Frieda, that's fixed.
The way to get partial charge data into .pdb files is to put it in the
temperature field. You can do that with:
{*}.temperature = {*}.partialcharge.all
Which will work on the revised Jmol that I haven't uploaded yet.
Which suggests to me that you might also try this in the version you have:
{*}.partialcharge = {*}.property_partialcharge.all
That copies all the property_partialcharge data into the real partialcharge
field of the atoms.
Then do the isosurface MEP business.
Bob
On Fri, Sep 19, 2008 at 4:32 PM, Reichsman Frieda <[EMAIL PROTECTED]> wrote:
> Hi Bob,
>
> Finally have my machine back and am catching up.
>
> The script below works for coloring the atoms by partial charge (very cool
> that Jmol can do that from two files!) but not for creating an isosurface
> that colors by mep. How can I get at the partial charges for that purpose?
>
> I tried the usual isosurface commands, but Jmol says it needs partial
> charges, so I would like to word the command to tell Jmol where to find
> them.
>
> Also tried to write the pdb file with the partial charges in it:
> write coords pdb "myfile.pdb"
> but no partial charges appear in the file.
>
> Frieda
>
>
> On Sep 13, 2008, at 1:00 PM, Robert Hanson wrote:
>
> If that's all you want to do, try this:
>
> load "xxxx.pdb"
> set propertydatafield 9
> x = load("xxxx.mol2")
> data "property_partialcharge @x"
> color property_partialcharge
>
>
>
>
> On Sat, Sep 13, 2008 at 8:22 AM, Reichsman Frieda <[EMAIL PROTECTED]>wrote:
>
>> That sounds very interesting. Yes, if I could take the partial charges
>> from the mol2 file and "put" them in the pdb file inside Jmol, that would do
>> the trick!
>>
>> In doing this, I do not usually need to remove atoms. While it might be
>> useful to be able to do so, removing atoms is done so easily by editing the
>> pdb file that I usually go that route, either deleting or just commenting
>> them out.
>>
>> I am not sure if mol2 files that are saved from pdb files have their atoms
>> in exactly the same order. I guess this would be important? Certainly I can
>> test this. Another issue is, if one has a mol2 file and no exact duplicate
>> pdb file. If the mol2 file did have residue names, numbers, and atom names
>> that included the .CA etc, perhaps one could "tell" Jmol where exactly to
>> find these items in this file?
>>
>> Frieda
>>
>> On Sep 13, 2008, at 5:48 AM, Robert Hanson wrote:
>>
>> Frieda, I'm working on a new system that will allow you to merge file
>> formats -- take the PDB/bonding information from one file and combine it
>> with the coordinate data from another file. This sounds to me like it might
>> be exactly what you are after.
>>
>> Question: in doing this, do you reduce the number of atoms from what they
>> were in the original PDB file?
>>
>> Bob
>>
>> On Fri, Sep 12, 2008 at 3:45 PM, Reichsman Frieda <[EMAIL PROTECTED]>wrote:
>>
>>> The program I am using at present is AtomSmith, but many other programs
>>> also apparently write mol2 files. Would that be a problem, since they may
>>> not all write them correctly? Or can we focus on the mol2 files written by
>>> AtomSmith?
>>> Some mol2 files are supplied with the AtomSmith program, but yes,
>>> starting with a pdb file I can save it as a mol2 file. I generally do this
>>> after creating an electrostatic potential surface so that the partial
>>> charges get saved there, so then I can display it in Jmol, and this is my
>>> primary motivation for making this request.
>>>
>>> For the amino acids page that I think you saw, I had to define every
>>> backbone atom in every file (there was no real pattern to the atomno
>>> designations) in order to make certain displays.
>>>
>>> Just yesterday I learned how to use python to extract characters from
>>> text files so theoretically I could soon take the partial charges out of a
>>> mol2 file and put them in the temperature field of a pdb file. And I am very
>>> willing to go that route if this mol2 thing is not worth the effort.
>>>
>>> I can send you a few files that are supplied as well as some that are
>>> exported form pdbs, if this makes sense to pursue.
>>>
>>> -Frieda
>>>
>>>
>>>
>>> On Sep 12, 2008, at 4:30 PM, Robert Hanson wrote:
>>>
>>>
>>>
>>> On Fri, Sep 12, 2008 at 3:21 PM, Reichsman Frieda <[EMAIL PROTECTED]>wrote:
>>>
>>>> On Sep 12, 2008, at 4:04 PM, Robert Hanson wrote:
>>>>
>>>> Well, what about the documentation at
>>>> http://www.tripos.com/data/support/mol2.pdf
>>>> I was assuming that this document is of no use in this regard, since you
>>>> seemed to know of this documentation already. It states at the beginning,
>>>> Mol2 files are written out in a *free format *to avoid the restrictions
>>>> created by
>>>> fixed format files.
>>>>
>>> To me, this sounds like a definitive statement that, forget it, anybody
>>>> can write anything they want in a mol2 file. But, then on page 12 the
>>>> document does lay out what the atom records can or should contain. I do not
>>>> understand from the language of this documentation, whether these are
>>>> considered recommendations or are a more hard-and-fast thing. Do you?
>>>>
>>>
>>> "free format" just means space characters separate fields rather than
>>> designated columns where one number can abut another.
>>>
>>>
>>>
>>>>
>>>> I would like to try to answer the questions you posed. If this format is
>>>> too loosey-goosey to be reliably readable for protein-level info, I am very
>>>> willing to let it go! Anyway - was anything I sent in the last email of use
>>>> in this regard?
>>>>
>>>
>>> Tell me again what program is producing these? Must be a PDB file going
>>> in, right? Or not....
>>>
>>>
>>>
>>>>
>>>> -Frieda
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Sep 12, 2008 at 12:29 PM, Reichsman Frieda <[EMAIL
>>>> PROTECTED]>wrote:
>>>>
>>>>> Hi Bob,
>>>>> Sending this off-list as I am not sure it is relevant for most users.
>>>>>
>>>>> Programs that write mol2 files: As you know, mol2 was created for SYBYL
>>>>> (Tripos). I have not found a comprehensive list of programs that read mol2
>>>>> files, but in searching I have found web pages from manuals, etc., that
>>>>> refer to the following programs that can output files in mol2 format:
>>>>> AtomSmith
>>>>> XLOGP
>>>>> GOLD
>>>>> Open Babel
>>>>> Chimera
>>>>> X-Score
>>>>> Mercury
>>>>>
>>>>> Interestingly, there is a powerpoint slide presentation by Roger Sayle
>>>>> (!) about reading mol2 files in OEChem called "Mol2 for Dummies" :) He
>>>>> points out several pitfalls, which may answer some of your questions. My
>>>>> problem is that the relevance/implications of some points are not clear to
>>>>> me.
>>>>> www.eyesopen.com/about/events/archives/cup_v/sayle/ Sayle*Mol2*For*
>>>>> Dummies*.ppt
>>>>>
>>>>> I do not know if the IDs are arbitrary. It does not seem clear (to me)
>>>>> from the documentation (pdf file linked below). Can you suggest how one
>>>>> would find out this sort of thing?
>>>>>
>>>>> I am currently looking for mol2 files in the variety of less usual
>>>>> structures as you suggest below. I'll send a bunch to you when I find
>>>>> them.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Frieda
>>>>>
>>>>>
>>>>> On Sep 10, 2008, at 2:10 PM, Robert Hanson wrote:
>>>>>
>>>>> We could set up the mol2 reader to do this. BUT I have to be convinced
>>>>> first that it's a real standard. What programs write these? Is it just
>>>>> totally arbitrary what these IDs are? Are the names standard? Try some
>>>>> more
>>>>> unusual structures, like DNA, RNA, nonstandard amino acids, 1BLU with its
>>>>> FeS4 sites. Hemoglobin.
>>>>>
>>>>> On Wed, Sep 10, 2008 at 8:51 AM, Angel Herraez <[EMAIL PROTECTED]>wrote:
>>>>>
>>>>>> Dear Frieda
>>>>>>
>>>>>> I've never tried that. From the doc
>>>>>> http://www.tripos.com/data/support/mol2.pdf
>>>>>> it seems that atoms can have IDs and residue IDs; they quote an
>>>>>> example:
>>>>>> 1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
>>>>>> BACKBONE|DICT|DIRECT
>>>>>> 1 CA -0.149 0.299 0.000 C.3
>>>>>> [...] the atom is named CA and is [...] It belongs to the
>>>>>> substructure with ID 1 which is named ALA1.
>>>>>>
>>>>>> So, Jmol should be able to interpret that, but maybe the file reader
>>>>>> has not been set for that.
>>>>>> As far as I know, the "protein" is determined based on bonding and
>>>>>> key atom names (N, CA, C) within the same residue.
>>>>>> Similarly for residue names.
>>>>>>
>>>>>> A quick test with a pdb file read into Accelrys DS Viewer 1.7 and
>>>>>> saved into mol2 shows that the atom IDs are read in Jmol (example:
>>>>>> select *.CA works), but not recognized as protein. "select ala"
>>>>>> doesn't work either.
>>>>>> So maybe it's just the residue ID part that is not being interpreted.
>>>>>> Notably, that goes after the coordinates, rather than before them as
>>>>>> in pdb.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------------------------
>>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>>> challenge
>>>>>> Build the coolest Linux based applications with Moblin SDK & win great
>>>>>> prizes
>>>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>>>> world
>>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>>> _______________________________________________
>>>>>> Jmol-users mailing list
>>>>>> [email protected]
>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> Northfield, MN
>>>>> http://www.stolaf.edu/people/hansonr
>>>>>
>>>>>
>>>>> If nature does not answer first what we want,
>>>>> it is better to take what answer we get.
>>>>>
>>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>> -------------------------------------------------------------------------
>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>> challenge
>>>>> Build the coolest Linux based applications with Moblin SDK & win great
>>>>> prizes
>>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>>> world
>>>>>
>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________
>>>>> Jmol-users mailing list
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> Northfield, MN
>>>> http://www.stolaf.edu/people/hansonr
>>>>
>>>>
>>>> If nature does not answer first what we want,
>>>> it is better to take what answer we get.
>>>>
>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr
>>>
>>>
>>> If nature does not answer first what we want,
>>> it is better to take what answer we get.
>>>
>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
