contacts in BUNCH

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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tmulhern
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Joined: 2007.11.21 08:08
Location: Australia

contacts in BUNCH

#1 Post by tmulhern » 2007.11.21 08:14

I am using the windows version of BUNCH 8.0 and it won't read my .cnd file. So, I tried the tutorial gst-dhfr and it also would not read the associated .cnd file. Is it just me or is this a bug?

SaxsMax
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#2 Post by SaxsMax » 2007.11.21 22:25

could you post your cnd file?
What is the error?

tmulhern
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Joined: 2007.11.21 08:08
Location: Australia

BUNCH contacts

#3 Post by tmulhern » 2007.11.23 02:15

This is the error message when attempting the GST-DHRF tutorial

- E -- worng format of conditions file
1 77 77 2 86 86

----------------------------------
Here is the contents of the condition file

dist 7.0
1 77 77 2 86 86
dist 7.0
1 69 69 2 97 97

This is unchanged from the files distributed.

I get the same sort of message for my own system. I have successfully used my own .cnd file in SASREF for another system, so I think I understand the syntax there. I have tried all sorts of interpretations of the ordiants numbers, but can get it to read anything.

SaxsMax
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#4 Post by SaxsMax » 2007.11.23 12:44

Hm, this is strange.
What is your operating system?
Do you use the answers file from the bunch package (gd01.ans)

Just in case (though it is not relevant),
there is a difference between the sasref and bunch contacts files:
for sasref the first and the fourth numbers are the subunit #,
for bunch they are chain # (and not domain #)

tmulhern
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Location: Australia

Problem solved!

#5 Post by tmulhern » 2007.11.26 00:44

It was a syntax problem after all. :D I was unaware the th 1st and 4th numbers were chain identifiers and not subunit identifiers. I have it working now. By the way, the tutorial contacts.cnd file for the gst-dhfr should be changed accordingly to 1 and 1, as that is a single chain multidomain example. It currently has the 1 and 2 as the 1st and 4th numbers, respectively -and also doesn't work.

I didn't see this difference between SASREF and BUNCH conditions syntax flagged anywhere in the BUNCH manual or readme file. Is it noted? Did I just not see it?

Thanks,

Terry

SaxsMax
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#6 Post by SaxsMax » 2007.12.11 16:12

By the way, the tutorial contacts.cnd file for the gst-dhfr should be changed accordingly to 1 and 1, as that is a single chain multidomain example
No, that is right. There is two-fold symmetry and therefore there are two chains

tankozavr
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#7 Post by tankozavr » 2010.11.12 17:11

Thanks to Terry!
I have also created a chimera sequence of a single polypeptide chain and forgot that all subunits are #chain 1# now.

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