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.

Morphing TRAP1

Q1:
in the past months I tried several times to us the multi-chain morph server for creating a movie of the heterodimeric protein TRAP1. I never got an e-mail back and when I used the old version of the server it does not seem to come to a result since more than 24 hours. It always gives the message not completed yet. I am wondering what the problem is.

A1:
Thank you for your query regarding the server. We’ll look into this, but may I ask why you are using the old version of our server specifically? I only ask because I ran tests on our newer multi-chain server on Sunday, and things worked very well there:

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

Having said that, we’ll check on things. Would you mind providing us with your Job ID (if you still have it), as well as the PBD files which you’d like to morph?

Q2:
I used the old server because I had used the new one before several times with the same job and never got an e-mail that it was finished. the job number is m716893-2511.

A2:
I was unable to find the directory corresponding to your morph, so our apologies for that. There are two possibilities I can think of:

1) We recently did some minor work on the server. Things were down for a short time, but when I checked over the weekend, things were back to normal. It is possible that your issue was a temporary one.

2) The second possibility is that your PDB files have formatting irregularities or some type of heteroatom which is not being processed or recognized by our server.

The best way to address the 1st possibility is for you to just re-submit your jobs on the newer server [ http://molmovdb.org/cgi-bin/beta.cgi ], and see if everything works. The easiest way to address the 2nd possible issue may be if you just send us your PDB files, and we can have a closer look at them.

Q3:
I tried the morph again in ran through this time but the movie file was empty and the pdb-files I could download just had "end" written in them. I also tried pdb-files of single chains. I also removed heteroatoms and made sure the number of amino acids is identical in both files. The message I get from the server is that it is not yet complete. The latest jog has the number 018936-29130. I do not understand what is wrong with these pdb-files. Please find enclosed the template pdbs that I have tried last. It would be great, if you would find out what is wrong with this.

A3:
Your PDB files look very good. It is not clear why your previous submission failed, but we were able to successfully generate your morph. You may view it here:

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=032929-30641

You may or may not find the attached image useful, but we have also produced a structure alignment for you (blue corresponds to low-RMSD regions of the alignment, and red corresponds to regions with higher RMSD between your two structures).

no output files from the multichain server

Q:
One of my friends recommended Molmovdb to me to calculate the morph conformation. As a test, I have successfully generated the morphing conformation from the single chain server.

Then I tried to use the "multichain server" to generate the morphing conformations of my target proteins last Friday. Everything goes well. However, I did not receive any mails reminding me the progress until today. So I am wondering if I should wait more days.

Just in case, I submitted the same job again today. The job No. is b337528-18153. Would you like to give me a favor to check the progress?

A:
Thank you very much for your query, and for your interest in our server. We have been having problems with our server not sending emails, and we have a notice on our website notifying users about these email issues.

However, the good news is that you should still be able to access morphs. The best approach would be to just append your job ID to the standard URL. Thus, in your case, this would be:

http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b337528-18153

If you are still unable to see your morphs, you may email me the structures, and I will try to generate them for you through our server.

data stored in molmovdb

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.

accessing Database of Macromolecular Movements

Q:

I am developing a software for assessing similarity among flexible proteins. I
would like to test the software on the Database of Macromolecular Movements
to test my software, however I found no means to download multiple files. I
was wondering whether it is possible to get a data set with files containing
protein motions without separately accessing each and every entry in your
database.

What I would like to have, if it is possible of course, is the curated
files of the conformational changes and the corresponding PDB IDs. Let
me know whether it is possible or not.

A:

This may be doable, but it depends on what exactly you need. Do you want the frame-by-frame morph files, the video files, or the PDB IDs, or some other form of the data? Also, we actually have two databases: one is a manually curated set of about 200 conformational changes, and the other database is user-submitted. If you tell me more about the kinds of things you may need, I can likely send you the compressed files.

At the first URL below, you will find the curated set of motions. The second URL is an outbox that’s prepared for you, which contains these morphs (frame-by-frame) from the curated motions:

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

http://homes.gersteinlab.org/people/dc547/.curated_morphs__G_Mate/

Please let us know if you have trouble getting access for any reason.