CVS log for ccp4/src/pdbset.f
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Increase dimension of spgnam string, see #4331

Patch from ClAuS, array bounds overrun messing with the sequence handling.
See 3353.

Put an extra space into the SEQRES output to be compatible with hydropro (Bugzilla #3165)

Put an extra space into the SEQRES output to be compatible with hydropro (Bugzilla #3165)

bug 3004, seqid3 is is initialised as 4-byte of characters, and compared to 4-bytes of characters, so declare it as such

New functionality to estimate the molecular weight from the sequence of
residues, invoked automatically when using the SEQUENCE keyword (Eleanor
Dodson).

Updated with changes that where lost from version 1.93 onwards after update
from Ian Tickle.

Updated with changes that where lost from version 1.93 onwards after update
from Ian Tickle.

Updated pdbset with spacgroup number problem fixed. CRYST card in output PDB
will now show the spacegroup rather than the spacgroup number even if the later
is specified in the  input to pdbset.

add OUTPUT PDB/CIF options

Used to convert output chainID to uppercase. But chain IDs can
be case-sensitive, so I have removed this.
Try e.g. "select chain A c" on 1fnt

Associate remark with input rather than output channel

update licence banners

Relax check on determinant of rotation transformation - user
reports 0.9998 from SSM server.
But also report determinant in every case, for user to check.

New keyword ATRENUMBER: renumbers atoms in the output file so that they
are sequential (in response to bug #828).

From Phil Evans: allow simple transformations even if the file doesn't have
CRYST line (the process is not fully checked for validity so it could fail
if eg there are anisotropic Bfactors). (Bug #612)

anisou cards caused translation to fail - bug 591

reinstate fix 1.78
i.e. extent should be for output file, not input file

add new licence banners

changes from Clemens

Fixed by pre for:
"You had the unsual (but allowable) case that the 1st residue of chain
3 (B) had residue number in sequence with the last of the previous
chain G (G1 then B2) & the program failed to test properly"

similar to last change - ro is no longer set

Fixed a bug from r1.79 - "rf" was no longer set but it was still used, and
broke the "tffc_procedure" example.

change to aniso check from EJD

changes from ejd mostly to correct cell from pdb or keyword conflicts.

uninitialised varoables in NOISE option - pre

Extent of coordinates was being calculated for input, should be for output.

we now allow longer spacegroup names

wbcell won't work for ncode 7

EJD: more corrections for BFAC AVERAGE option.

Fix for previous change, otherwise BFACTOR AVERAGE doesn't work.

ejd enhancing bfactor stuff

QREADX and QWRITX changed to QREAD and QWRITE

Minor bug - can't have empty string '' (picked up by Alpha).

(a) fixes up the atom type rom the first 2 characters of the new atom name
(b) gets the justification right I think. This is v confusing as s/r
xyzatom returns or takes atom names left-justified, but on writing
pushes them right 1 place if the 1st character of atmtyp is blank
PRE

Changes from Phil/Eleanor:
1. New subkey FILE from TRANSFORM - read from a formatted file containing a
   3x3 matrix followed by a translation vector
2. Chain selections now use ChId (previously used the first character of
   Segid, if non-blank); if Segid is blank, Segid is always set = ChID on
   output

EJD: calculates fractional limits of coordinates along x,y and z.

Subroutine MATMLN removed (now in modlib); subroutine TRNFRM removed and
replaced with calls to TRANSFRM (also in modlib).

EJD: pdbset now warns if there is an inconsistency between the specified
spacegroup and that from the CRYST1 or REMARK 290 cards in the file.

correction to allow compilation nder g77

Error with side chain selection corrected.

Random noise option added.  Selection by atom type, B-factor and Chain

EJD: new EXCLUDE WAT option added.

EJD: added EXCLUDE SIDE option, which excludes protein side chains.

Fix for TRANSFORM FRACTIONAL option (was broken) from PRE.

New OCCUPANCY RESET option from Phil.

Fix from Phil to not mess up negative residue numbers.

Fixes for broken EXCLUDE HEADERS option. Includes a call to new s/r
RWNOHEAD in rwbrook.f.

Very minor fix for REPLACE option.

Fix for broken SPACEGROUP option (Ezra Peisach).

New version from Phil Evans: changed s/r getorm to get the orthogonalization
matrices from rwbrook calls.

Reversed previous change.

Fixed recognition of hydrogen atoms in XPLOR mode.

fix for divide by zero if INVERT flag set from PRE

New version from Phil

Echoing of input/output pdb data lines commented out (EJD).

fis from EJD - all atom names with H were being excluded

Returned UTOB keyword - EJD

EJD a new version that uses rwbrook

PRE: fixes bug in SEQUENCE option (actually
problem in setting variable mchain)

PRE: small change prompted by Kim Henrick, take
        orthogonalization matrix from SCALE lines even if CELL
        present, to allow for cases in which SCALE has a non-zero
        translation.

files CLOSED.

Error when using COM keyword fixed. From Sheila.

Changes from LMB

Changes from LMB. SEQUENCE SINGLE and REPLACE RESI  added.

unused variables

30/12/95 PDBSET: added EXCLUDE HEADERS option  (Phil)
17/1/96  PDBSET: added SEQUENCE PDB option (Phil).

Don't ignore unknown keywords.

PRE: EXCLUDE option

192 symops

PRE: new option REPLACE ATOM

The last change regarded reading O datablocks (case-sensitivity and comment
records (?))

Changes from Phil 6/04/95.

PRE: fixed bug in s/r opnodb in reading format from O datablock

Calculate COM

PRE: new options BFACTOR MAXIMUM|RANGE, SELECT BFACTOR

date stamp only

3/1/95 PDBSET: added options SYMGEN NCS, SELECT OCCUPANCY,
	fixed bug in RENUMBER input  (Phil)

tidying

IJT: coding error in converting Us to Bs

bad formats

added REPLACE RESIDUE option (Phil).  And a fix to last change . . .

REORTHOGONALIZE option (PRE)

typo causing ref. of undef. var.

PRE: made internal working with CHAIN Ids char*4 to allow
it to handle Xplor SegIDs sensibly, so can now do eg
	xplor
	chain Seg1 D

PRE: add ELEMENT option to left-justify atomnames
containing 2-character element names according to the PDB convention

version pulled straight from york

PRE: added utob option

copy residue insert codes (column 27)  (Phil)

used to set chain ID to '*' from command without chain Id change  (Phil)

PRE:
	New facilities
	a) OUTPUT XPLOR  write chain ID into Xplor segid column
	b) SEQUENCE  write out sequence file (useful for Xplor & O)
	c) TRANSFORM ODB  read transformation from O datablock
	d) TRANSFORM|ROTATE|SHIFT  INVERT, invert transformation
before applying

PRE format fix

PRE: added "Pick atom_name1 atom_name2" option to PDBSET, eg for
selecting CA atoms only.

11/5/93 Renamed "SYMMETRY" keyword in PDBSET to "SYMGEN" to avoid
	confusion (Phil). New pdbset.for, pdbset.doc

PRE: added OCCUPANCY option (removed from BFACTOR option)
	Always copies TER lines to output.

new SHIFT FRACTIONAL & TRANSFORM FRACTIONAL command

PRE: prints coordinate range

PRE:
	1) recognized HETA as well as ATOM
	2) renumber atoms in output

PRE: Modified PDBSET to add chain ID change option to RENUMBER command.

add ccprcs

PRE: bug fix in pdbset to get RENUMBER . . . CHAIN to work

pdbset now subsumes xplor2pdb

new version from LMB

new version from LMB

from PRE: yet another little program to do simple things to Brookhaven files