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    Simon Bray
    @simonbray
    Also welcome @praveenkumarpgiindia and @Nitin0304Gupta_twitter, though I know you joined already a few weeks ago
    chrisbarnettster
    @chrisbarnettster
    :clap:
    chrisbarnettster
    @chrisbarnettster
    Hi everyone! Birds of a Feather session starts soon and looking forward to seeing you there! 9:15 UTC+2 22/07/2020 https://sched.co/d8A0
    Björn Grüning
    @bgruening
    Thanks @chrisbarnettster!
    Simon Bray
    @simonbray
    Just a reminder: the birds-of-a-feather session is on now
    Simon Bray
    @simonbray
    Congratulations @tsenapathi and @chrisbarnettster on the new paper!
    Tharindu Senapathi
    @tsenapathi
    Thanks @simonbray !!
    chrisbarnettster
    @chrisbarnettster
    Thanks @simonbray. Also waiting in anticipation for our j chem informatics one to be released as well 🙏🏻
    Jamshaid-2020
    @Jamshaid-2020
    Congratulations @chrisbarnettster and @tsenapathi
    Tharindu Senapathi
    @tsenapathi
    Thanks @Jamshaid-2020
    George Kobakhidze
    @Kokobashky36_twitter
    Hi @simonbray , I am working through your Protein-ligand docking tutorial on Galaxy training. However I cannot find some of the tools such as "Search ChEMBL database", "Prepare receptor" or "Calculate the box parameters..." when I search through Tools on the left. I would really appreciate any help!
    sometimes the Galaxy search behaves a bit strangely
    George Kobakhidze
    @Kokobashky36_twitter
    Oh maybe it's because I'm on Galaxy Australia. Sorry I'm new to Galaxy. Are the tools different for different regions?
    George Kobakhidze
    @Kokobashky36_twitter
    OK I just registered for Galaxy Europe and I can find them all now. Thanks for the help!
    Simon Bray
    @simonbray
    Oh yes that would be the reason
    There are multiple separate Galaxy servers and they all have a slightly different selection of tools available
    chrisbarnettster
    @chrisbarnettster
    Thanks @simonbray, @Kokobashky36_twitter glad you are able to get going with these tools on Galaxy EU !
    ARMI CHAUDHARI
    @ARMIFS97_gitlab
    hello everyone.

    I performed protein RNA complex simulation in Schrodinger, and want to study DCC for the same.

    I covert Schrodinger trajectories to the DCC in VMD. I uploaded the pdb files and DCD file and was able to generate the graph for C-alpha atoms for protein.

    for nucleic acid i was facing problem as i have tottle 48 nucleotide but DCC graphs was showing 1522 resides,which is due to atoms selection. i rectify that error using selecting the Atom id 'P'. which generated the graph for only 48 residues which i want.

    Now the last step which i want is combine graph of protein and RNA residues, I have tabular file for booth as a different but i want combine graph for protein. I tried using CA and P for nucleic acid., but end up getting error.

    It will be great help to generate the combine graph for protein and RNA.

    chrisbarnettster
    @chrisbarnettster
    Hi @ARMIFS97_gitlab This is a great usecase and not sure if supported in the current tool. Maybe we can improve it, @tsenapathi do you have any ideas.
    ARMI CHAUDHARI
    @ARMIFS97_gitlab
    so is there is anyway to form correlation graph of combine protein and RNA?
    chrisbarnettster
    @chrisbarnettster
    @ARMIFS97_gitlab are you able to share a history with myself or @tsenapathi , we could have a look at the system and try help out?
    ARMI CHAUDHARI
    @ARMIFS97_gitlab
    sure. As I mentioned above simulation was performed in Schrodinger, meanwhile then i followed below mention steps. 1. where .out-cms file is converted in dcd format through VMD. 2. Used galaxy europe BIO3D i uploded respective DCD file of trejcetory and PDB file. 3. Selelcted Atoms CA for protein then got DCC for protein. 4. In another run selected atoms name P and got DCC for RNA. 5. as i want to get combine graph i typed P and CA but got error. (R-studio i installed bio3D where the issue is same i am able to select 'inds' for protein and RNA seperatly but not combine. if will be really great if this issue can be resolved.
    ARMI CHAUDHARI
    @ARMIFS97_gitlab
    image.png
    instead of CA I type P for RNA and i got DCC for RNA but further I type CA and P combine graph it is giving error. (if any other data is required please tell me)
    ARMI CHAUDHARI
    @ARMIFS97_gitlab
    trj <- read.dcd(trtfile, cell = FALSE)
    NATOM = 30378
    NFRAME= 1002
    ISTART= 0
    last = 1002
    nstep = 1002
    nfile = 1002
    NSAVE = 1
    NDEGF = 0
    version 24
    |======================== | 21%Error in readBin(trj, "numeric", size = 8, n = (a/8), endian = head$end) :
    invalid 'n' argument
    In addition: Warning messages:
    1: In readBin(trj, "integer", 1, endian = head$end) :
    closing unused connection 3 (wt.dcd)
    2: In rbind(x, y, z) :
    number of columns of result is not a multiple of vector length (arg 3) this is warning in reading pdb file.
    Simon Bray
    @simonbray
    Maybe an interesting read for some people here: https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.9b00779
    Björn Grüning
    @bgruening
    Cool, thanks @simonbray
    Jamshaid-2020
    @Jamshaid-2020
    Interesting, thanks @simonbray
    Simon Bray
    @simonbray
    Hi @trachtok, could you post those example InChIs again? I'll try and test the tool out
    Karolína Trachtová
    @trachtok
    @simonbray :D you are super fast! I am still fighting with how to put it here in some reasonable way...

    Hi, I have a question regarding tool Remove counterions and fragments in chemicaltoolbox. When I use SMILES as an input, it seems to work fine but when I input InChI nothing happens.

    Original InChI
    InChI=1S/C13H14N4O3S.Na/c1-8-6-13(12(15)7-11(8)14)17-16-9-2-4-10(5-3-9)21(18,19)20;/h2-7H,14-15H2,1H3,(H,18,19,20);/q;+1/p-1
    InChI after removing counterions and fragments
    InChI=1S/C13H14N4O3S.Na/c1-8-6-13(12(15)7-11(8)14)17-16-9-2-4-10(5-3-9)21(18,19)20;/h2-7H,14-15H2,1H3,(H,18,19,20);/q;+1/p-1

    Simon Bray
    @simonbray
    Not really, just confused by why a message kept appearing and disappearing :)
    you can try putting slanted quotes on each side of the string like this `
    Karolína Trachtová
    @trachtok
    Yeah, that was me exploring how to post things in gitter :D sorry for the confusion...
    Simon Bray
    @simonbray
    Hi @trachtok, after some testing, it seems this is a bug in OpenBabel. I made a bug report here: openbabel/openbabel#2288
    As a workaround, I suggest you try converting to SMILES before running the 'remove counterions' tool
    Karolína Trachtová
    @trachtok
    Hi @simonbray, thanks for looking into this!
    Karolína Trachtová
    @trachtok
    And I have another question which is more general, is there any tool within Galaxy that can, given InChI/SMILES, recognize that the input is inorganic/organometallic/mixture and mark this compound as such? I am currently trying to translate compounds (from InChI) to QSAR-ready SMILES (basically SMILES without stereoisomerism, neutralized, without salts) which can be done using chemicaltoolbox, but I would also like to remove any inorganic/organometallic/mixture compounds completely. I can pretty much do this using simple grep but why write something if there is already such a tool :)
    Simon Bray
    @simonbray
    Hm, we don't have such a tool as far as I remember. But it shouldn't be difficult to do the same with the general grep and filter tools, as you suggest
    We have a public workflow which downloads compounds from a number of online databases and standardises them, which uses those tools several times
    but probably a simple grep is indeed the best solution
    Martin Cech
    @martenson
    This is potentially very helpful, thanks @simonbray !
    Simon Bray
    @simonbray
    You are welcome!
    We have a few different workflows under the 'cheminformatics' tag here: https://usegalaxy.eu/workflows/list_published
    If you are working on QSAR stuff maybe this one is also of interest: https://usegalaxy.eu/u/sbray/w/cheminformatics-ml