Path to the loops archive in coral

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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bnolen
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Path to the loops archive in coral

#1 Post by bnolen » 2012.01.18 19:41

I have installed the ATSAS (2.4.2) package on linux CentOS 5.7 and am having some trouble getting Coral to work. Upon startup the command line input asks:

Enter dir name (path) to the loops archive:

I’m assuming (and maybe this is where I’m wrong!) that the loops archive is in the /atsas/lib/

But when I enter that path, I get:

STOP Cannot find the loop database

I’ve tried pointing it to all of the other directories under /atasas without success.

I’ve also installed ATSAS on my mac (OS X lion 10.7.2) and am having the same problem.

My apologies if this has been addressed, but I haven’t run into any thread that covers this yet…

Alex
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#2 Post by Alex » 2012.01.18 20:20

Hi

I am not a MAC expert. Essentially, CORAL is trying to find a DB generated
by RANLOGS, which is named 'dbloop.zip'.

I suggest you find it in the directory where ATSAS was installed and
provide absolute PATH when CORAL is asking for it.

Please, report here if this could fixed your problem.

Thanks, Alex

bnolen
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path to the loops archive in coral

#3 Post by bnolen » 2012.01.19 19:29

I could not find the dbloop.zip file on either the mac or linux installation, either in the atsas directory or anywhere else on the hard drive. We have a PC with atsas installed, so I moved copied the dbloops.zip file from the windows installation onto both the mac and the linux machines. I provided the absolute path when coral asked for it and it worked!

However, I ran into another problem and again, this problem occurred on both the mac and linux installations.

File name with objects info ............ <con>: coral
caution: filename not matched: 011/*
At line 37 of file /home/franke/svn/atsas-current-release-branch/atsas/coral/read_db_linux.for
Fortran runtime error: Bad integer for item 1 in list input

At first I thought this might be a problem with the .con file, but I've gotten the same error with .con files that work on our windows atsas installation. I also get the error when using the example .con file in /atsas/share/doc/atsas-2.4.2/coral/example

Any ideas?

SaxsMax
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Download CORAL loop library for Linux/Mac

#4 Post by SaxsMax » 2012.01.20 12:23

The archives with the loops database are somewhat different for Win and Linux/Mac.
Please download the Linux/Mac loops database.

Paige
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Re: Path to the loops archive in coral

#5 Post by Paige » 2012.05.25 16:03

I've been running into the same problems with directing into the path (I'm running ATSAS 2.4.2-4 on my Mac, Lion OS 10.7.4,).
It tells me that it can not find the loop database.

* I've downloaded the the Linux/Mac loops database
* Put it in a folder that I want to put my CORAL Data in
* During the step where it ask "Enter dir name (path) to the loops archive":
* I simply provided the full path: Volumes/Macintosh\ HD/Users/paige/Research/HWI/saxs/coral/dbloop.zip

I have tried different variations, such as:
* Volumes/Macintosh\ HD/Users/paige/Research/HWI/saxs/coral/
* I unzipped the zip file provided the path Volumes/Macintosh\ HD/Users/paige/Research/HWI/saxs/coral/dbloop

I am wondering if it matters where I put the loops database or if I'm doing anything wrong that I just can't see.
Last edited by Paige on 2012.05.30 19:38, edited 2 times in total.

Alex
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Re: Path to the loops archive in coral

#6 Post by Alex » 2012.05.26 18:59

i would have tried putting db to a PATH which does not have empty spaces.

I also created a version of CORAL that does not depend on the loop DB - it
should be available in the future as a part of the ATSAS suite - so stay tuned.

HTH
Alex

Paige
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Re: Path to the loops archive in coral

#7 Post by Paige » 2012.05.26 19:09

I can't control the name for the Macintosh HD --> it came on my mac that way

I am looking forward it the new release of CORAL. When do you think that would be?

Andrew
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Re: Path to the loops archive in coral

#8 Post by Andrew » 2012.05.30 03:18

Paige wrote:* I simply provided the full path: Volumes/Macintosh\ HD/Users/paige/Research/HWI/saxs/coral/dbloop.zip

I have tried different variations, such as:
* Volumes/Macintosh\ HD/Users/peihang/Research/HWI/201204_saxs/coral/
* I unzipped the zip file provided the path Volumes/Macintosh\ HD/Users/peihang/Research/HWI/201204_saxs/coral/dbloop

I am wondering if it matters where I put the loops database or if I'm doing anything wrong that I just can't see.


You have specified a relative path i.e. should be /Volumes/..... not Volumes/....

In any case, why can't you just specify: /Users/paige/Research/HWI/saxs/coral/dbloop.zip ? The /Volumes/Macintosh\ HD/ is redundant for the local boot disc.

Paige
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Re: Path to the loops archive in coral

#9 Post by Paige » 2012.05.30 15:01

It worked! You have to believe me when I say I thought tried something like that before I started diving into the whole Volumes/Macintosh thing.

Thanks Andrew!

mwilce
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Re: Path to the loops archive in coral

#10 Post by mwilce » 2012.08.13 14:52

Hi,
regarding the loops database for coral05 run on either linux or OSX - is there an environmental variable that can be defined to point the location of the loop database?
Cheers,
Matt

Alex
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Re: Path to the loops archive in coral

#11 Post by Alex » 2012.08.28 23:30

no, there is no. But you can indicate it in your answer file:
coral < ans.txt

in the future, hopefully, there will be a version of CORAL which does
not rely on the loop db.

Best, Alex

mwilce wrote:Hi,
regarding the loops database for coral05 run on either linux or OSX - is there an environmental variable that can be defined to point the location of the loop database?
Cheers,
Matt

lwc
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Re: Path to the loops archive in coral

#12 Post by lwc » 2014.11.24 04:02

Going to bump an ancient post for my stupid question, rather than make a whole thread.

In ATSAS 2.6.0 it seems to no longer be possible to specify the loop path in the interactive mode. I assume this is because it's supposed to know where the loops are. Unfortunately, the CentOS 6.xx release is giving "Cannot find the loop database at coral/dbloop" and then exiting, and since the interactive option is gone, I can't see a way to correct it.

I've simply unzipped the tar archive into a folder where I keep my applications, haven't renamed anything. The loop db is definitely present at $apps/ATSAS-2.6.0-1/share/atsas/coral/dbloop/, including .pdb files in ./005/ ./010/ etc. My PATH and LD_LIBRARY_PATH variables point to $apps/ATSAS-2.6.0-1/bin and $apps/ATSAS-2.6.0-1/lib64, respectively.

Any chance another environment variable has been added in the last couple of years? Any other workaround?

- Lachlan

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AL
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Re: Path to the loops archive in coral

#13 Post by AL » 2014.11.24 11:54

lwc wrote:Any chance another environment variable has been added in the last couple of years?
Yes! Try

Code: Select all

$ export ATSAS=$apps/ATSAS-2.6.0-1

lwc
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Re: Path to the loops archive in coral

#14 Post by lwc » 2014.11.26 02:01

Great, that worked. Thanks Al.

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