Re: [ccp4bb] CHAINSAW ERROR

[Tim Gruene]

Dear Vicky,

did you possibly edit this file with Word or some other text formatting 
program? A file .aln is a pure text file. What you sent is a binary file, hence 
not interpretable as alignement file.

There are proper text editors even for windows. Notepad is one option.

Best,
Tim


On Sunday, September 3, 2017 6:05:21 PM CEST Vicky Tsirkone wrote:
> Dear,
> 
> You may find attached the corresponding file.
> It does not contain the real sequences (I replaced every aa with ALA) but
> overall this is how it looks like.
> 
> Best,
> 
> Vicky
> 
> On Sun, Sep 3, 2017 at 5:53 PM, Eleanor Dodson 
> 
> wrote:
> > Can you attach the alignment file - there is a plethora of formats and it
> > is hard to debug them all.
> > 
> > Eleanor
> > 
> > On 3 September 2017 at 15:18, Vicky Tsirkone  wrote:
> >> Dear all,
> >> 
> >> I faced a strange issue while I was trying to run CCP4-chainsaw. I used
> >> EBI-Clustal omega to prepare the desired alignement. Next, I copied the
> >> output into a text file and renamed it to alignment.aln. When I chose
> >> this
> >> file in chainsaw it gave me back this kind of error:
> >> 
> >> format error in ALN/Clustal file
> >> No CLUSTAL keyword
> >> 
> >> 
> >> This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
> >> alignment*
> >> 
> >> I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same
> >> error message.
> >> 
> >> Any suggestion will be appreciated.
> >> 
> >> Kindly,
> >> 
> >> Vicky

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Paul Scherrer Institut
Tim Gruene
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OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

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Re: [ccp4bb] CHAINSAW ERROR

[Vicky Tsirkone]

Dear,

You may find attached the corresponding file.
It does not contain the real sequences (I replaced every aa with ALA) but
overall this is how it looks like.

Best,

Vicky

On Sun, Sep 3, 2017 at 5:53 PM, Eleanor Dodson 
wrote:

> Can you attach the alignment file - there is a plethora of formats and it
> is hard to debug them all.
>
> Eleanor
>
> On 3 September 2017 at 15:18, Vicky Tsirkone  wrote:
>
>> Dear all,
>>
>> I faced a strange issue while I was trying to run CCP4-chainsaw. I used
>> EBI-Clustal omega to prepare the desired alignement. Next, I copied the
>> output into a text file and renamed it to alignment.aln. When I chose this
>> file in chainsaw it gave me back this kind of error:
>>
>> format error in ALN/Clustal file
>> No CLUSTAL keyword
>>
>>
>> This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
>> alignment*
>>
>> I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same
>> error message.
>>
>> Any suggestion will be appreciated.
>>
>> Kindly,
>>
>> Vicky
>>
>
>


align.aln
Description: Binary data

Re: [ccp4bb] CHAINSAW ERROR

[Eleanor Dodson]

Can you attach the alignment file - there is a plethora of formats and it
is hard to debug them all.

Eleanor

On 3 September 2017 at 15:18, Vicky Tsirkone  wrote:

> Dear all,
>
> I faced a strange issue while I was trying to run CCP4-chainsaw. I used
> EBI-Clustal omega to prepare the desired alignement. Next, I copied the
> output into a text file and renamed it to alignment.aln. When I chose this
> file in chainsaw it gave me back this kind of error:
>
> format error in ALN/Clustal file
> No CLUSTAL keyword
>
>
> This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
> alignment*
>
> I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same
> error message.
>
> Any suggestion will be appreciated.
>
> Kindly,
>
> Vicky
>

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[ccp4bb] CHAINSAW ERROR

[Vicky Tsirkone]

Dear all,

I faced a strange issue while I was trying to run CCP4-chainsaw. I used
EBI-Clustal omega to prepare the desired alignement. Next, I copied the
output into a text file and renamed it to alignment.aln. When I chose this
file in chainsaw it gave me back this kind of error:

format error in ALN/Clustal file
No CLUSTAL keyword


This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
alignment*

I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same error
message.

Any suggestion will be appreciated.

Kindly,

Vicky

Re: [ccp4bb] Postdoctoral opening in structural biology (protein crystallography and drug discovery) at KU Leuven, Belgium

[Vicky Tsirkone]

Dear all,

I faced a strange issue while I was trying to run CCP4-chainsaw. I used
EBI-Clustal omega to prepare the desired alignement. Next, I copied the
output into a text file and renamed it to alignment.aln. When I chose this
file in chainsaw it gave me back this kind of error:

format error in ALN/Clustal file
No CLUSTAL keyword


This is the first line of my file : *CLUSTAL O(1.2.4) multiple sequence
alignment*

I also typed CLUSTAL W instead of CLUSTAL O but ccp4 gave me the same error
message.

Any suggestion will be appreciated.

Kindly,

Vicky