[cmview-users] Problem running various pdb files+dssp error

[M. F.]

Hi

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.

Thanks a million 
Maryam



________________________________
 From: Jose Duarte <jose.duarte at psi.ch>
To: cmview-users at bioinformatics.org 
Sent: Friday, June 7, 2013 12:06 PM
Subject: Re: [cmview-users] Problem running various pdb files+dssp error
 


Hi Maryam

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.

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. 

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.

Cheers

Jose



On 06/06/2013 10:19 AM, M. F. wrote:

Hi there,
>
>I have been struggling with running cmview now for awhile, I am
        very happy to findout about this group and ask my question here. 
>
>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!
>
>
>Maryam% cmview.sh
>Starting CMView 1.1.1
>Loading configuration file cmview.cfg
>Using temporary directory
          /var/folders/JN/JNvt1vfbH4CRpqOfuMtdQk+++TI/-Tmp-/
>Connecting to PyMol...
>Starting PyMol...
>Connected.
>Using DSSP executable ../dssp-2.1.0/src
>Loading from Pdb file
>Filename:    /Users/Maryam/Desktop/10ns-3.pdb
>Model serial:    1
>Chain code:    NULL
>Contact type:    Ca
>Dist. cutoff:    8.0
>Min. Seq. Sep.:    none
>Max. Seq. Sep.:    none
>(Re)assigning secondary structure using DSSP
>Failed to assign secondary structure: Cannot run program
          "../dssp-2.1.0/src": error=13, Permission denied
>Warning: 89 unobserved or non-standard residues
>Warning: Chain NULL is now called A
>Contact map 2kunA loaded.
>
>
>
>
>
>
>_______________________________________________
cmview-users mailing list cmview-users at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/cmview-users 

_______________________________________________
cmview-users mailing list
cmview-users at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/cmview-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/cmview-users/attachments/20130607/7515e62e/attachment.html>