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

[Jose Duarte]

 From your original output:

...
Using DSSP executable ../dssp-2.1.0/src
...

There seems to be 2 problems: you need to make the path absolute (it has 
to be the full path starting with "/" instead of "..") and then you need 
to point to the dssp executable file (it looks like you are pointing to 
the source folder). In Linux it looks like: /opt/programs/dssp/dssp

Hope it helps

Jose



On 06/12/2013 12:10 PM, M. F. wrote:
>
> 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> <mailto:jose.duarte at psi.ch>
>> *To:* cmview-users at bioinformatics.org 
>> <mailto: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  <mailto:cmview-users at bioinformatics.org>
>>> http://www.bioinformatics.org/mailman/listinfo/cmview-users
>>
>>
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>>
>
>
>

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