Issue in Alignment and how to use Amber trajectory?

[Abbas Khan]

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="[e-mail]")) 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.

[Xinqiu Yao]

You should use a vector not separate arguments for input pdb files. Try pdbaln(c("SigH.pdb", "G15.pdb"), web.arg=list(email="[e-mail]")).

Try trajectory analysis, please read the tutorial here http://thegrantlab.org/bio3d/tutorials/trajectory-analysis.

[Abbas Khan]

aln <- pdbaln(c(files), web.arg=list(email="[e-mail]")) 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

[Xinqiu Yao]

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'.

[Abbas Khan]

aln <- pdbaln(c(files), web.arg=list(email="[e-mail]")) 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)

[Xinqiu Yao]

Please switch the order of modes <- aanma(pdbs, rtb=TRUE) and plot(modes, pdbs = pdbs). You can't use the object that you haven't generated!

[Abbas Khan]

aln <- pdbaln(c(files), web.arg=list(email="[e-mail]"))

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

[Xinqiu Yao]

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).