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> -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Joel Bard > Sent: 20 January 2006 00:15 > To: [email protected]; [EMAIL PROTECTED] > Subject: Re: [ccp4bb]: electron density map & Pymol <snip> > # generate a pdb with just our ligand > awk '$1 == "ATOM" && $5 == "'$ligID'"' $pdbin > ligmap_lig${ligID}.pdb This is a potentially error-prone way of extracting lines from a PDB file, because the PDB record format is inherently not free (i.e. space-separated with no data allowed to be blank; rather the data are in fixed columns). awk is designed to process free-format data so is totally unsuited to the task. Consider for example how the above script would handle the following cases: HETATM 1234 CD1 LIG X 1 -2.389 -15.315 14.234 0.537 10.66 (PDB requires non-amino acids to be keyed as HETATM) HETATM12345 CD1 LIG X 1 -2.389 -15.315 14.234 0.537 10.66 (Atom number has 5 digits) ATOM CD1 LIG X 1 -2.389 -15.315 14.234 0.537 10.66 (Atom number column is blank) ATOM 1234 CD1ALIG X 1 -2.389 -15.315 14.234 0.537 10.66 (Alternate location indicator) ATOM 1234 CD1 LIG 1 -2.389 -15.315 14.234 0.537 10.66 (Chain ID is blank) ATOM 1234 CD1 LIG X1234 -2.389 -15.315 14.234 0.537 10.66 (Residue number has 4 digits) ... and of course all combinations of the above! Admittedly 1 or 2 of these examples that contain blank columns break the rules but most are valid (but then people who write programs that output PDB files are not known for sticking to the rules!). Unix provides a versatile utility for handling fixed-format records that many people don't seem to be aware of, namely egrep (or grep -E), i.e. grep with extended regular expressions. The following command will handle all of the above cases very neatly, and is easily generalised to perform similar tasks: egrep "^(ATOM |HETATM).{15}$ligID" $pdbin -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
