<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><div><span><div><span>Hi</span><br><br>I checked the pdb file and yes, it is missing the SEQRES, so I am going to add it and try again. Actually the header is very brief. Meanwhile, what else in the header could be crucial as an input to cmview? It would be good if we could skip many lines in the header and keep only crucial ones because there are many files to generate.<br><br>Thanks a million <br>Maryam</div><div><br></div></span></div><div><br></div> <div style="font-size: 14pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Jose Duarte <jose.duarte@psi.ch><br> <b><span style="font-weight:
bold;">To:</span></b> cmview-users@bioinformatics.org <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="y_msg_container"><br><div id="yiv5077537805">
<div>
<div class="yiv5077537805moz-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>
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<blockquote type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: 'times new roman', 'new york', times, serif; ">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>
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