blast.pdb problem

[Ahmed Adel Ezat]

I have a problem with plast.pdb function.

I am trying to reproduce "Part I: Ensemble NMA of E.coli DHFR structures tutorial" and I get this error.

library(bio3d) aa <- get.seq("1rx2_A") trying URL 'http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&val=1rx2_A&report=fasta&retmode=text' Content type 'text/plain' length unknown downloaded 210 bytes

Warning message: In get.seq("1rx2_A") : Removing existing file: seqs.fasta

blast <- blast.pdb(aa) Searching ... please wait (updates every 5 seconds) RID = 9UKCSCE501R Error in if (any(chain.ind)) { : missing value where TRUE/FALSE needed sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=Arabic_Egypt.1256 LC_CTYPE=Arabic_Egypt.1256
[3] LC_MONETARY=Arabic_Egypt.1256 LC_NUMERIC=C
[5] LC_TIME=Arabic_Egypt.1256

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] bio3d_2.2-4

loaded via a namespace (and not attached): [1] parallel_3.3.1 tools_3.3.1 grid_3.3.1

Best, Ahmed A Ezat

[Lars Skjærven]

Please update to the last version of bio3d, e.g. with

devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

[Ahmed Adel Ezat]

I tried to run this command but it fails and I don't why.

devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/") Downloading bitbucket repo Grantlab/bio3d@master trying URL 'https://cran.rstudio.com/bin/windows/Rtools/Rtools33.exe' Content type 'application/x-msdos-program' length 129680178 bytes (123.7 MB) downloaded 22.8 MB

Installation failed: Could not find build tools necessary to build bio3d Warning message: In utils::download.file("https://cran.rstudio.com/bin/windows/Rtools/Rtools33.exe", : downloaded length 23928832 != reported length 129680178

devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/") Downloading bitbucket repo Grantlab/bio3d@master trying URL 'https://cran.rstudio.com/bin/windows/Rtools/Rtools33.exe' Content type 'application/x-msdos-program' length 129680178 bytes (123.7 MB) downloaded 123.7 MB

Installation failed: Could not find build tools necessary to build bio3d

devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/") Downloading bitbucket repo Grantlab/bio3d@master Installation failed: Failure when receiving data from the peer devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/") Downloading bitbucket repo Grantlab/bio3d@master Installation failed: Failure when receiving data from the peer

Best and Thanks for help,

Ahmed A Ezat

[Lars Skjærven]

Are you on windows? Looks like you need to install Rtools to be able to compile the package.

Try first with install.packages("bio3d"). This will give you bio3d v2.3-3 that should have this fix installed.

[Ahmed Adel Ezat]

Thanks Dr. Lars. It works with me.

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[Ahmed Adel Ezat]

Sorry Dr. Lars, but I get this problem again.

When trying to reproduce the tutorial, I got this result and also for other problem, I got this result.

The hits I got after blast search doesn't contain any pdb ids.

Warning message: package ‘bio3d’ was built under R version 3.4.3 Warning message: In get.seq("1rx2_A") : Removing existing file: seqs.fasta Searching ... please wait (updates every 5 seconds) RID = AHZWUZBF01R

Reporting 100 hits * Possible cutoff values: -5 Yielding Nhits: 100

• Chosen cutoff value of: 225 Yielding Nhits: 0

[Lars Skjærven]

Looks like the format has changed from NCBI. subjectids are seperated with a "_" instead of "|".

Ahmed: you can use the hmmer() function until we sort out this issue.

[Lars Skjærven]

issue with parsing results from NCBI. Lines 53-60 in get.pdb

[Ahmed Adel Ezat]

Also, hmmer() function gives me this issue.

Warning message: In get.seq("1rx2_A") : Removing existing file: seqs.fasta * Trying 193.62.193.80... * Connected to www.ebi.ac.uk (193.62.193.80) port 80 (#0) Host: www.ebi.ac.uk Accept:text/xml Content-Length: 181 Content-Type: application/x-www-form-urlencoded

• upload completely sent off: 181 out of 181 bytes < HTTP/1.1 301 Moved Permanently < Content-Type: text/html < Location: https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan < Connection: Keep-Alive < Content-Length: 0 <
• Connection #0 to host www.ebi.ac.uk left intact
• Issue another request to this URL: ' https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan'
• Switch from POST to GET
• Found bundle for host www.ebi.ac.uk: 0x89975d0
• Trying 193.62.193.80...
• Connected to www.ebi.ac.uk (193.62.193.80) port 443 (#1)
• successfully set certificate verify locations:
• CAfile: C:/Users/Ahmed Adel/Documents/R/win-library/3.4/RCurl/etc/ca-bundle.crt CApath: none
• SSL connection using TLSv1.0 / ECDHE-RSA-AES128-SHA
• Server certificate: Institute; OU=European Bioinformatics Institute; CN=www.ebi.ac.uk
• subjectAltName: www.ebi.ac.uk matched
• issuer: C=BM; O=QuoVadis Limited; CN=QuoVadis Global SSL ICA G2
• SSL certificate verify ok. Host: www.ebi.ac.uk Accept:text/xml

< HTTP/1.1 500 Internal Server Error < Server: Apache/2.2.15 (Red Hat) < Content-Type: text/html; charset=iso-8859-1 < Strict-Transport-Security: max-age=0 < Access-Control-Max-Age: 1000 < Access-Control-Allow-Origin: * < Connection: close < Access-Control-Allow-Methods: HEAD, POST, GET, OPTIONS, DELETE, PUT < Access-Control-Allow-Headers: x-requested-with, Content-Type, origin, authorization, accept, clie$ < Content-Length: 614 < * Closing connection 1 Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 15 and body Opening and ending tag mismatch: body line 4 and html Premature end of data in tag html line 2 Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Opening and ending tag mismatch: hr line 15 and body 5: Opening and ending tag mismatch: body line 4 and html 6: Premature end of data in tag html line 2

[Lars Skjærven]

I just tested this multiple times with the newest code. and it works here. What R version are you on now? Also, windows or linux?

[Ahmed Adel Ezat]

windows, R version 3.4.1

[Lars Skjærven]

which bio3d version? copy and paste the result from sessionInfo()

[Ahmed Adel Ezat]

R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=Arabic_Egypt.1256 LC_CTYPE=Arabic_Egypt.1256 LC_MONETARY=Arabic_Egypt.1256 [4] LC_NUMERIC=C LC_TIME=Arabic_Egypt.1256

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] tools_3.3.1

[Lars Skjærven]

you need to load the bio3d package before running sessionInfo()

[Ahmed Adel Ezat]

Warning message: package ‘bio3d’ was built under R version 3.4.3 R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] bio3d_2.3-3

loaded via a namespace (and not attached): [1] compiler_3.4.1 parallel_3.4.1 tools_3.4.1 Rcpp_0.12.12 grid_3.4.1

[Lars Skjærven]

You need the bugfix released in the development version. It should say bio3d_2.3-3.9000.

I believe you need to install RTools.exe, and then use command line to build it. see e.g. https://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html

or alternatively, install a virtual machine with ubuntu on, and install with devtools::install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

we should put up some info on how to compile bio3d in windows.

[Lars Skjærven]

fixed with commit 08afbd1