Problems running Ranch90

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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David
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Joined: 2008.06.14 20:36
Location: Imperial College London

Problems running Ranch90

#1 Post by David » 2012.01.28 23:24

Dear all,

I am not able to run Ranch90 using two fixed domains. The program runs ok fixing one domain, but fails to run with both domains fixed. I would appreciate very much if anyone could tell me what I am doing wrong. Attached I am sending the input files.

Thanks,

David
Attachments
Nter.pdb
N-terminal domain
(68.23 KiB) Downloaded 416 times
Cter.pdb
C-terminal domain
(116.14 KiB) Downloaded 377 times
102-sA.dat
experimental data
(96.87 KiB) Downloaded 392 times
seq.seq
sequence file
(383 Bytes) Downloaded 389 times

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Giancarlo
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Location: EMBL Hamburg, Germany

Problems running Ranch90

#2 Post by Giancarlo » 2012.01.30 12:01

Hi David,

We just noted that Ranch90 has some problems reading sequence file with Windows characters codification. Maybe, you use Windows. I tried your test case on my machine (Unix) and it works perfectly.
I am going to fix this bug anyway. Thanks for reporting it.

Meanwhile, if you want to continue to use Ranch90 please use the sequence file in attached. It's apparently exact the same, but with Unix characters codification. Please, note that if you open the file and save it again on your machine, such characters will be replied again by the Windows ones (if you use Windows).

Ciao,
Giancarlo
Attachments
seq.seq
sequence file
(383 Bytes) Downloaded 388 times

David
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Location: Imperial College London

#3 Post by David » 2012.01.30 12:24

Thanks Giancarlo for your quick reply,

Unfortunately the sequence file is not the issue, since Ranch90 runs fine when using either 1 domain or 2 domains (one fixed, one not fixed). The problem appears when using 2 fixed domains. (I am using Windows).

Thanks,

David

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Giancarlo
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Location: EMBL Hamburg, Germany

#4 Post by Giancarlo » 2012.01.30 12:30

David wrote: Unfortunately the sequence file is not the issue, since Ranch90 runs fine when using either 1 domain or 2 domains (one fixed, one not fixed). The problem appears when using 2 fixed domains. (I am using Windows).
For some strange reasons the sequence file becomes a problem as described in the previous post. I tried your case exactly as specified by you (both domains fixed) and it works.
Try to use the file sequence I sent you.

Keep me posted. :)

Ciao,
Giancarlo

David
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Posts: 6
Joined: 2008.06.14 20:36
Location: Imperial College London

#5 Post by David » 2012.01.30 13:22

Giancarlo wrote:
David wrote: Unfortunately the sequence file is not the issue, since Ranch90 runs fine when using either 1 domain or 2 domains (one fixed, one not fixed). The problem appears when using 2 fixed domains. (I am using Windows).
For some strange reasons the sequence file becomes a problem as described in the previous post. I tried your case exactly as specified by you (both domains fixed) and it works.
Try to use the file sequence I sent you.
Dear Giancarlo,

It is very strange, I tried (twice) with your sequence file using Windows. The program runs, but does not progress beyond [ 1%]. Follow the link bellow to download the output files. Is there a binary for Mac I could try? Would you be so kind to send me the outputs to my e-mail account (davidalbesa (at) gmail.com).

http://dl.dropbox.com/u/15846600/logs.zip

Thank you,

David

bnolen
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Location: University of Oregon

problems running Ranch90 . . . revisited

#6 Post by bnolen » 2012.02.05 00:04

Hi David and Giancarlo,
I am having the same issue with ranch90 (on Windows). I tried generating a sequence file in a linux text editor to avoid potential issues with windows characters codification, but the problem persists- I can use identical input files for two runs, and the run with two domains fixed gets stuck at 1%, never outputting any pdb file, while the run with only one domain fixed runs without any problems.
I was wondering if anyone had been able to resolve this issue.

Thanks!
Brad

mdelcamp
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Joined: 2010.07.13 20:18
Location: USA

Re: Problems running Ranch90

#7 Post by mdelcamp » 2012.05.02 20:54

I have to say that I am running into the same issue here with a structure split into 3 PDB files. Ranch90 will only run properly if one of the PDB files is not fixed. The moment I try to fix all the PDB files the program hangs on 1% completion and does not output any models.

Mark

PhD_fm
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Joined: 2012.05.08 11:58

Re: Problems running Ranch90

#8 Post by PhD_fm » 2012.05.08 12:39

Hi,
I had done all thats you describe above, and after have been solved the problems with seq.seq, the program hangs on 1% yet, despite I fixed only one domain and the not the second ones, and chose Non pdb output. I have worked with a oligomers, maybe , could be a reason for don´t run properly the program??

Thank you.

Pablo.

PhD_fm
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Joined: 2012.05.08 11:58

Re: Problems running Ranch90

#9 Post by PhD_fm » 2012.05.08 17:13

Hi,

I tried only with one monomers and RAnch90 run succesfull,fixing one domain, but not with oligomer protein, in this case is hanging always ...

If some one found any solution, help me please.!!

Pablo.

PhD_fm
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Posts: 11
Joined: 2012.05.08 11:58

Re: Problems running Ranch90

#10 Post by PhD_fm » 2012.05.08 17:31

I have found the answer in another topic !!!. I have to choose Symetric, in firts opcions. (and also all that you have been described up)

thank you.

Pablo.

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