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

[M. F.]

Dear Jose,

Thanks I added chain A as you said and it works. I am happy that it helped to find out about the bug. 



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.

Cheers
Maryam


________________________________
 From: Jose Duarte <jose.duarte at psi.ch>
To: M. F. <mfaridun at yahoo.com> 
Cc: cmview-users at bioinformatics.org 
Sent: Monday, June 10, 2013 6:10 PM
Subject: Re: [cmview-users] Problem running various pdb files+dssp error
 


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.

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.

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.

Cheers

Jose



On 06/10/2013 05:10 PM, M. F. wrote:

Dear Jose,
>
>Unfortunately it didn't work. Could you please take a look at
        the attached file? 
>
>Thanks a lot in advance
>
>
>
>
>
>
>________________________________
> 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/20130612/79c7a98c/attachment.html>