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On 02/18/2011 07:42 AM, Vellieux Frederic wrote: Arp Warp used to want a blank line between the > MALDH title, and the first line of the sequence.. Not sure if that still holds. Eleanor a> Hi Careina, > > Just an example of a pir file which I just generated (using Bart Hazes > program mcfman): > > P1;>MALDH_ > Just a title > TKVSVVGAAGTVGAAAGYNIALDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVR > QGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNP > VDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVP > VFSKVSVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTG > EVLPASVKLEGEFGHEDTAFGVPVSLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDK > IS* > > I don't think the pir format has changed much since the subroutine that > extracts the sequence from a coordinate file was written. As you will > see the (ASCII) format is pretty simple, one start record, one title > record followed by records containing the sequence in the one-character > abbreviation, 60 characters per line, with "*" to end the sequence. The > start record is P1;> followed by 6 characters. > > I never had any problems with the pir files generated by mcfman, and I > always have used an editor (vi is the one I use) to convert other > formats to this format. > > Fred. > > Careina Edgooms wrote: >> Dear CCP4 mailing list >> >> I have a relatively simple question. How do I get sequence file in >> .pir format which is required for many programs? I normally use fasta >> format but some programs eg arpwarp do not allow me to use that >> >> Thanks for your help >> >> Careina >>