[cmview-users] Problem running various pdb files

Mon Jul 1 12:13:00 EDT 2013

To be honest I can't see why it goes wrong there. If you can send me the 
PDB file I could have a look and maybe find out what's happening exactly.

Cheers

Jose

On 07/01/2013 01:20 PM, M. F. wrote:
>
> Dear Jose and other users and developers,
>
>
> Thanks for previous helps on this matter, but it appears that the 
> problem in running the cmview for my pdb files is still persisting. 
> How can I generate a pdb file that cmview likes? I changed the header 
> to the one that was working, and I added chainA to the column 22. When 
> I wanted to load I still got two options for chain (A & NULL (attached 
> as NULL). I solved that by adding numbers from the main pdb file.
> Then, I loaded again and I got wrong number format error. Could you 
> please let me know how can I solve it? How can I have the right format?
>
> Best regards
> Maryam
>
>
> ------------------------------------------------------------------------
> **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> <mailto:jose.duarte at psi.ch>
>> *To:* M. F. <mfaridun at yahoo.com> <mailto:mfaridun at yahoo.com>
>> *Cc:* cmview-users at bioinformatics.org 
>> <mailto: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.
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
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>>
>>
>>
>
>
>
>
>

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