pymol-users

[PyMOL] manual update

[Dr. M. M. <ma...@ma...>]

Dear Warren,

I would second Dirk's statement below. The manuals on web are a 
couple of years out of date now, and while the wiki and bulletin 
board are very useful sources of information, I too would prefer to 
have good up to date documentation, rather than more and more 
improvements with poor documentation


this little thread points nicely to the major problem that I have 
quite often with PyMol: it is a really powerful program, but the 
documentation is somewhere scattered between various incomplete 
sources (manual, reference list, wiki, bulletin board, user home 
pages, ...). This makes it very difficult for the average user like 
me to make full use of PyMol's capabilities. I would _really_ prefer 
to have a good and up-to-date documentation available, at least for 
the last official version, rather than more and more improvements 
with poor documentation.


-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

Re: [PyMOL] manual update

[Stephane G. <sg...@rs...>]

Dear Warren,

I could not agree more with Mark and Dirk. I recently received my "PyMOL=20
Subscription Renewal" email from DeLano Scientific, and I must admit I=20
will not renew my subscription, and for only one reason; the=20
documentation is not up-to-date! Especially since (according to the=20
Manual page on the PyMOL web site, see below) the manuals are=20
"Incentives Products" designed to spur sponsorship. Well, in my case,=20
the manuals have resulted in the withdrawal of my sponsorship for a=20
product that is otherwise  excellent!

Sincerely,

St=E9phane



 From http://pymol.sourceforge.net/html/index.html :

*The PyMOL manuals are undergoing revision and reorganization.* Because=20
of the resources required to accomplish this, we have decided to make=20
new versions of the PyMOL manual available as /*Incentive Products*/,=20
designed to spur sponsorship which can make improved documentation possib=
le.

*PyMOL Incentive Manuals are only "free" for a one-year evaluation.* By=20
the time your first year is up, we will trust you to have purchased a=20
PyMOL maintenance or support subscription=20
<http://www.pymol.org/funding.html>, in order to secure a continued=20
right to use these manuals and other Incentive Products. We settled on=20
this particular approach because it seems like the best way of=20
encouraging sponsorship without significantly limiting anyone's ability=20
to learn and apply the software. However, please don't wait a year to=20
begin sponsoring the project if you're willing to sponsor it today!

*Note that these terms only apply to PyMOL manuals and other Incentive=20
Products, but not to Open-Source PyMOL software, * which itself remains=20
available under an open-source license, without mandatory costs. It will=20
always be FREE to download, compile, and use Open-Source PyMOL.

*This arrangement is on the "honor" system.* If you do your part to=20
sponsor the project, then you will have access to all PyMOL products. If=20
not, then we ask you to /willingly/ refrain from taking advantage of=20
PyMOL Incentive Products, except for evaluation purposes.



--=20

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
St=E9phane M. Gagn=E9, Ph.D.
Professeur agr=E9g=E9, biochimie et CREFSIP
3255 pavillon Marchand
Universit=E9 Laval, Qu=E9bec, Canada     G1K 7P4
T=E9l=E9phone (bureau)   : (418) 656-7860
T=E9l=E9phone (labo)     : (418) 656-2131, poste 4530
T=E9l=E9copieur (Fax)    : (418) 656-7176
courrier =E9lectronique: sg...@rs...
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20

Avis relatif =E0 la confidentialit=E9 / Notice of Confidentiality
http://www.rec.ulaval.ca/lce/securite/confidentialite.htm

Re: [PyMOL] manual update

[Peter A. M. <pa...@co...>]

> this little thread points nicely to the major problem that I have
> quite often with PyMol: it is a really powerful program, but the
> documentation is somewhere scattered between various incomplete
> sources (manual, reference list, wiki, bulletin board, user home
> pages, ...). This makes it very difficult for the average user like
> me to make full use of PyMol's capabilities. I would _really_ prefer
> to have a good and up-to-date documentation available, at least for
> the last official version, rather than more and more improvements
> with poor documentation.

In my experience, pymol's build in help system is a very good guide.  Most
of the questions I get from local users, as well as my own questions, can
be resolved that way.  When that fails, it's generally because I'm trying
to do something that isn't directly supported (so I fall back on grep -nir
$whatever in the source directory or the mailing list/list archives).  I
completely agree that having good documentation is important; but I
haven't found pymol to be significantly lacking in that regard.

I wouldn't mind more comments in the source code (particularly the
underlying c modules), but that's probably due to lack of experience with
3d graphics programming on my part than anything else.

just my opinion...

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University