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<div class="moz-cite-prefix">To be honest I can't see why it goes
wrong there. If you can send me the PDB file I could have a look
and maybe find out what's happening exactly.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<br>
On 07/01/2013 01:20 PM, M. F. wrote:<br>
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<blockquote
cite="mid:1372677637.83805.YahooMailNeo@web140705.mail.bf1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:arial,
helvetica, sans-serif;font-size:12pt">
<div><span><br>
</span></div>
<div style="color: rgb(0, 0, 0); font-size: 16px; font-family:
arial,helvetica,sans-serif; background-color: transparent;
font-style: normal;">Dear Jose and other users and developers,<br>
<br>
<br>
Thanks for previous helps on this matter, but it appears that
the problem in running the cmview for my pdb files is still
persisting. How can I generate a pdb file that cmview likes? I
changed the header to the one that was working, and I added
chainA to the column 22. When I wanted to load I still got two
options for chain (A & NULL (attached as NULL). I solved
that by adding numbers from the main pdb file.<br>
Then, I loaded again and I got <span style="font-weight:
bold;">wrong number format</span> error. Could you please
let me know how can I solve it? How can I have the right
format?<br>
<br>
Best regards<br>
Maryam<br>
<br>
<br>
</div>
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font-size: 12pt;">
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<hr size="1"><font size="2" face="Arial"><b><span
style="font-weight:bold;"></span></b></font>On
06/12/2013 12:10 PM, M. F. wrote:<br>
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id="yiv2988709245yui_3_7_2_33_1371031368009_60" style="font-family:times
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serif;font-size:14pt;">
<div
id="yiv2988709245yui_3_7_2_33_1371031368009_115"
class="yiv2988709245yui_3_7_2_33_1371031368009_63"
style="font-family:times new roman, new
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id="yiv2988709245yui_3_7_2_33_1371031368009_114"
class="yiv2988709245y_msg_container">
<div id="yiv2988709245">
<div
id="yiv2988709245yui_3_7_2_33_1371031368009_113">
<blockquote type="cite">
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_70"
style="color:#000;background-color:#fff;font-family:times
new roman, new york, times,
serif;font-size:14pt;">
<div><span><br>
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<div
class="yiv2988709245yui_3_7_2_33_1371031368009_71"
style="color:rgb(0, 0,
0);font-size:18.6667px;font-family:times
new roman, new york, times,
serif;background-color:transparent;font-style:normal;">Dear
Jose,<br>
<br>
Thanks I added chain A as you
said and it works. I am happy
that it helped to find out
about the bug. <br>
</div>
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_72"
style="color:rgb(0, 0,
0);font-size:18.6667px;font-family:times
new roman, new york, times,
serif;background-color:transparent;font-style:normal;"><br>
</div>
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_73"
style="color:rgb(0, 0,
0);font-size:18.6667px;font-family:times
new roman, new york, times,
serif;background-color:transparent;font-style:normal;"><br>
</div>
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_74"
style="color:rgb(0, 0,
0);font-size:18.6667px;font-family:times
new roman, new york, times,
serif;background-color:transparent;font-style:normal;">One
more problem that I have and I
do not know how to solve it,
is about running dssp. I don't
know what directory I should
put in the configure file for
the dssp file. I had done it
once and it was working but
now I can't make the same
configure file again! Could
you give me a hint? I will
appreciate it a lot? Or is it
a bug that dssp is not
running, since I read
something about it while I was
looking through the problem.<br>
<br>
Cheers<br>
Maryam<br>
</div>
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_75"
style="font-family:times new
roman, new york, times,
serif;font-size:14pt;">
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_76"
style="font-family:times new
roman, new york, times,
serif;font-size:12pt;">
<div dir="ltr">
<hr size="1"> <font
size="2" face="Arial"> <b><span
style="font-weight:bold;">From:</span></b> Jose Duarte <a
moz-do-not-send="true"
rel="nofollow"
class="yiv2988709245moz-txt-link-rfc2396E"
ymailto="mailto:jose.duarte@psi.ch" target="_blank"
href="mailto:jose.duarte@psi.ch"><jose.duarte@psi.ch></a><br>
<b><span
style="font-weight:bold;">To:</span></b>
M. F. <a
moz-do-not-send="true"
rel="nofollow"
class="yiv2988709245moz-txt-link-rfc2396E"
ymailto="mailto:mfaridun@yahoo.com" target="_blank"
href="mailto:mfaridun@yahoo.com"><mfaridun@yahoo.com></a>
<br>
<b><span
style="font-weight:bold;">Cc:</span></b>
<a
moz-do-not-send="true"
rel="nofollow"
class="yiv2988709245moz-txt-link-abbreviated"
ymailto="mailto:cmview-users@bioinformatics.org" target="_blank"
href="mailto:cmview-users@bioinformatics.org">cmview-users@bioinformatics.org</a>
<br>
<b><span
style="font-weight:bold;">Sent:</span></b>
Monday, June 10, 2013
6:10 PM<br>
<b><span
style="font-weight:bold;">Subject:</span></b>
Re: [cmview-users]
Problem running various
pdb files+dssp error<br>
</font> </div>
<div
class="yiv2988709245y_msg_container"><br>
<div id="yiv2988709245">
<div>
<div
class="yiv2988709245moz-cite-prefix">Thanks
a lot for sending
the file. So I've
managed to track it
down to a problem
with the chain code
used for the ATOM
lines (your file has
an empty chain code)
and the one used for
the SEQRES lines
(chain code A). It
is a bug in CMView:
it does not match
the 2 sequences up
and then tries to
guess a sequence
from the residue
numbers in ATOM
lines, instead of
using the SEQRES
one.<br>
<br>
In any case the
problem is solved if
you use the chain
code A for your ATOM
lines (replacing the
blank in column 22),
then you get the
correct contact map
displayed. Also I've
noticed that your
coordinates end at
TYR 226, but the
SEQRES sequence has
a few more residues.
It would be good if
you also removed
those from SEQRES so
that you don't have
a few trailing
unobserved (empty
coordinates)
residues.<br>
<br>
We'll try to fix the
bug at some point,
but that will take
some time as at the
moment we are bit
short of time.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<br>
On 06/10/2013 05:10
PM, M. F. wrote:<br>
</div>
<blockquote
type="cite">
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_83"
style="color:#000;background-color:#fff;font-family:times
new roman, new
york, times,
serif;font-size:14pt;">Dear
Jose,<br>
<br>
Unfortunately it
didn't work. Could
you please take a
look at the
attached file? <br>
<br>
Thanks a lot in
advance<br>
<div><span><br>
</span></div>
<div><br>
</div>
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_84"
style="font-family:times
new roman, new
york, times,
serif;font-size:14pt;">
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_85"
style="font-family:times
new roman, new
york, times,
serif;font-size:12pt;">
<div dir="ltr">
<hr size="1">
<font size="2"
face="Arial">
<b><span
style="font-weight:bold;">From:</span></b>
Jose Duarte <a
moz-do-not-send="true" rel="nofollow"
class="yiv2988709245moz-txt-link-rfc2396E"
ymailto="mailto:jose.duarte@psi.ch" target="_blank"
href="mailto:jose.duarte@psi.ch"><jose.duarte@psi.ch></a><br>
<b><span
style="font-weight:bold;">To:</span></b>
<a
moz-do-not-send="true"
rel="nofollow"
class="yiv2988709245moz-txt-link-abbreviated"
ymailto="mailto:cmview-users@bioinformatics.org"
target="_blank" href="mailto:cmview-users@bioinformatics.org">cmview-users@bioinformatics.org</a>
<br>
<b><span
style="font-weight:bold;">Sent:</span></b>
Friday, June
7, 2013 12:06
PM<br>
<b><span
style="font-weight:bold;">Subject:</span></b>
Re:
[cmview-users]
Problem
running
various pdb
files+dssp
error<br>
</font> </div>
<div
class="yiv2988709245y_msg_container"><br>
<div
id="yiv2988709245">
<div>
<div
class="yiv2988709245moz-cite-prefix">Hi
Maryam<br>
<br>
I would say
that this is a
known problem
with the
program that
doesn't cope
well when the
sequence
numbering
starts at a
high number.
If I
understand
from the
output you
show, your
model is based
on PDB code
2kun, isn't
it? I've tried
the original
2kun PDB file
and it worked
alright.<br>
<br>
My guess is
that in your
case it
doesn't work
because there
is no SEQRES
records
indicating
what the exact
sequence is
for the PDB
file. Do you
have SEQRES
records in
your file? If
not you can
add them from
the original
PDB file and
try it again.
Another way to
solve the
issue is to
renumber your
residue
serials in the
ATOM lines to
start at 1. <br>
<br>
Let us know if
that helps. If
not it would
be useful to
have a look at
your PDB file
to be able to
track down
exactly what
went wrong
with the
program.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<br>
On 06/06/2013
10:19 AM, M.
F. wrote:<br>
</div>
<blockquote
type="cite">
<div
class="yiv2988709245yui_3_7_2_33_1371031368009_91"
style="color:#000;background-color:#fff;font-family:times
new roman, new
york, times,
serif;font-size:14pt;">Hi
there,<br>
<br>
I have been
struggling
with running
cmview now for
awhile, I am
very happy to
findout about
this group and
ask my
question here.
<br>
<br>
I have changed
my generated
pdb file
format,
already for
several times
and it is
still giving a
weird sort of
graph and
loosing some
info probably.
This is the
error I get
and the result
image is
attached.
Please let me
know if you
need more
info. Thanks
in advance!<br>
<br>
<div
style="margin-left:40px;">Maryam%
cmview.sh<br>
Starting
CMView 1.1.1<br>
Loading
configuration
file
cmview.cfg<br>
Using
temporary
directory
/var/folders/JN/JNvt1vfbH4CRpqOfuMtdQk+++TI/-Tmp-/<br>
Connecting to
PyMol...<br>
Starting
PyMol...<br>
Connected.<br>
Using DSSP
executable
../dssp-2.1.0/src<br>
Loading from
Pdb file<br>
Filename:
/Users/Maryam/Desktop/10ns-3.pdb<br>
Model
serial: 1<br>
Chain code:
NULL<br>
Contact
type: Ca<br>
Dist.
cutoff: 8.0<br>
Min. Seq.
Sep.: none<br>
Max. Seq.
Sep.: none<br>
(Re)assigning
secondary
structure
using DSSP<br>
Failed to
assign
secondary
structure:
Cannot run
program
"../dssp-2.1.0/src":
error=13,
Permission
denied<br>
Warning: 89
unobserved or
non-standard
residues<br>
Warning: Chain
NULL is now
called A<br>
Contact map
2kunA loaded.<br>
<br>
</div>
<div><br>
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