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Stein, ND (Norman) wrote:
Hi Dan
If I run areaimol on 1ej6.vdb (rather than 1ej6_full.vdb) I get the following
warning message, which seems more appropriate:
*** Warning(s): point code unit function
*** 1 16512 1 MMDB_F_Atom
*** file : 1ej6.vdb
*** warning: unknown form factor encountered
atom type found and not recognised =
ZN H2000
$TEXT:Warning: $$ comment $$
WARNING: Unknown atom type: adding to list with default radius 1.8 A
$$
This is caused by the last atom in the vdb file. For some reason, someone has
taken the original 1ej6 pdb file and changed the last record (the zinc atom)
from a HETAM to an ATOM record in creating the vdb file. It is these zinc atoms
that are giving the warning messages you see.
Norman Stein
CCP4
Thanks for the information. It seems that all the HETATM lines have been
changed to ATOM lines in ViperDB.
Can I bug you again about the Icode / AltLoc fields and AREAIMOL? How
does it handle these attributes with regard to input / output? I guess
all AltLocs are dropped when the atoms with fractional occupancy are
dropped, but what about Icodes?
Thanks for any help,
Dan.
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of
Dan Bolser
Sent: 14 November 2006 13:20
To: Dan Bolser
Cc: CCP4
Subject: Re: [ccp4bb]: Some questions about Areaimol?
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Dan Bolser wrote:
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I am calculating the ASA of some virus structures downloaded from
VIPERdb.
I get the following error when processing some of the 'full capsid'
structures (after tweaking MAXNET as appropriate)...
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1ej6_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 34487
*** warning: unknown form factor encountered
*** position unavailable, serial number 34487
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1ej6_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 34487
*** warning: unknown form factor encountered
*** position unavailable, serial number 34487
... (and many many more).
I tried Googling, but I couldn't find the cause of this error.
Following the errors (many thousands), the ASA appears to be
calculated correctly (for at least some of the files that I have).
Actually the above structure in particular is problematic in other
ways...
ERROR: Dimension of parameter MAXNET is too small
Currently it is : 200000000
Needs to be at least: 1368998631
Which I think is impossibly large - Not sure though.
My question is, what is this warning? Is it safe to ignore? Is it
related to issues with Areaimol or rather the structure from VIPERdb?
I had thought this warning was related to 'ALT LOC' codes in the
files, for example,
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 668
*** warning: unknown form factor encountered
*** position unavailable, serial number 668
atom type found and not recognised =
THR A 13
$TEXT:Warning: $$ comment $$
WARNING: Unknown atom type: adding to list with default radius 1.8 A
$$
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 669
*** warning: unknown form factor encountered
*** position unavailable, serial number 669
*** Warning(s): point code unit function
*** 1 16576 1 MMDB_F_Atom
*** file : DBd/ViperDb/structures/1a34_full.vdb.gz
*** warning: atom serial number does not match position
*** position unavailable, serial number 670
*** warning: unknown form factor encountered
*** position unavailable, serial number 670
....
The above warnings appear to be co-localized with 'alternate location
codes' in the PDB. How does Areaimol handle AltLocs (and Icodes)?
Cheers,
Dan.
Does Areaimol simply ignore the ALTLOC codes?
