[cmview-users] Problem running various pdb files
M. F.
mfaridun at yahoo.com
Mon Jul 1 07:20:37 EDT 2013
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>
>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
>>
>>
>>
>
>
>
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