Hi,
Here is the perl script which is good enough
to extract the sequences from the PDB file.
best,
Sekar
> Hi, I have vague recollection that one of the Uppsala package
> programs (xutils ??) does that. I could be wrong of course. Boaz
>
> -------- Original message --------
> From: Reza Khayat
> Date: 10/08/2016 21:57 (GMT+02:00)
> To: [log in to unmask]
> Subject: [ccp4bb] PDB sequence extract
>
> Hi,
>
> Is anyone familiar with a program that can extract the sequence from the
> PDB chains while respecting the missing regions for the chain? For
> example, the output of such a program would use hyphens or some other
> ASCII character to indicate that there is no model for residues 13-20,
> rather than output a sequence that is contiguous. Thanks.
>
> Best wishes,
> Reza
>
> PS I don't think phenix.print_sequence or pdb-extract perform this, but I
> could be wrong.
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Cheng
> Zhang [[log in to unmask]]
> Sent: Wednesday, August 10, 2016 12:16 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Benchtop microscope
>
> We are pretty happy with Leica M125. In many cases, we saw tiny crystals
> probably smaller than 5um with this microscope.
>
> Cheng
>
> On Wed, Aug 10, 2016 at 10:48 AM, Joe Patel wrote:
> Hi Folks,
>
> I searched the archives but did not find anything particularly current.
> What have people bought recently for a high end microscope for crystal
> observation and manipulation?
>
> Not looking for automation or CCD camera functionality and all the models
> I have used in the past are no longer available.
>
> What else should I be looking at:
>
> Leica M125 (8x to 100x)
>
> Nikon SMZ1270
>
> Mitegen V81 (which is a Zeiss Stereo discovery V8)
>
> Many thanks,
>
> Joe P
>
>
>
>
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>
>
> --
> ---------------------
> Cheng Zhang
>
Could you kindly confirm the safe
receipt of the mail please.
All best wishes and regards,
Yours sincerely,
Dr. K. Sekar, Ph.D.
Associate Professor
Department of Computational and Data Sciences
Room No. 341, old Ecological Sciences Building
Second Floor
Indian Institute of Science
Bangalore 560 012
INDIA
E-mail: [log in to unmask]
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