Thanks Jose,
It is a weird problem of editor!! Everytime I add chainA (manually), every 6 space (in the columns) change to a tab. Probably, cmview cannot translate it back to space, so the formatting error occurs.
For the moment, I don't have any problem any more.
Cheers
Maryam
________________________________
From: Jose Duarte <jose.duarte at psi.ch>
To: M. F. <mfaridun at yahoo.com>
Cc: "cmview-users at bioinformatics.org" <cmview-users at bioinformatics.org>
Sent: Monday, July 1, 2013 6:13 PM
Subject: Re: [cmview-users] Problem running various pdb files
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>
>>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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