Issue in Alignment and how to use Amber trajectory?
Hi I'm new and using Bio3d a very good package but I'm having problems in using Bio3d. First using an online alignment source (EMBL-EBI) the alignment is always showing the following error;
pdbaln("SigH.pdb", "G15.pdb", web.arg=list(email="abbaskhan@sjtu.edu.cn")) Reading PDB files: SigH.pdb .
Extracting sequences
pdb/seq: 1 name: SigH.pdb Error in if (fit) s$xyz <- pdbfit(s) : argument is not interpretable as logical In addition: Warning message: In seqaln(s, id = files, ...) : nothing to align
Further please explian how to use Bio3d for Amber trajectory Analysis?
Thanking you.
Comments (8)
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reporter aln <- pdbaln(c(files), web.arg=list(email="abbaskhan@sjtu.edu.cn")) Reading PDB files: split_chain/1rx2_A.pdb split_chain/1df7_A.pdb split_chain/4kne_A.pdb split_chain/3sgy_B.pdb PDB has ALT records, taking A only, rm.alt=TRUE .. PDB has ALT records, taking A only, rm.alt=TRUE ..
Extracting sequences
Will try to align sequences online...
Job successfully submited (job ID: muscle-R20170111-040222-0641-99291228-pg) Waiting for job to finish...
pdb/seq: 1 name: split_chain/1rx2_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 2 name: split_chain/1df7_A.pdb pdb/seq: 3 name: split_chain/4kne_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 4 name: split_chain/3sgy_B.pdb Warning message: running command 'muscle -version' had status 127
pdbs <- read.all(aln) pdb/seq: 1 name: split_chain/1rx2_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 2 name: split_chain/1df7_A.pdb pdb/seq: 3 name: split_chain/4kne_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 4 name: split_chain/3sgy_B.pdb plot(modes, pdbs=pdbs) Error in plot(modes, pdbs = pdbs) : object 'modes' not found modes <- aanma(pdbs, rtb=TRUE) Error in (function (aln, id = NULL, profile = NULL, exefile = "muscle", : You do not have muscle installed/working locally on your machine. We can attempt to use the EBI webserver if you provide an email address (required by the EBI). Please note that the EBI states (see their Terms of Use): 'Using fake e-mail address may result in your jobs being killed and your IP, Organisation or entire domain being black-listed.' In addition: Warning message: running command 'muscle -version' had status 127
Again Error
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Can you organize your command and output and re-post them? There are a few buttons on the top of the text box you wrote down your issues. Use the one named 'code' (which looks like '<>') and use the language 'r'.
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reporter aln <- pdbaln(c(files), web.arg=list(email="abbaskhan@sjtu.edu.cn")) Reading PDB files: split_chain/1rx2_A.pdb split_chain/1df7_A.pdb split_chain/4kne_A.pdb split_chain/3sgy_B.pdb PDB has ALT records, taking A only, rm.alt=TRUE .. PDB has ALT records, taking A only, rm.alt=TRUE ..
Extracting sequences Will try to align sequences online... Job successfully submited (job ID: muscle-R20170111-040222-0641-99291228-pg) Waiting for job to finish...
pdb/seq: 1 name: split_chain/1rx2_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 2 name: split_chain/1df7_A.pdb pdb/seq: 3 name: split_chain/4kne_A.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 4 name: split_chain/3sgy_B.pdb Warning message: running command 'muscle -version' had status 127
Error in plot(modes, pdbs = pdbs) : object 'modes' not found modes <- aanma(pdbs, rtb=TRUE)
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Please switch the order of
modes <- aanma(pdbs, rtb=TRUE)
andplot(modes, pdbs = pdbs)
. You can't use the object that you haven't generated! -
reporter aln <- pdbaln(c(files), web.arg=list(email="abbaskhan@sjtu.edu.cn"))
Reading PDB files: split_chain/1rx2_A.
pdb split_chain/1df7_A.pdb split_chain/4kne_A.
pdb split_chain/3sgy_B.pdb
PDB has ALT records, taking A only, rm.alt=TRUE ..
PDB has ALT records, taking A only, rm.alt=TRUE ..
Extracting sequences Will try to align sequences online...
Job successfully submited (job ID: muscle-R20170111-040222-0641-99291228-pg) Waiting for job to finish...
Warning message: running command 'muscle -version' had status 127
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This is a warning message indicating you don't have muscle installed. It shouldn't affect you because your alignment is done online. Check the aln object and see if it is what you want (simply type
aln
and return will show the alignment). -
- changed status to resolved
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You should use a vector not separate arguments for input pdb files. Try
pdbaln(c("SigH.pdb", "G15.pdb"), web.arg=list(email="abbaskhan@sjtu.edu.cn"))
.Try trajectory analysis, please read the tutorial here http://thegrantlab.org/bio3d/tutorials/trajectory-analysis.