I tried to check the molecular movements database at this address

http://www.molmovdb.org/cgi-bin/browse.cgi

I got error msg when i opened morph button:

"Your request could not be processed. The following error was detected:
Morph va1cbuB-1c9kB not found in database.
Please email protmot if you think this message was caused by a server error.

Last year, we developed a probabilistic model for detecting rigid domains.

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw442

We use Dyndom database for benchmarking which contain a lot of redundancies. I am looking for alternative database for benchmarking our methods.

A:
Would you mind sending me the PDB files you submitted, as well as you job ID, and we’ll investigate. In the meantime, we’ve compiled a list of related resources that may be of interest:

http://www2.molmovdb.org/wiki/info/index.php/Related_Resources

Also — what do you mean when you say it does not work?

it no longer sends out acknowledgement emails. However save the morph ID and come back later (sometimes as long as a day later) to check on it.

You can also use my macromoleculebuilder (MMB) software. It’s good if you have a very large complex undergoing a large scale conformational change.

problem with server MolMovDB

Posted on by
Reply

Q:
It has been a while i am uploading my pdb files on morph server but did no receive any answer. I have checked both files and the atoms are the same. i am afraid what is the problem??

Is it possible to check my uploaded jobs and tell me what is the error causing the problem? it would be very helpful to solve my pdb files problem. Here is the code of last job 755599-30494.

A:
There seems to be something wrong with your PDB files, because when we try running the single-chain server using other PDB pairs, it seems to work fine with those PDBs. For instance, when running the PDBs attached to this email, the following morph is generated (using Safari to visualize the morph):

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=800501-5588

At first glance, your PDBs do not seem to have chain fields. May we ask how you produced your PDB files? Would it be possible for you to re-build the files with the chain fields set to the letter "A" (or any other arbitrary letter)? Then we will continue from there.

Macromolecular Database Question

Posted on by
Reply

Q:
I have come across the Macromolecular Database and I
was curious to how a degree of motion is quantified in this site. In the
following link for one of the entries (HIV protease:
http://www.molmovdb.org/cgi-bin/motion.cgi?ID=hivprot), the third box from
the top entitled ‘Description’ says of HIV protease:

"Two large loop regions, that together comprise one quarter of the
structure, move CA atoms ~7 Angstroms"

Is this referring to a RMSD value of an ensemble of structures? Is this a
RMSD value of the whole protein, or only for the domain of those two large
loop regions?

A:
This is described in the DB paper
(http://papers.gersteinlab.org/papers/molmovdb2).