<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><div id="yiv3867718763"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:14pt;">Hi Jose,<br><br>Thanks for the tip. I had written down the directory as ../dssp-2.1.0/dssp and it was working, which was because mkdssp command could run. I don't know what happened after I installed the cmview again, but it was not working, and in one of the blind tries, I changed the directory to what you saw.<br><br>So, I again corrected it to what you said but it is not working. <br>No DSSP executable found.<br><br>I read somewhere mac 10.6.8 has a problem with dssp but I cannot that information back to see if there was a solution given. Maybe I am making some mistake or forgot a step about making executable dssp?<br><br>Best regards,<br>Maryam<br><br><br> <hr size="1"> <font
face="Arial" size="2"> <b><span style="font-weight:bold;"></span></b></font><br><br><b><span style="font-weight:bold;">From:</span></b> Jose Duarte <jose.duarte@psi.ch><br><div class="yiv3867718763yui_3_7_2_33_1371031368009_59" id="yiv3867718763yui_3_7_2_33_1371031368009_60" style="font-family:times new roman, new york, times, serif;font-size:14pt;"><div id="yiv3867718763yui_3_7_2_33_1371031368009_115" class="yiv3867718763yui_3_7_2_33_1371031368009_63" style="font-family:times new roman, new york, times, serif;font-size:12pt;"><div dir="ltr"><font face="Arial" size="2"> <b><span style="font-weight:bold;">To:</span></b> M. F. <mfaridun@yahoo.com> <br><b><span style="font-weight:bold;">Cc:</span></b> "cmview-users@bioinformatics.org" <cmview-users@bioinformatics.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Wednesday, June 12, 2013 12:42 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 id="yiv3867718763yui_3_7_2_33_1371031368009_114" class="yiv3867718763y_msg_container"><br><div id="yiv3867718763">
<div id="yiv3867718763yui_3_7_2_33_1371031368009_113">
<div id="yiv3867718763yui_3_7_2_33_1371031368009_112" class="yiv3867718763moz-cite-prefix">From your original output:<br>
<br>
...<br>
Using DSSP executable ../dssp-2.1.0/src<br>
...<br>
<br>
There seems to be 2 problems: you need to make the path absolute
(it has to be the full path starting with "/" instead of "..") and
then you need to point to the dssp executable file (it looks like
you are pointing to the source folder). In Linux it looks like:
/opt/programs/dssp/dssp<br>
<br>
Hope it helps<br>
<br>
Jose<br>
<br>
<br>
<br>
On 06/12/2013 12:10 PM, M. F. wrote:<br>
</div>
<blockquote type="cite">
<div class="yiv3867718763yui_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>
</span></div>
<div class="yiv3867718763yui_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="yiv3867718763yui_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="yiv3867718763yui_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="yiv3867718763yui_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="yiv3867718763yui_3_7_2_33_1371031368009_75" style="font-family:times new roman, new york, times, serif;font-size:14pt;">
<div class="yiv3867718763yui_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 face="Arial" size="2"> <b><span style="font-weight:bold;">From:</span></b> Jose
Duarte <a rel="nofollow" class="yiv3867718763moz-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 rel="nofollow" class="yiv3867718763moz-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 rel="nofollow" class="yiv3867718763moz-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="yiv3867718763y_msg_container"><br>
<div id="yiv3867718763">
<div>
<div class="yiv3867718763moz-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="yiv3867718763yui_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="yiv3867718763yui_3_7_2_33_1371031368009_84" style="font-family:times new roman, new york, times, serif;font-size:14pt;">
<div class="yiv3867718763yui_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 face="Arial" size="2">
<b><span style="font-weight:bold;">From:</span></b>
Jose Duarte <a rel="nofollow" class="yiv3867718763moz-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 rel="nofollow" class="yiv3867718763moz-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="yiv3867718763y_msg_container"><br>
<div id="yiv3867718763">
<div>
<div class="yiv3867718763moz-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="yiv3867718763yui_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>
</div>
</div>
<br>
<fieldset class="yiv3867718763mimeAttachmentHeader"></fieldset>
<br>
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