Category Archives: structures

Conformation Explorer

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Q:
I’m trying to use Conformation Explorer.

I have submitted a job, but looks like Proxy error. Is this server still working?

Server message:
The job ce199231-3887 is not yet completed. Please check again a few minutes to a day from the time of your initial submission.

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /cgi-bin/morph.cgi.

Reason: Error reading from remote server

Here’s the URL and job ID: http://molmovdb.org/cgi-bin/morph.cgi?ID=ce199231-3887&type=choosehinge

Server message:
The job ce199231-3887 is not yet completed. Please check again a few minutes to a day from the time of your initial submission. If this job is older than a day or so, please contact the server administrator. Email: Mark.Gerstein _at_ yale.eduI wanted to know how conformation of protein changes due to ligand addition.

A:
Unfortunately, the server is experiencing problems and we do not have a developer maintaining this right now. All files generated and related to your submission are in http://www.molmovdb.org/uploads/ce199231-3887/ . The PDB movie file looks like it consists of one frame when viewed in VMD so I do not think a movie was successfully produced by the server.

Genodock

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Q1:
We are running some docking and would like to use genodock for some experiments too. Is it something that we can install on our servers to run? who should we talk to for more details? I have also noticed that the server is currently down. We would actually like to even run on our cloud environment for some more intensive computation. Is there a github or sth or any documentation about it? or would you happen to know more about it?

A1:
The webserver was in a hung state at the moment, but will be back up shortly.

Q2:
We are trying out Genodock on http://genodock.molmovdb.org/calculation/0. But unfortunately none of the models worked.

A2:
There’s enough file space in the device and nothing obviously and immediately stands out to me why the 77 print(….) line should fail. Nothing in his user history indicates that any other service should be running.

I restarted it and it now works. See below for details:

The error probably was due to the function ‘print’ which couldn’t find its stdout handle to log. I have restarted the server with this command:

nohup python3.6 manage.py runserver 0.0.0.0:80 >nohup.out 2>&1 </dev/null &

This should be the same as how the server previously started:
root 25966 25965 0 2020 ? 00:00:00 python3.6 manage.py runserver 0.0.0.0:80
root 25968 25966 2 2020 ? 1-05:19:32 /usr/bin/python3.6 manage.py runserver 0.0.0.0:80

Hopefully the nohup, redirects and background execution, which previously may or may not have it all, together can prevent this problem from happening again. You probably know but just fyi, the way that it started (which is now restarted) might not be fully production level:
https://docs.djangoproject.com/en/2.2/ref/django-admin/#runserver

Request for example input and output files of Hotspot Community pipeline

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Q:
We are interested in using the HotCommics pipeline to identify hotspot
communities from our own cancer mutation data. However, we have
difficulty in running the pipeline because we could not find
description of the input files in the snpMapping and the
hotSpotCalculation step. Could you kindly help to provide us some
example input files so that we can appropriately format our input?

A:
Thank you for your interest in our work. The input file for SNP
mapping step is the input file for VAT tool, which can be the vcf file
that you. are working with. Alternatively, you can also use a
tab-separated file with header information described below.

#CHROM hg19_pos ID Ref Alt Tumor_Sample_Barcode
Matched_Norm_Sample_Barcode Info

http://vat.gersteinlab.org

For the hotspot community identification, you will have to run the
community identification module for each PDBs on which your mutations
have mapped to

https://github.com/gersteinlab/HotCommics/tree/master/communityIdentification

Once you have generated these communities and have a list of PDBs on
which mutations have mapped to then you will need to provide the list
of PDBs for hotspot calculation.

Question re. Yale Morph Server

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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

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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.

A question about 3V

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Q:
Regarding your paper entitled "3V: cavity, channel and cleft volume calculator and extractor", which I read carefully.

I’ve a question for you. In the abstract, it is written the following:"It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces,…", but I think you mean "two imaginary rolling-probe solvent-excluded surfaces" because after looking at your code, I haven’t seen any analytic SES formulation therein. I guess you are just using two probe spheres of distinct radii to account for cavities, not the analytic SES themselves. Am I right?

A:
I am not certain about your use of the term "imaginary", but I would say my method is a "discrete approximation" to the SES. And because it is discrete (i.e. a 3D grid) one can simply subtract one grid from another. See attached figures.

With small grid sizes (0.2 A), I see very little discrepancy to the analytical solution.

voxel_analytical2.pdf

voxel_exclude_hires2.pdf

voxel_exclude_lowres2.pdf

pnas paper supplement duplication

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Q1:
I am reading with interest your recent paper (Kumar, Clarke, and Gerstein, PNAS), but I suspect that supplement 1 and 2 are the same, and neither has a list of 434 genes. Could you please supply the list?

A1:
Thank you very much for your interest in the paper. Supplement 1 includes hotspot communities based on pan-cancer analysis (i.e., when will compute statistics over multiple cancer cohorts in TCGA). In contrast, supplement 2 lists out putative driver genes with hotspot communities for specific cancer types. If you note in supplement2, column F list out the name of particular cancer cohorts.

Regarding the number of genes, 434 genes are based on the pan-cancer analysis.
For each gene, there are multiple PDB entries. For analysis in our paper, we selected a representative structure with the highest residue coverage. However, to be exhaustive and allow researchers to analyze protein of their interest, in our supplement, we include all PDB entries for a given gene. We have tried to explain this in our method section.

Q2:
Thanks for your quick reply; but, no, this does not remove my confusion. Please take a moment to check the link from your paper at PNAS. When I download pnas.1901156116.sd01.xlsx, the file has 217 lines (not 434) and includes the column F that breaksdown by cancer type.

A2:
I am attaching our original tables with the email. It appears that the table has been somehow duplicated on the PNAS website. We will work with the PNAS team to get it fixed.

Supplemental_tables.xlsx

HingeAtlas (2007)

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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.

MolmovDB job ID b956969-31750

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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.