MorphServer job

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)

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

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

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

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

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

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).

molmovdb job 014670-22217

Q:
I submitted a job to your morph server but after 4-5 days it is not yet completed. Could you please check if there is a problem or if I made a mistake in my submission?

I just gave two PDB codes for different conformations of maltose-binding protein (MBP). The two codes were 1OMP and 3MBP. They are both monomers and have the same number of residues, but 3MBP has a ligand bound.

A:
Indeed, it appears as if the issue has to do with PDB format irregularities. We have corrected these issues, and your morph may viewed by clicking the link below (please use Safari to view morphs, as Chrome and Firefox no longer support java):

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=057837-877

Feel free to let us know if you experience any further difficulties. Also, if you like, we’d be happy to send you all of the accessory files associated with this morph.

molmovdb.org reboot?

Q:
Still getting this message after several days.

The job 072540-24927 is not yet completed

The two files were 1ohu chain A

1ty4 chain A

A:
It appears as if the issue has to do with PDB format irregularities. Specifically, the sequences within ATOM fields do no match the residues reported in the PDB file’s SEQRES field. In any case, we have corrected these, and your morph may viewed by clicking the link below (please use Safari to view morphs, as Chrome and Firefox no longer support java):

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=056703-32536

Question about morph jobs “not yet completed” and errors

Q:
Greetings. Apologies for bothering you, but your morphing site suggests that
I contact you if a job is not finished in a day or so. The following jobs
were submitted last Friday:
– 692711-16199
– 692809-16356
– b692486-16007

For b692486-16007, at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.molmovdb.org_cgi-2Dbin_morph.cgi-3FID-3D&d=AwIFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=GXLLd-iiiG3R6K6OQPuu_LKCNRF_WFNNajU6UPeecr0&m=Pa2aCcufMFrEjabZ9RvhKK7vIb2V8KTTaDj5TsR6n7E&s=W6R2HgNPIB0eB-w_lOkuCjLbCf_3TMwfNsDf9Nr1lUQ&e=
I get the following message: "Your request could not be processed. The
following error was detected: Morph not found in database.”

A:
An investigation into your morphs has been completed, and we have identified likely causes of these errors. In all cases, it appears as if the errors are a consequence of the PDB file formats. Details on specific morphs are given below:

For kb protein: 2qke_monomer.pdb —> fsTB_avg_min.pdb —> 2qke_monomer.pdb
At least one major issue identified was the fact that there appear to be pathological residue formats. For instance, have a look at the beginning of the ATOM records for the PDB 2qke_monomer.pdb:
ATOM 1 N MET A 1 -8.932 -20.214 2.255 1.00129.79 N
ATOM 2 CA MET A 1 -8.182 -19.102 2.920 1.00129.79 C
ATOM 3 C MET A 1 -8.441 -19.104 4.433 1.00129.79 C
ATOM 4 O MET A 1 -8.910 -18.109 4.991 1.00129.79 O
ATOM 5 CB MET A 1 -8.608 -17.750 2.326 1.00129.79 C
ATOM 6 CG MET A 1 -8.651 -17.719 0.800 1.00129.79 C
ATOM 7 SD MET A 1 -9.005 -16.077 0.094 1.00129.79 S
ATOM 8 CE MET A 1 -10.801 -15.970 0.277 1.00129.79 C

Everything appears to be perfectly fine with this MET residue. But have a look at the corresponding MET (again, the first residue in the file) within the PDB file to which we are trying to morph (ie, MET 1 in fsTB_avg_min.pdb):
ATOM 1 N MET 1 -10.344 9.596 10.785 1.00999.99
ATOM 2 HT1 MET 1 -10.167 8.615 10.490 1.00999.99
ATOM 3 HT2 MET 1 -9.599 10.204 10.388 1.00999.99
ATOM 4 HT3 MET 1 -11.263 9.902 10.406 1.00999.99
ATOM 5 CA MET 1 -10.344 9.693 12.268 1.00999.99
ATOM 6 HA MET 1 -10.330 10.740 12.539 1.00999.99
ATOM 7 CB MET 1 -11.608 9.045 12.838 1.00999.99
ATOM 8 HB1 MET 1 -11.402 8.006 13.048 1.00999.99
ATOM 9 HB2 MET 1 -12.394 9.105 12.100 1.00999.99
ATOM 10 CG MET 1 -12.105 9.700 14.117 1.00999.99
ATOM 11 HG1 MET 1 -11.283 9.762 14.816 1.00999.99
ATOM 12 HG2 MET 1 -12.888 9.087 14.538 1.00999.99
ATOM 13 SD MET 1 -12.756 11.359 13.840 1.00999.99
ATOM 14 CE MET 1 -11.572 12.350 14.748 1.00999.99
ATOM 15 HE1 MET 1 -10.811 12.710 14.072 1.00999.99
ATOM 16 HE2 MET 1 -11.114 11.749 15.519 1.00999.99
ATOM 17 HE3 MET 1 -12.078 13.190 15.200 1.00999.99
ATOM 18 C MET 1 -9.108 9.019 12.853 1.00999.99
ATOM 19 O MET 1 -8.352 9.629 13.609 1.00999.99

Of course, the morph server is trying to morph each residue into the corresponding residue of the other PDB file. However, it is very difficult to do this, most likely because the residues given are actually completely different (your MET residue in fsTB_avg_min.pdb seems to have ~3 times the number of atoms, making it impossible to perform the morph). Notably, the MET 1 residue is not unique in this regard — it appears as if there are many other residues with completely different numbers of atoms and formats.

I would also mention that all morphs are pairwise (rather than being annotated as 3-way morphs in the way that you have this one) — thus, what we tried to generate was really the following: 2qke_monomer.pdb —> fsTB_avg_min.pdb

For ka protein:
truncated5c5e.pdb —> KaiA_transitionState.pdb —> kaiA_fromTernary.pdb —> KaiA_transitionState.pdb —> truncated5c5e.pdb

Again, one immediate issue here is that all morphs are pairwise. Thus, the following individual pairwise morphs are possible
truncated5c5e.pdb —> KaiA_transitionState.pdb
KaiA_transitionState.pdb —> kaiA_fromTernary.pdb
kaiA_fromTernary.pdb —> KaiA_transitionState.pdb
KaiA_transitionState.pdb —> truncated5c5e.pdb

However, a single continues morph between all 5 structures given (really a cycle between 4 morphs) is not possible.

Secondly, if you look closely at the files kaiA_fromTernary.pdb and KaiA_transitionState.pdb, these seem to be completely different sequences (ie, the sequence of residues are very different). Some sequence differences can indeed be tolerated by the morph server, but beyond a certain degree of sequence homology, morphing becomes unreliable and eventually impossible.

For kc protein: c1_from_BCcomplex.pdb —> c1_from_40om.pdb —> c1_from_BCcomplex.pdb

Here, one immediate issue is (as with the first morph), the residue formats seem to be completely different and incompatible. For instance, have a look at VAL 19 in c1_from_BCcomplex.pdb:
ATOM 1 N VAL A 19 41.315 27.606 60.932 1.00 43.58 N
ATOM 2 CA VAL A 19 40.989 28.635 59.949 1.00 41.68 C
ATOM 3 C VAL A 19 42.235 29.400 59.515 1.00 24.69 C
ATOM 4 O VAL A 19 42.771 30.221 60.265 1.00 37.44 O
ATOM 5 CB VAL A 19 39.924 29.626 60.510 1.00 46.84 C
ATOM 6 CG1 VAL A 19 39.678 30.796 59.562 1.00 31.21 C
ATOM 7 CG2 VAL A 19 38.613 28.894 60.761 1.00 49.29 C
ATOM 8 HA VAL A 19 40.613 28.209 59.163 1.00 50.01 H
ATOM 9 HB VAL A 19 40.237 29.983 61.356 1.00 56.21 H
ATOM 10 HG11 VAL A 19 39.011 31.383 59.952 1.00 37.45 H
ATOM 11 HG12 VAL A 19 40.509 31.279 59.434 1.00 37.45 H
ATOM 12 HG13 VAL A 19 39.360 30.452 58.712 1.00 37.45 H
ATOM 13 HG21 VAL A 19 37.962 29.523 61.109 1.00 59.15 H
ATOM 14 HG22 VAL A 19 38.296 28.519 59.924 1.00 59.15 H
ATOM 15 HG23 VAL A 19 38.766 28.185 61.405 1.00 59.15 H

Now compare this to the corresponding residue VAL 19 in the file c1_from_40om.pdb:
ATOM 1 N VAL A 19 -23.156 44.101 -9.426 1.00 64.75 N
ATOM 2 CA VAL A 19 -22.022 43.812 -10.291 1.00 58.63 C
ATOM 3 C VAL A 19 -21.671 42.331 -10.275 1.00 54.58 C
ATOM 4 O VAL A 19 -21.400 41.761 -9.218 1.00 55.90 O
ATOM 5 CB VAL A 19 -20.783 44.627 -9.874 1.00 52.74 C
ATOM 6 CG1 VAL A 19 -19.630 44.361 -10.818 1.00 47.35 C
ATOM 7 CG2 VAL A 19 -21.116 46.109 -9.837 1.00 61.62 C

The VAL 19 within this second file looks good, but there seems to be something wrong with the format of the VAL19 in the first file. It is likely that the errors are a result of a) the incompatible residue formats, and b) the unrecognizable format given in the 1st file. Here, again, I just use VAL19 as an example — many other residues in your file seem to have this issue.

In sum, we advise ‘homogonizing’ the file formats, and adopting conventional residue formats, if possible. You might want to run a python script to extract out the atoms that are consistent with standard formats, for instance. We cannot guarantee with 100% that this will fix everything, but we can guarantee that this is the ideal starting point for resolving these errors.

Thank you again for using the server, and please do not hesitate to contact us if you have further questions or experience further difficulty.