Important Considerations
-Please submit no more than 20 jobs at a time
FTMap Help
Welcome to FTMap! This page offers support for each facet of the FTMap server. Feel free to use one of the test cases from the Examples Page or use a protein of your own. The images below use the Angiotensin Converting Enzyme example.
Contents
- Login
- Sign Up
- Mapping
- Advanced Options
- Queue
- Status
- Status Abbreviations
- Results List
- Results Detail
- Probes
- Preferences
- Publications
- Contact
Login
When you arrive at the FTMap page, the first screen you see is the login screen, shown here:
- If you already have a username and password, fill in the boxes and click Login. Proceed to Mapping.
- If you prefer not to use an account, click the option below Login to use the server without an ID. Know that your job submissions will be publicly accessible.
- If you would like to sign up for an account, click the Sign Up option at the bottom of the screen. Proceed to Sign Up.
- If you are a returning user, but have forgotten your password, click Reset Password to have a new password emailed to you
Sign Up
Use the form on this page to create a new user account. Provide your First Name, Last Name, a unique Username, your Affiliation, and your Email. Enter the text in the image to Word Verification and click the Agreement checkbox, and then click Create Account. If you have entered everything correctly, an email will be sent to you with a password to Login. You can change this password later in Prefereences.
Mapping
This is the server home screen. From this page you can submit a new job. See below for descriptions of the information to enter into each box. Jump to Advanced Options to find further information.
- Job Name: [Optional] Provide a job name for this submission. If you choose to leave this blank, a unique ID will be created for this field.
- PDB: [Choose one]
The FTMap algorithm, regardless of the use of a PDB ID or an uploaded PDB file, removes all ligands, non-standard amino acid residues, and small molecules before mapping.
- PDB ID: Enter the four digit ID of a PDB or click Upload PDB.
- Upload PDB: Select Browse to upload a file containing a structure in PDB format. Please note that the server is unable to process jobs containing previous mapping results.
- Chains: Designate specific chains to be used by the server with whitespace separated chain IDs or leave blank for all chains.
- Advanced Options: Click here to see detailed information about Advanced Options.
- Map: Click the Map button when all the fields are filled to your satisfaction to submit your job. Your job will enter the Queue
Advanced Options
Click the Advanced Options label on the Map page to see more options.
- Protein Mask: Upload a file to mask specified atoms as non-interacting. See this guide for how to create a mask file.
- PPI Mode: Detect binding hot spots for protein-protein interactions using an alternative set of parameters.
- Nucleic Acids: PDB includes nucleic acids. This option uses a specific set of parameters and must be selected for any file containing nucleic acids.
Queue
Use this page to see the status of your submitted jobs. Jobs are run in order of there submission. Runtime will vary by job. Click on a job ID to see a detailed Status Page. See the Status Abbreviation table for a description of the various job statuses and their meanings.
Status
This page shows the detailed status of a job that is currently running.
- Job ID: Unique job ID number and job name.
- Job Info: Information about this job including status, submission time stamp, and PDB ID. Definitions of statuses can be found in this table.
- Input: Pictoral representations of the uploaded and processed inputs.
- Probe Status: Status for each small molecule probe. See the Probe Status Abbreviation table.
Status Abbreviations
This table shows a list of job statuses and their descriptions that are seen on the Queue and Status pages.
| Status | Description |
|---|---|
| processing pdb files | downloading pdbs from the PDB web site, processing chain information, extracting the chains the user specified |
| pre-docking minimization | running charmm to add missing atoms and polar hydrogens, minimizing the added atoms in the presence of the protein |
| calculating PB potential | using charmm to calculate the Poisson-Boltzmann potential around the protein |
| copying to supercomputer | copying the pdbs and PB potential to the cluster where FTMap will run |
| held on supercomputer | files are on cluster, but job is not yet submitted |
| in queue on supercomputer | jobs for all probes have been submitted on the cluster, but they have not started running |
| running on supercomputer | jobs have begun running on the cluster |
| finished on supercomputer | all probes have run FFT and minimization on the cluster |
| coping to local computer | results are being copied from the cluster back to the FTMap server |
| clustering and minimization | individual probes are clustered, then consensus sites are generated by clustering across probes |
| calculating interactions | calculate nonbonded and hydrogen bonded interactions between probes and the protein using HBPlus |
| finished | everything is complete |
This table shows a list of probe statuses that can be found on the Status Page.
| Status | Description |
|---|---|
| Queued | waiting in the cluster queue to run FFT |
| Running FFT | probe is running FFT on the cluster |
| Clustering | post-FFT clustering of probes |
| Queued for minimization | waiting in the cluster queue to minimize probes |
| Running Minimization | probe is being minimized on the cluster |
| Finished | probe has finished minimization on the cluster |
Results List
See a list of your completed jobs. Click a job ID to see Result Details. Click next-> or <-prev to see more completed jobs.
Results Detail
See detailed information about a completed job.
- Job Details: Job name.
- Download: Download your results in PDB format or as a PyMol Session.
- Contact Graphs: Bar graphs show contact frequency per residue from FTMap results.
- Probe Summary: Download a text file summary of clusters and their probe compositions.
Contact Graphs
The contact graphs display the contact rate of structure residues as a percent of total contacts. One graph is for nonbonded residue interactions, the second for hydrogen bond interactions. These results can be downloaded as a tab separated file with exact residue contact counts by click the link located directly beneath each respective graph.
Probes
| ID | Name |
|---|---|
| 1acd | acetamide |
| 1acn | acetonitrile |
| 1act | acetone |
| 1ady | acetaldehyde |
| 1amn | methylamine |
| 1bdy | benzaldehyde |
| 1ben | benzene |
| 1but | isobutanol |
| 1chx | cyclohexane |
| 1dfo | N,N-dimethylformamide |
| 1dme | dimethyl ether |
| 1eol | ethanol |
| 1eth | ethane |
| 1phn | phenol |
| 1ths | isopropanol |
| 1ure | urea |
Preferences
Set options for your FTMap account.
- Enter a new password for your account.
- Select or deselect email notification for completed jobs.
Publications
Please cite these papers in any publications that make use of FTMap.
Contact
Feel free to contact us with any additional questions.
