On 08/06/2015 11:15 PM, Robert Hanson wrote:
> On Thu, Aug 6, 2015 at 7:12 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
>
>> Hi all,
>>
>> I explored the 'plot PROPERTIES' command in Jmol 14.3.14_2015.06.06 and
>> noticed some odd behaviour and have a few suggestions.
>>
>> As example an mmCIF format file was loaded, temporarily available at
>> "http://www.fli-leibniz.de/~rhuehne/jmol/plot_example.cif";.
>>
>> The "_struct_conn" bond records are ignored. But I hope this will change
>> soon. (At least Bob admitted some time ago on this list that it should
>> have higher priority with regard to the plans of the PDB to drop PDB
>> format files from their FTP site soon.)
>>
>
> I am not ready to jump for this. What code is producing this file? I'm
> guessing you are usurping the mmCIF format for your own purposes, right? I
> think it is very clever to use _atom_site.auth_seq_id for these purposes,
> and we could consider that, though it cannot be a default to read this data
> block, since it is not the same as CONECT, and it is not consistent with
> Jmol's standard autobonding business.
>
It is true that the example mmCIF file here is generated within Jmol for
pseudoatoms. But I tried to make it similar to the mmCIF files used by
the PDB. And as far as I have seen they use the '_struct_conn' record to
provide bonding information like they provide it in the 'CONECT' records
in the PDB format (see example below). And about 80% of the PDB entries
contain 'CONECT' records. So if Jmol should still be usable consistently
as a viewer for structure database sites like the PDB or JenaLib/Jena3D
in a few months (when no PDB format files will be provided any more) it
should be able to read '_struct_conn' records as default.
Bob, I thought we had discussed this here in a thread on the mmCIF
format earlier this year and you agreed to it. But I seem to have
misunderstood this.
--- Example '_struct_conn' record from PDB entry 1DEH ----------
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc1 metalc ? C ZN . ZN ? ? ? 1_555 A CYS 97 SG ? ? A ZN 375 A
CYS 97 1_555 ? ? ? ? ? ? ? 2.370 ?
metalc2 metalc ? C ZN . ZN ? ? ? 1_555 A CYS 100 SG ? ? A ZN 375 A
CYS 100 1_555 ? ? ? ? ? ? ? 2.312 ?
metalc3 metalc ? C ZN . ZN ? ? ? 1_555 A CYS 111 SG ? ? A ZN 375 A
CYS 111 1_555 ? ? ? ? ? ? ? 2.260 ?
------------------------------------------------------------------
>
>>
>> --- Example commands ---
>> load "plot_example.cif"
>> hover "[%[group]]:%[atomName] #%[atomno] temp=%[temperature]"
>> plot PROPERTIES atomno temperature
>> ------------------------
>>
>> Oddities:
>> 1) Negative temperature values are plotted as zero (e.g.: atom 17).
>>
>
> it's not that it is zero, only that it is on the axis. Hover over it, and
> you will see that it has the proper value.
>
It is quite unexpected that the axis doesn't indicate zero, especially
if there is no label indicating the non-standard value.
>
>
>>
>> 2) Zero temperature values are plotted with a shift in the z-axis (500
>> instead of -100) and the y-axis (-22.7 instead of -100), e.g. atom 1 and
>> 16:
>> $ print {2.1 and @1}.xyz
>> {-100.0 -22.6938 500.0}
>> $ print {2.1 and @2}.xyz
>> {-92.0 19.6863 -100.0}
>> $ print {2.1 and @3}.xyz
>> {-84.0 15.9963 -100.0}
>> $ print {2.1 and @16}.xyz
>> {20.0 -22.6938 500.0}
>>
>>
> That's a bug due to the longer-than-three-character residue names. (fixed,
> or at least those are truncated to 3 char)
>
>
>
>
>> 3) Residue names with more than three letters are truncated in the plot
>> to three letters, e.g.: "OB_INC" -> "OB_"
>>
>> This format cannot support long names.
>
Q: Does 'this format' mean 'plot format' or something else?
I tested if Jmol could handle residue names with six characters and I
didn't observe any problems, for example with selection commands or labels.
>
>
>
>> Suggestions:
>> B) In extension to A) it would be nice if also other atom properties
>> would be transferred, but at least those that are plotted. Then for
>> example a 'hover' like the one defined in the example above would show
>> the same in the plot and the model frame. And one could look up the
>> exact values of the plotted properties.
>>
>
> Can't have it both ways, unfortunately.
>
I am not sure what 'both ways' means here. Maybe I wasn't clear enough.
I just wanted that properties are transferred from the model to the plot
while it is created. Afterwards properties might differ because of user
interactions.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail: rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de
Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein
VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228
------------------------------------------------------------------------------
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
