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

[Jose Duarte]

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.
>>
>>
>>
>>
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>
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