Pipeline Pilot Interface to FlexS User Guide
Contents
1. Parallel Processing Options True via SSH FlexS Configuration Implementation Parameters Figure 3 2 ops Connect to an FlexS Installation on the Pipeline Pilot Server Configuration file config_sp dat ic e Requirement FlexS is installed on a Linux machine available to the Pipeline Pilot server via ssh e General Steps 1 Set lt Run FlexS gt to via SSH 2 For the parameter lt Run FlexS gt via SSH gt Executable gt enter the path to the FlexS installation on the Linux machine For example software BioSolveIT flexs bin flexs 3 For the parameter lt Run FlexS gt via SSH gt Configuration gt enter the path to the FlexS configuration file For example software BioSolveIT FlexS config_sp dat 4 For the parameter lt Run FlexS gt via SSH gt Host gt enter the Linux machine host name e User specific steps 1 For the parameter lt Run FlexS gt via SSH gt User gt enter the user login name for ssh on the Linux machine 2 For the parameter lt Run FlexS gt via SSH gt Password gt enter the user password for ssh on the Linux machine 3 There are more advanced options to be found under lt Run FlexS gt via SSH gt Options gt for more specific ssh parameters Note the option lt Run FlexS gt via SSH gt Options gt Delete Results gt this may be useful for trouble shooting later You can save these settings in the compo2. FlexS Pipeline Pilot Interface to FlexS Version 2 1 0 1 User Guide for FlexS version 2 1 0 and above and Pipeline Pilot version 6 1 and above Edgar Derksen Sally Hindle HH FH Al Institut Algorithmen und Wissen schaftliches Rechnen 110 Fraunhofer Contents Contents 1 Quick Start Steps 1 1 Install FlexS dk ok oe Oe oO 1 2 Create or Update Protocols 2 1 About Flex 3 5 gale eee ee ee er 2 2 FlexS Component in Pipeline Pilot 2 2 1 Superpositioning 2 2 2 Virtual screening 4 9 as 3 The Internal and External FlexS Installations 3 1 BioSolvelT Web Installation 3 2 Using the FlexS Installation Component 3 3 Using Global Variables 3 4 Using Custom External FlexS Installations 3 4 1 To Connect to a FlexS Installation on the Pipeline Pilot Server 3 4 2 To Connect to a FlexS Installation on a Remote Linux Server 3 5 Running FlexS in Parallel in Pipeline Pilot 3 5 1 Running in Parallel on the Pipeline Pilot Server 3 5 2 Running in Parallel on a Remote Linux Cluster 3 5 3 Example Scenarios and Required Settings 3 6 Uninstallation 4 Trouble Shooting 4 1 Problems connecting to the external installation 4 2 Problems using the ssh Method 4 3 Further help and BioSolveIT PDF Reporter 5 Tips and Tricks 5 1 Other Significant Pa
3. The full error report can be found in the Jobs tab Tips and Tricks 5 1 Other Significant Parameters in the FlexS Components For detailed documentation of all parameters refer to the documentation you find in the Help area of the Pipeline Pilot window We list here particularly interesting parameters those that greatly influence the workflow or change the outcome of calculations or those that may help you understand what is hap pening in the component 5 1 1 lt Has Same File System gt FlexSImplementation lt Run FlexS gt via SSH gt Options gt Has Same File System gt The name of this parameter stands for ssh Has Same File System Normally for an ssh job Pipeline Pilot must first copy all the data required by FlexS to the lt Run FTrees gt via SSH gt Host gt using scp This is time consuming Itis possible that the Pipeline Pilot Server and lt Run FTrees gt via SSH gt Host gt actually share the same file system rendering the scp process unnecessary Select True if the Pipeline Pilot Server and lt Run FTrees gt via SSH gt Host gt share the same File System no copying of data is necessary Selecting False means Pipeline Pilot copies all the data to and back from the lt Run FTrees gt via SSH gt Host gt this is just a little slower but will always still work Leave the parameter set to False if you are uncertain 5 2 Accessing Other Domains within Pipeline Pilot Often in house da
4. The second variable file_server_FlexS_config must be set to the full path of FlexS configura tion Example C Program Files x86 BioSolveIT FTrees config_ft dat In comparison to FlexS auto installation see section 2 you need to check the compatibility between your defined installation and the components 3 4 Using Custom External FlexS Installations You can also use an existing external installation of the FlexS software This means you also have the opportunity to use settings different to those set by default To do this you must already have FlexS installed somewhere on your system outside of Pipeline Pilot To install FlexS yourself visit the download page at BioSolvelT http www biosolveit de download and fetch the download package for your system for the latest FlexS package Follow the instructions in the package to install FlexS and receive your licenses Enter the license infor mation for FlexS as described in the package and not using the parameter lt Run FlexS gt on PP Server gt License Server or License File gt as for the internal installation To use an external installation of FlexS you must change the value of the parameter lt Run FlexS gt on PP Server gt Use gt in the Implementation tab to preinstalled FlexS There are actually two ways to use FlexS with an external installation These are by using FlexS installed directly on the Pipeline Pilot server you are or by accessing a remote ma chine
5. Administrator user name and password e In the last field of the table Maximum number of simultaneous parallel processing subprotocols allowed change the value click Save and log out again 3 5 3 Example Scenarios and Required Settings ssh ops Parallel Processing Options Number of PP servers in list Number of ssh Hosts in list Number of Processes ops False 1 Behavior The calculation will run as one complete job on the Pipeline Pilot server ssh ops ssh Parallel Processing Options False Number of PP servers in list Number of ssh Hosts in list 1 Number of Processes Behavior The calculation will run as one complete job on the ssh host ssh ops ops Parallel Processing Options True Number of PP servers in list 1 Number of ssh Hosts in list Number of Processes 1 Behavior Default Induces the pipeline effect the job will run in chunks on the server processor s ssh ops ops Parallel Processing Options True Number of PP servers in list 1 Number of ssh Hosts in list Number of Processes gt 1 Behavior A true parallel effect the job will be run in chunks on the server processors ssh ops ops Parallel Processing Options True Number of PP servers in list Number of ssh Hosts in list 4 each with two processors 2 2 2 2 Number of Processes Behavior A true parallel effect the job will run in chunks in par allel split across 8 processors ssh ops ssh Parallel Processing Options
6. Installer component Download BioSolvelT in PipelinePilot package from http www biosolveit de download Read UserGuide within that package for fur ther details Note that both PP Client and PP Server need web access to run BioSolveIT Web Installer Without web access you need to follow one of the following sections in this chapter 3 2 Using the FlexS Installation Component The FlexS components are set by default to use a so called auto installation of FlexS This works as follows When you run either of the FlexS Calculator or Similarity components and the parameter lt Run FlexS gt is set to on PP Server and the parameter lt Run FlexS gt on PP Server gt Use gt is set to FTrees Auto Installation they search for a FlexS installation in the directory lt scitegic install directory gt public bin BioSolvelT and use this installation to run the calculation A html report pupup shows if a FlexS instal lation is not found in this directory Use FlexS installer component to install FlexS prior to run calculations In case of a default setup you don t need administrator rights to do this as it is actually Pipeline Pilot that car ries out the installation and not you as a user In special cases your system administrator prevents installations by PP and you need to ask him to install FlexS As this installation knows nothing about the licenses you may have for FlexS you have to supply the license information separately Thi
7. True Number of PP servers in list 1 Number of ssh Hosts in list 5 each with 2 processors Number of Processes 10 Behavior A true parallel effect the job will run in chunks in par allel split across 10 processors 3 6 Uninstallation Use the FlexS installer component to uninstall previous FlexS versions by switching Param eter Uninstall Previous Versions to True Use BioSolvelT Uninstaller component to uninstall all FlexS versions Note that this kind of deinstallation only removes FlexS versions installed by FlexS installer component or BioSolvelT web installer component Trouble Shoofing 4 1 Problems connecting to the external installation Other most commonly seen problems with FlexS in Pipeline Pilot is with the connection to the external FlexS installation For one thing FlexS itself must be correctly installed on the system independently of Pipeline Pilot it is essential first to make sure this is the case especially to make sure that FlexS can locate the licenses Once FlexS runs fine on your system the remaining key task is to make sure the paths to the executable and configuration file are correct within the Pipeline Pilot component When the error messages pop up they may contain an FlexSError in the error message box as in figure Go to the Jobs tab below the Protocol workspace and check under the last run job for a file called FlexSComponent Debug as in figure 4 2 Clicking on the link br
8. arameter to read all molecule records from the file 3 Set up FlexS component as described in Change the lt Number of Solutions gt parameter to 1 If you want to take more poses into account you have to do some extended analysis of the results after the superpo sition calculation using the components available to you in Pipeline Pilot check the Pipeline Pilotdocumentation for more information The result will now be one pose per input molecule The resulting poses need to be sorted to create a ranked list of your library Drag and drop a Sort Data component and connect it to FlexS component Set the parameter lt SortProperty1 gt to value BSIT_FlexS_Total_Score The lowest scores are the best in FlexS so set the parameter lt SortDirection1 gt to Increasing To select a subset of the resulting ranked list you can add a filter In this example we want to filter the 100 best results Drag and drop the component Range filter and connect it to the Sort Data component Set the paramter lt List gt to 1 100 Finally add a viewer or a writer component to view and or save your results Your pipeline may look like the example in figure 2 Change the workflow to your needs and for example try out some more detailed analysis The Internal and External FlexS Installations 3 1 BioSolvelT Web Installation The easiest way to download and install BioSolveIT packages and tools is to download and run BioSolveIT Web
9. e Mol2 Reader to your empty pipeline area Select a MOL2 file in the parameter tab with the parameter lt Source gt You can try out a MOL2 file in the examples folder of this package 2 Set the lt Maximum gt parameter to 1 to ensure you start with only one molecule This will form a quick example as a first test 3 Drag and drop FlexS component to your pipeline area and connect the output port of the molecule reader to the input port of FlexS component Go to FlexS component and define a query molecule file with the parameter lt Query gt in the parameter tab 4 By default 10 different docking poses will be calculated You can change this value at the paramter lt nofPoses gt be aware that FlexS can create hundreds of poses 5 To see a simple visual result of the poses with their scores drag and drop the com ponent HTML Table Viewer to your pipeline Connect the output pass port of FlexS component to the input port of HTML Table Viewer 6 Your workflow should look like the example in figure 2 1 and is ready to run hol2 Reader FlexS Sort Data Range Filter HTML Table Viewer Figure 2 2 Starting example for virtual screening 2 2 2 Virtual screening 1 Start with a molecule reader as described in In this example the reader de fines the library you want to screen You can also replace the MOL2 reader with any molecule reader available in the Pipeline Pilot collection Remember to change the lt Maximum gt p
10. ed list of the host names in the Linux cluster Then you must choose how many batchs in total you want the job to be split into and enter this total in the lt Processes gt parameter Remember to change the lt Batch Size gt to fit with the number of processes Figure B 5lmay help clarify how the method works 8 y help y 10 Processes 1 Server 10 ssh logins 5 ssh hosts Host 1 ad Z pe Host 2 PP Server mil Host 3 m Host 5 Figure 3 5 The method of parallel processing on Linux clusters in the FlexS component The Pipeline Pilot server is given 10 processes The 10 processes start an ssh job respectively distributed amongst the ssh hosts The Pipeline Pilot server will run with the number of processes given in lt Processes gt However in this case the processes the server receives are not the FlexS calculations them selves but instructions for starting the ssh jobs The server iterates through its 10 jobs each time spawning an ssh job on a Linux host Beware that the Pipeline Pilot server does not know how many processors the Linux hosts have so make sure you choose the number of lt Processes gt to fit the number of Linux hosts and their number of processors respectively be careful not to overload the Linux hosts Figure 3 6 shows the detailed settings required to set up the calculation as in figure 3 5 8 gs req Pp 8 Implementation User Mode Expert v a BE Run FlexS via SSH v E via SSH Executable flexs exe so
11. elf to see if you can recognize the problem In this case you can look in the temporary folders Pipeline Pilot sets up inter nally to find the output or if you are working with the ssh method set the parameter lt Run FTrees gt via SSH gt Options gt Delete Results gt to False so that you may then find the files retained on the ssh host these will be in the directory set under the ssh parameter lt Run FTrees gt via SSH gt Options gt Temp Path gt see the help text associated with this param eter to find its default value essentially a cryptically named folder whose name begins with the date and time of the job If you still do not know what is causing the errors write down as much information as possi ble relating to your installation scheme You can also create a PDF Report unsing BioSolveIT PDF Reporter component which summarizes installation data into one pdf file Send all the information to support biosolveit de Last error mex FlexS Poses Error FlexS executable run into Error FlexS Exit Code not 0 See Jobs Window gt FlexS_Poses_Debug for more Information OK Help Locate Error Details gt gt Figure 4 1 An error box reporting that the FlexS exited with error Protocol Name Status Start e 7 4 New Protocoll Finished Tue Oct 0 E New Protocoll Finished Tue Oct 0 E New Protocoll Errors txt FlexS Poses Debug v Jobs Help Error Figure 4 2
12. exS configuration file on the Pipeline Pilotserver For example C Programs BioSolveIT FlexS config_sp dat You can save these settings in the component 3 4 2 To Connect to a FlexS Installation on a Remote Linux Server Your existing FlexS installation could be on a Linux computer remote from the Pipeline Pilot server in this case we offer an alternative so you can use the remote installation in stead Here the calculations carried out by FlexS will be done on the remote Linux machine Pipeline Pilot logs into the Linux machine using ssh having copied all relevant files to the machine and will run the calculation there finally copying back all data it needs to the Pipeline Pilot server to continue with the pipeline This method is given the label via ssh You can see an example in figure 3 3 El Pipeline Pilot Professional Client Eile Edt View Tools Window Help paati meee SulPOA mA fal m Generic J Chemistry eder Prot Comp A z Help Jobs Parameters Information Error Ready Figure 3 1 See where your Pipeline Pilot Server is installed User Mode Default v E Run FlexS on PP Server v E on PP Server Use Preinstalled FlexS License Server or License File riz Custom Install Destination Ring Conformation Generator corina exe Executable flexs exe software BioSolvelT flexs flexs ve i software BioSolvelT flexs config_sp dat
13. ftware BioSolvelT flexs flexs Configuration file config_sp dat software BioSolvelT flexs config_sp dat E Host hostl host2 host3 host4 host5 User userl Password Options E Parallel Processing Options True v Batch Size 1 Server Processes 10 Implementation Parameters Figure 3 6 The options for parallel processing for the example shown in figure 8 5 would look similar to these As you may already have realised you could enter more than one Pipeline Pilot server at the lt Server gt parameter along with another entry for number of lt Processes gt as a comma separated list to execute a doubly parallel calculation Note to get this method to work you will need to change the maximum number of processes per Pipeline Pilot server The Pipeline Pilot Client will let you enter any number for the lt Processes gt parameter and does not warn you if this number is above the maximum Changing the maximum number requires Administrator rights The number of processes per Pipeline Pilot server is usually restricted to the number of processors of the server You must override this maximum to be able to set the number of processes you want for your parallel calculation In the above example the maximum must be set to 10 or more Take the following steps e Go to the Scitegic Server Home Page for example via the Help menu in your Pipeline Pilot client e Click on Pipeline Pilot Administration Portal and log in with the
14. have If you only have a single license then parallel calculations will not be possible Further choices in the set up of the parallel computing computing calculation depend on the number of Pipeline Pilot licenses you have plus your choice of connection to the external FlexS installation on PP Server or via SSH Implementation User Mode Expert v 4 BE Run FlexS on PP Server v E on PP Server Use Preinstalled FlexS v Executable flexs exe software BioSolvelT flexs flexs a Configuration file config_sp dat software BioSolvelT flexs config_sp dat El Parallel Processing Options True Mi Batch Size 1 B localhost Processes 1 Preserve Order True v r Implementation Parameters Figure 3 4 The options for tuning parallel processing are found in the Implementation tab It is important to note that a balance must be achieved between the overhead caused by running several calculations instead of one and the size of the calculation there is a lot of overhead involved in sending all the essential data to different computers and collecting the results For the FlexS component however we still think parallel computing will work also for parallel jobs with batch size 1 Of course these figures depend on the speed of your machines and network experiment with your set up if you intend to carry out large calcu lations often Also we advise you to read the Pipeline Pilot documentation about parallel processing to understand more fully how it
15. ings up HTML report with input and output data in a browser A correctly started FlexS job outputs the following header if there is a problem you will see some of this header and the point where the problem occurs Flexs Copyright Prediction of Ligand Superposition BioSolveIT GmbH Version L203 22 08 06 An der Ziegelei 79 Modules PVM CSUPER 53757 St Augustin Germany Authors C Lemmen M Rarey T Lengauer C Hiller B Kramer M Lilienthal F Sonnenburg M Zimmermann www biosolveit de Contact flexs biosolveit de Additional copyright notes Software basis C 2001 by Fraunhofer Gesellschaft FhI SCAI Getline library C 1993 by Chris Thewalt PVM library C 1997 by University of Tennessee Knoxville TN Torsion angle data C by GMD SCAI CCDC BASF AG 21 gt gt Running on gamma Linux 2 6 25 11 0 1 pae with 4 processors gt gt FlexS configuration file software BioSolveIT flexs config_sp dat loaded gt gt FlexS_base license check BioSolveIT keys succeeded 4 2 Problems using the ssh Method You may also experience problems using the ssh login for example the user name is un known or the host is not found 4 3 Further help and BioSolvelT PDF Reporter More complicated errors may arise during the running of FlexS Again though the errors will be collected and as much information shown as possible If you are familiar with FlexS you may want to take a look at all the output of the job yours
16. nent be sure not to save your own user specific login details in components available to others Implementation User Mode Default v EI Run FlexS via SSH El via SSH Executable flexs exe software BioSolvelT flexs flexs Configuration file config_sp dat software BioSolvelT flexs config_sp dat Host hostl User userl Password Implementation Parameters Figure 3 3 ssh Connect to an FlexS Installation on a Remote Linux Server via ssh All files necessary for the FlexS calculation will be transferred via scp between the Pipeline Pilot server and ssh Linux machine Files copied and files created the remote server are automatically deleted at the end of the job leaving no trace However in case the user would like to leave a copy of the calculation and result files on the Linux machine or for trouble shooting as mentioned above it is possible to set a parameter to tell Pipeline Pilot not to delete these files lt Run FlexS gt via SSH gt Options gt Delete Results gt False 3 5 Running FlexS in Parallel in Pipeline Pilot FlexS in Pipeline Pilot takes advantage of the parallel computing options available in Pipeline Pilot to speed up longer calculations This section tells you how to adjust the op tions to your system and needs You will find the options in the Implementation tab as in figure The most important limitation to a parallel processing calculation is the number of FlexS licenses that you
17. r of lig ands FlexS predicts the conformation and orientation of one ligand relative to the other which is known as the reference ligand The reference ligand is assumed to be rigid thus it should be given in a conformation which is similar to the bound state For further infor mation and references please visit http www biosolveit de FlexS The two main applications of FlexS are ligand superpositioning for example for COMFA QSAR and vir tual screening 1 Ligand superpositioning If you have a protein and a small molecule binding to it so called reference ligand but no structure of the protein you can take the structure of the reference as a negative fingerprint of the active site So in contrast to a docking calculation FlexS determines the structure of a test ligand by flexibly aligning to the reference The result is scored according to the similarity between the test and the reference structure To use FlexS for superpositioning within Pipeline Pilot see the example in section 2 Virtual screening with a reference ligand and a set of compounds to hand you want to rank the set of compounds according to how similar their structures are to the refer ence structure To use FlexS for virtual screening within Pipeline Pilot see the example in section 2 2 2Jand setup for parallel processing in section B 5 2 2 FlexS Component in Pipeline Pilot The component for FlexS in Pipeline Pilot is called flexs alignment xxx xml where x
18. rameters in the FlexS Components 5 11 lt Has Same File System gt 2 5 2 Accessing Other Domains within Pipeline Pilot Quick Start Steps Download current FlexS in PipelinePilot package on http www biosolveit de download 2 Extract FlexS package to a custom directory 3 From the custom directory import all components xml using PP Client via drag and drop to your components collection Install FlexS Drag and drop FlexS installation component from the components collection to an empty protocol Add your license for the executable of FlexS in the field for the parameter lt Run FlexS gt on PP Server gt License Server or License File gt in the Implementation tab if your license is available from a license server simply type in the name of the server in this format servername or if you have a license file then you may browse for it using the facility 3 Run protocol once it will result into a html report showing installation success For alternative installations and more details see chapter 3 Create or Update Protocols Drag and drop new components into a new protocol Update via a right click drag and drop of new component onto component reference in a protocol Now you are ready to setup the new components and run your protocol Introduction 2 1 About FlexS FlexS is a computer program for predicting ligand superpositions For a given pai
19. s is supplied using the parameter lt Run FlexS gt on PP Server gt License Server or License File gt as described above in the section i 11 The installation is carried out once only for that FlexS version and only once per server not per user The software is available to all users once it is installed 3 3 Using Global Variables Use global variables as an alternative to the FlexS installation component decribed in section Note that global variables will only be used if components are set to run auto installation see section 3 2 but no installation is done by an FlexS installation component yet Goto Administratin Portal accessible through the Server Home Page at http localhost 9944 if PP Server is installed on your local machine The Server Home Page is also available through your PP Client in menu lt Help gt Server Home Page gt Use default name scitegicadmin and password scitegic if you have not changed it yet Browse to lt Setup gt Globals gt Add Custom Global Protocol Properties Note that defining parameters within your protocol will override global variables if they are named the same Use parameters within your protocol instead of global variables only if you want to use a custom installation for that protocol The first variable file_server_FlexS_executable must be set to the full path of FlexS exe cutable available by the PP Server Example C Program Files x86 BioSolveIT FTrees ftrees exe
20. ta or even your own working data are accessible from a windows com puter via a domain a path starting for example z or A which you cannot find from within Pipeline Pilot That means you must first literally transfer the data to the Pipeline Pilot Server itself If you are using a Linux Pipeline Pilot server this hint does not apply 25 To get around this problem and make the Pipeline Pilot working environment much more flexible you can allow users access to domains you need Administrator rights to be able to do this Also check first that you should change these settings as they may have already been set to fit the current environment e Go to the Scitegic Server Home Page for example via the Help menu in your Pipeline Pilot client e Click on Pipeline Pilot Administration Portal and log in with the Administrator user name and password e In the Security tab go to Authentification e For the Authentification Method choose DOMAIN and a set of parameters will ap pear e Enter the domain name in the field Domain and choose Full for Impersonation e Choose DOMAIN for Retrieve Groups and leave Limit access to listed domains set to No e click Save and log out again After you have done this you will need to enter your domain login details when you start the Pipeline Pilot Client
21. where FlexS is installed using ssh The method is selected using the parameter lt Run FlexS gt Both methods are covered in more detail below 3 4 1 To Connect to a Flex Installation on the Pipeline Pilot Server The most common scenario is that you will have an installation of FlexS on the Pipeline Pilot server If you choose this option you just have to enter the path to the executable and configuration file as parameters in the Implementation tab Pipeline Pilot will then just start FlexS whenever it is required by making a call to the executable that you entered This method is given the name on PP Server On Pipelinepilot Server You can see an exam ple in figure 2 e Requirement FlexS is installed on the Pipeline Pilot server You can see which machine is the Pipeline Pilot server by starting your copy of Pipeline Pilot Client on your own workstation and find the name or IP of the server shown at the bottom right of the status bar see figure 1 You must find where the FlexS installation is on that machine e General Steps 1 Set lt Run FlexS gt to on PP Server 2 Set lt Run FlexS gt Use gt to Preinstalled FlexS 3 For the parameter lt Run FlexS gt on PP Server gt Executable gt enter the path to the FlexS installation on the Pipeline Pilotserver For example C Programs BioSolveIT FlexS bin flexs exe 4 For the parameter lt Run FlexS gt on PP Server gt Configuration gt enter the path to the Fl
22. works Note to set up large parallel processing jobs you will need Administrator rights to change one setting 3 5 1 Running in Parallel on the Pipeline Pilot Server You may have a multi processor machine as your Pipeline Pilot server If you also have the appropriate number of Pipeline Pilot and FlexS licenses the simplest way to start a parallel calculation is to raise the number of processes to the number of processors of the machine You could also have more than one Pipeline Pilot server available in your network If so you can enter a list of the server names at the parameter lt Server gt Below that for the parameter lt Processes gt enter a list of the number of processes each server should receive The lists are both comma separated and must be in corresponding order Remember to adjust also the lt Batch Size gt accordingly Note the path to the external installation of FlexS must be same on all servers 3 5 2 Running in Parallel on a Remote Linux Cluster We have developed an implementation in the component whereby a large cluster can be incorporated to run FlexS jobs without them having to be Pipeline Pilot servers However it must be a Linux cluster and the component must use the ssh method You must also have enough FlexS licenses available to the cluster The settings in the Implementation tab must be made as for running the ssh method with two important changes Instead of one lt sshHost gt enter a comma separat
23. xx is the version number Once you have installed the component See chapter 1 and you can drag and drop the FlexS component from your components window to your workflow area The reference ligand in FlexS in Pipeline Pilot is called the Query You must set the lt Query gt parameter of the FlexS component to specify the reference ligand to be used in 7 the calculation The query should be a molecule file readable by the standard reader com ponents of Pipeline Pilot You can also select a multi molecule file to align the test ligands against different reference ligands The test ligands are the incoming molecules from the pipeline You can find examples of molecule files within this package Now the FlexS com ponent is ready to run For each incoming molecule the FlexS component runs a calculation using the query which results in a set of poses These are ranked by the FlexS score Only the best lt Number of Solutions gt are output from the component You can change this optional parameter to set the number of poses to keep If the calculation for the input molecule fails the input molecule will be passed to error port The following two examples form a first simple tutorial to see how the FlexS component works 2 2 1 Superpositioning Mol Reader Flexs HTML Table Viewer Figure 2 1 Starting example for superpositioning 1 First you need a source for the input molecules Drag and drop a molecule reader component lik
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