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

[Jose Duarte]

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.
>
>
>
>
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