Re: [PyMOL] [Apbs-users] Plan for FreeMOL: APBS/PQR2PDB + MENGINE + MPEG movie creation

[Nathan B. <nat...@ma...>]

Hi Warren --

That's fantastic news!  It sounds like a great plan; please let me  
know if we can do anything to help out, particularly with the  
interface, annoying "ObjectMapLoadDXFile-Error" messages and related  
verbosity, etc.

Thanks!

-- Nathan

On Sep 18, 2008, at 2:32 PM, DeLano Scientific wrote:

>
>> This might be a good reason to start moving towards distribution of
>> APBS and PDB2PQR with PyMOL! :)
>
> Indeed, along those lines, here is the plan:
>
> Starting with PyMOL 1.2, we will start distributing an accompanying
> open-source compilation named FreeMOL, which includes several  
> packages many
> users would like to be able to call upon when using PyMOL.  They are:
>
> (a) an electrostatics package (APBS / PDB2PQR of course).
>
> (b) an MMFF forcefield & minimizer (mengine) for small molecule  
> building and
> peptide modeling.
>
> (C) an MPEG movie generator (mpeg_encode, most likely).
>
> In each case, we are doing the upfront compilation, integration, and  
> testing
> to ensure that what ships actually interoperates reliably, on Mac, on
> Windows, and on Linux.  With this effort, I am determined that we  
> will get
> to a point where all this stuff "just works" together without major  
> issues.
>
> Well.  That is the plan at least.  Nothing in software can ever be  
> taken for
> granted until it has shipped.  At present, we about two thirds of  
> the way
> there, so hopefully the rest will have come together before the end  
> of the
> year.  Betas will be out much sooner of course...
>
> By the way, just to be absolutely crystal clear:  FreeMOL is and  
> will remain
> a 100% free-software  open-source project, distributed under full  
> compliance
> with each component's own open-source licensing terms.  As such,  
> FreeMOL is
> and must be kept well-separated from our closed-source PyMOL  
> derivatives.
>
> Cheers,
> Warren
>
> PS. I suspect I am not the only one looking forward to the day when  
> we stop
> seeing all those repeated "ObjectMapLoadDXFile-Error"s clogging up  
> the APBS
> & PyMOL mailing lists...
>
>> -----Original Message-----
>> From: pym...@li... [mailto:pymol-users-
>> bo...@li...] On Behalf Of Nathan Baker
>> Sent: Thursday, September 18, 2008 11:54 AM
>> To: DeLano Scientific
>> Cc: apb...@li...; gil...@cg...;  
>> pymol-
>> us...@li...
>> Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
>>
>> Hi Warren --
>>
>>> Strictly speaking, the issue may be with PDB2PQR itself, not APBS.
>>> Furthermore, we don't yet know whether a combined development
>>> version of all
>>> three packages would still reproduce the problem.
>>
>> This might be a good reason to start moving towards distribution of
>> APBS and PDB2PQR with PyMOL! :)
>>
>>> As an aside, a good reason for PyMOL to see PQR files is for
>>> diagnostic
>>> visualization:  to enable the user to inspect and modify or
>>> manipulate what
>>> is being fed directly into APBS.
>>
>> I agree completely.  However, I think we can remain flexible with the
>> PQR format while still allowing this.
>>
>>> PyMOL can read & write PQR directly, though we may have issues  
>>> reading
>>> non-PDB-like PQR files.  I would generally agree that use of PDB2PQR
>>> to
>>> convert PDBs to PQRs is the preferred route, since PyMOL doesn't do
>>> any
>>> checking or optimization.
>>
>> OK.
>>
>>> Anyway, based on reported symptoms alone, the problem appears to be
>>> that
>>> some component in the PyMOL->APBS pipeline assumes that the input
>>> PDBs are
>>> space-delimited rather than column-delimited.  This guess is based
>>> on the
>>> observation that a B-factor of 100 or greater eliminates the space
>>> between
>>> the occupany and the B factor in spec-compliant PDB files, and the
>>> calculation fails.
>>
>> This seems like a reasonable guess but I can't think of a component  
>> of
>> PDB2PQR that is sensitive to this.  Gilles, can you confirm that you
>> used PDB2PQR to generate the PQR file for your calculation?
>>
>> Thanks,
>>
>> Nathan
>>
>
>
>
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/