pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Ray-tracing inner surface backside

[Paul W. E. <pa...@un...>]

Hi folks,


what I did for now is that I selected a subset of residues that sit
around a cavity. Then I showed the surface of the original protein
inside the selection to get only the inside surface of the cavity. Now
it looks sort of like a hose with inside and outside just as I wanted.


Now I'd like to raytrace this and I find no texture on the outside
surface, which is actually just the back of the inside. I put a picture
on http://pwe.no-ip.org/other/Pymol.png to illustrate my problem. See
how the inner surface has texture and its back doesn't!


How can I get this fixed? Any ideas?


Paul

[PyMOL] documentation vs features

[Seth H. <se...@gm...>]

Just to pipe up for the other side, while I would by no means defend the
lack of documentation as a good thing, given limited resources I actually
prefer new features at the expense of documentation. I realize there is a
large range of computer expertise in the pymol user community, and obviousl=
y
there are many who prefer more documentation, but even with an occasional
frustration of not finding something I need, I personally am pretty happy
with the users list archive, the wiki, and the "help" command within pymol.
And at "worst" (i.e. least immediate), I've found that this list gives
pretty helpful and rapid responses.
So without knowing anything of the timetable for development, I'd suggest
the lack of a full up-to-date manual is excusable (or at least not grounds
for removal of support) at least in the drive to version 1.0 or some simila=
r
landmark release.

To reiterate, I'm not trying to force this view on anyone, just provide som=
e
representation for the alternate (possibly minority) enjoyment of exciting
and useful new features that take a bit more effort to learn to use given
the lack of documentation...and therefore encourage us to help each other
out in the meantime.

Also motivated to speak up since my last message appeared a catalyst for th=
e
documentation requests...and that being said, I too would like to request
more documentation! (...at some point when it fits in).

Cheers,
Seth
(

RE: [PyMOL] manual update

[Warren D. <wa...@de...>]

PyMOL Users,

I concur with both of the statements below -- lack of good documentation =
and training materials has become much more limiting of PyMOL's utility =
than lack of functionality.

Furthermore, as illustrated by St=E9phane's post, if DeLano Scientific =
LLC is to continue to thrive as a business, then we must focus on =
meeting the needs of our customers, first and foremost.  We have heard =
directly from some important sponsors on such matters, and in response, =
we are implementing a number of changes in policy and practice leading =
up to the release of PyMOL 1.0. =20

In the meantime, we invite all current and/or past PyMOL sponsors and =
contributors to voice their thoughts and opinions to su...@de.... =
 Please help us find that optimal path through which PyMOL can =
eventually thrive in both commercial and open-source contexts. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Dr. Mark Mayer
> Sent: Tuesday, April 04, 2006 6:23 AM
> To: pym...@li...
> Subject: [PyMOL] manual update
>=20
> Dear Warren,
>=20
> I would second Dirk's statement below. The manuals on web are=20
> a couple of years out of date now, and while the wiki and=20
> bulletin board are very useful sources of information, I too=20
> would prefer to have good up to date documentation, rather=20
> than more and more improvements with poor documentation
>=20
>=20
> this little thread points nicely to the major problem that I=20
> have quite often with PyMol: it is a really powerful program,=20
> but the documentation is somewhere scattered between various=20
> incomplete sources (manual, reference list, wiki, bulletin=20
> board, user home pages, ...). This makes it very difficult=20
> for the average user like me to make full use of PyMol's=20
> capabilities. I would _really_ prefer to have a good and=20
> up-to-date documentation available, at least for the last=20
> official version, rather than more and more improvements with=20
> poor documentation.
>=20
>=20
> --
> 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=20
> 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov
>=20
> Send packages, Fedex and anything requiring a signature to:
>=20
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>=20
>=20

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

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

[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

[PyMOL] Surface atoms again

[Piter_ <x....@gm...>]

Dear all.
I need to select surface atoms. Friend of mine recommended me this way:



For solvent accessible surface one can try Molmol:
Load your molecule, say " SelectAtom '' " in command line, say "CalcSurface=
"
- select the solvent radius (1.4A for water by default), put "by atom" radi=
o
button on and then save and import the text output into spreadsheet of your
choice. Unfortunately output has solvent accessibility data for all the
atoms of the molecule - you use spreadsheet to filter those atoms which are
exposed most (i.e. - on the surface of the molecule).

In case you need a VdW surface you can try to decrease the solvent radius.

After that I selected needed atoms in command line.

Is is possible to do it everything in pymol and automatically?
Thanks
Petro

[PyMOL] Re: PyMOL-users digest, Vol 1 #1176 - 1 msg

[Liu S. <sy...@md...>]

http://www.ebi.ac.uk/~gareth/pymol/images/walls.png

how to draw this walls.png ?


On Mon, 3 Apr 2006 pym...@li... wrote:

> Send PyMOL-users mailing list submissions to
> 	pym...@li...
>
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> or, via email, send a message with subject or body 'help' to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
>   1. RE: Angstrom-squared values for solvent/protein contact surface per residue (Seth Harris)
>
> --__--__--
>
> Message: 1
> Date: Mon, 3 Apr 2006 15:56:23 -0700
> From: "Seth Harris" <se...@gm...>
> To: pym...@li...
> Subject: [PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue
>
> ------=_Part_19793_7876172.1144104983332
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> Just to throw my 2 cents in following Warren's invitation, I think
> Mark Gerstein's programs work well for this (calcsurf.exe or
> something...they're on his web site)
> ccp4's areaimol does something similar, though I can't recall whether
> its output was atom by atom.
> In either case, you may have to add up the component atom parts if you
> want residue by residue.
>
> Despite Warren's comment, I think last time I was doing this Pymol's
> results compared well with the above methods, but that was for large
> areas of a protein interface
> and perhaps if you want very fine residue level resolution you'd heed
> his caveat. I though, which is reiterated in the notes accompanying a
> former post of his...
>
> -Seth
>
> if I may quote Warren:
>
> For a solvent accessible PSA approximation:
>
> set dot_density, 3
> remove hydro
> remove solvent
> show dots
> set dot_solvent, on
> get_area elem N+O
> get_area elem C+S
> get_area all
>
> For molecular PSA approximation
>
> set dot_density, 3
> remove hydro
> remove solvent
> set dot_solvent, off
> get_area elem N+O
> get_area elem C+S
> get_area all
>
> Showing dots isn"t mandatory, but it"s a good idea to confirm that you"re
> getting the value for the atom dot surface you think you"re using.
>
> Please realize that the resulting numbers are only approximate, reflecting
> the sum of partial surface areas for all the dots you see.  To increase
> accuracy, set dot_density to 4, but be prepared to wait...
>  Cheers,
>  Warren
>
>
>
>
>
> ---------------------------------------------------------------------------=
> --------------------
> Melanie,
>
> At present, PyMOL isn't the right tool for this, but perhaps someone
> on the mailing list will know what is...
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Melanie Rogers
>> Sent: Monday, April 03, 2006 10:36 AM
>> To: pym...@li...
>> Subject: [PyMOL] Angstrom-squared values for solvent/protein
>> contact surface per residue
>>
>> Dear Pymol Users,
>>
>> Is it possible to extract numerical values, (i.e. Angstrom-squared per
>> residue)
>> for the solvent/protein contact surface for individual
>> residues in a crystal structure using Pymol?
>>
>> Thank you,
>>
>> Melanie Rogers
>> University of Leeds
>>
>>
>
> ------=_Part_19793_7876172.1144104983332
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> <pre>Just to throw my 2 cents in following Warren's invitation, I think Mar=
> k Gerstein's programs work well for this (calcsurf.exe or something...they'=
> re on his web site)<br>ccp4's areaimol does something similar, though I can=
> 't recall whether its output was atom by atom.=20
> <br>In either case, you may have to add up the component atom parts if you =
> want residue by residue. <br><br>Despite Warren's comment, I think last tim=
> e I was doing this Pymol's results compared well with the above methods, bu=
> t that was for large areas of a protein interface=20
> <br>and perhaps if you want very fine residue level resolution you'd heed h=
> is caveat. I though, which is reiterated in the notes accompanying a former=
> post of his...<br><br>-Seth<br><br>if I may quote Warren:<br><br>For a sol=
> vent accessible PSA approximation:
> <br> <br> set dot_density, 3<br> remove hydro<br> remove solvent<br> show d=
> ots<br> set dot_solvent, on<br> get_area elem N+O<br> get_area elem C+S<br>=
> get_area all<br> <br> For molecular PSA approximation<br> <br> set dot_den=
> sity, 3
> <br> remove hydro<br> remove solvent<br> set dot_solvent, off<br> get_area =
> elem N+O<br> get_area elem C+S<br> get_area all<br> <br> Showing dots isn&q=
> uot;t mandatory, but it&quot;s a good idea to confirm that you&quot;re<br>
> getting the value for the atom dot surface you think you&quot;re using.  <=
> br> <br> Please realize that the resulting numbers are only approximate, re=
> flecting<br> the sum of partial surface areas for all the dots you see.  To=
> increase
> <br> accuracy, set dot_density to 4, but be prepared to wait...<br>  Cheers=
> ,<br>  Warren<br><br><br><br><br><br>--------------------------------------=
> ---------------------------------------------------------<br>Melanie,<br>
> <br>At present, PyMOL isn't the right tool for this, but perhaps someone on=
> the mailing list will know what is...<br><br>Cheers,<br>Warren<br><br>--<b=
> r>Warren L. DeLano, Ph.D.                     <br>Principal Scientist<br>
> <br>. DeLano Scientific LLC  <br>. 400 Oyster Point Blvd., Suite 213       =
>    <br>. South San Francisco, CA 94080 USA   <br>. Biz:(650)-872-0942  Tec=
> h:(650)-872-0834     <br>. Fax:(650)-872-0273  Cell:(650)-346-1154<br>. mai=
> lto:
> <a href=3D"mailto:wa...@de...">wa...@de...</a>      <br> <br><b=
> r>&gt; -----Original Message-----<br>&gt; From: <a href=3D"mailto:pymol-use=
> rs-...@li...">pym...@li...</a>
> <br>&gt; [mailto:<a href=3D"mailto:pym...@li...=
> ">pym...@li...</a>] On Behalf Of <br>&gt; Melani=
> e Rogers <br>&gt; Sent: Monday, April 03, 2006 10:36 AM<br>&gt; To: <a href=
> =3D"mailto:pym...@li...">
> pym...@li...</a><br>&gt; Subject: [PyMOL] Angstrom-squ=
> ared values for solvent/protein <br>&gt; contact surface per residue<br>&gt=
> ; <br>&gt; Dear Pymol Users, <br>&gt; <br>&gt; Is it possible to extract nu=
> merical values, (
> i.e. Angstrom-squared per<br>&gt; residue)<br>&gt; for the solvent/protein =
> contact surface for individual <br>&gt; residues in a crystal structure usi=
> ng Pymol?  <br>&gt; <br>&gt; Thank you,<br>&gt; <br>&gt; Melanie Rogers
> <br>&gt; University of Leeds <br>&gt; <br>&gt; </pre>
>
> ------=_Part_19793_7876172.1144104983332--
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>

Re: [PyMOL] RE: making a movie from saved scenes

[Dirk K. <dir...@ps...>]

Dear Warren,

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.

Best regards,

Dirk.

Seth Harris wrote:
> Hi Sun,
> 
> Warren (and others?) has posted some text before about this. A simple
> template for it is as follows with the key being that mview interpolate
> command at the end. This works, but I haven't been through it recently to
> remind myself of the nuances of the animate=0 options and the view=0 options
> at their respective occurences, but if you play around with it I think
> you'll find it a treat.  Don't forget that the mset 1 x180 should be
> replaced by however many total frames you want in the movie, and repeat the
> little blocks for however many scenes you have. If you don't mind equal
> sized steps between scenes you can automate the whole thing in a little
> python loop for X number of scenes. Also replace 001, 002, etc. with
> whatever your scenes are stored as. Use the mview store, YY to pinpoint at
> which frame you want that scene to be set.
> 
> mset 1 x180
> scene 001, animate=0
> mview store, 1
> scene 002, animate=0
> mview store, 60
> mview interpolate
> mdo 1: scene 001, view=0
> mdo 2: scene 002, view=0
> 
> There are other non-scene based movie mechanisms that allow fancier fades
> and things, but this way is certainly much easier to work with.
> 
> -Seth
> 


-- 

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: 	+41-56-310-4722
Fax: 	+41-56-310-5288
E-mail:	dir...@ps...
http://sb.web.psi.ch
****************************************

RE: [PyMOL] Atom type selection with the *

[Kerff <fk...@ul...>]

Thank you very much to both of you for your help.
Have a good day.

Fred

> Matt,
>
> There isn't an escape sequence, but PyMOL will automatically disable the
> asterisk as a wildcard for atom names if any PDB file loaded contains an
> asterisk in that field.
>
> To manually choose another wildcard for that field, issue something like
>
> set atom_name_wildcard, %
>
> As for coloring atoms by element, use of wildcards should be avoided --
> use the "elem" operator instead.
>
> color red, elem o
> color blue, elem n
> color green, elem c
>
> etc.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Mat...@im...
>> Sent: Monday, April 03, 2006 8:37 AM
>> To: Kerff Frédéric
>> Cc: pym...@li...; Warren DeLano
>> Subject: Re: [PyMOL] Atom type selection with the *
>>
>>
>> pym...@li... wrote on 04/03/2006
>> 09:49:51 AM:
>>
>> > Hi Pymol users,
>> >
>> > I'm experiencing some trouble with the selection of atom type using
>> > the "*". Sometimes it works and sometimes it doesn't...
>> > I used for example:
>> > color red, object////o*
>> > 'color red, name o*' give the same result.
>> > Any idea why it's happening and more interesting what
>> should I do to
>> > fix
>> it.
>> > Thank you very much.
>> >
>> > Fred
>> >
>>
>> Hi Fred -
>>
>> I don't have the answer to your question, but I did want to
>> point out that "*" is a perfectly valid part of the atom name
>> in some PDB files - the PDB expects you to use it for atoms
>> in the ribose ring of nucleotides.  For example, this is from
>> a structure I did a while ago:
>>
>> HETATM 8021  O5* TTP     1       0.035  48.396  15.975  1.00 50.15
>> O
>> HETATM 8022  C5* TTP     1      -0.048  49.462  14.957  1.00 40.93
>> C
>> HETATM 8023  C4* TTP     1       0.565  50.743  15.416  1.00 38.78
>> C
>> HETATM 8024  O4* TTP     1      -0.194  51.219  16.565  1.00 36.44
>> O
>> HETATM 8025  C3* TTP     1       1.977  50.628  15.948  1.00 38.12
>> C
>> HETATM 8026  O3* TTP     1       2.988  50.525  14.996  1.00 44.69
>> O
>> HETATM 8027  C2* TTP     1       2.084  51.848  16.841  1.00 33.48
>> C
>> HETATM 8028  C1* TTP     1       0.693  51.871  17.477  1.00 33.26
>> C
>>
>>
>> So watch out!
>>
>>
>>
>> Warren - is there a way of escaping the "*" if you want to
>> use it for selection?  Let's say I wanted atom C5* but not C5M.
>>
>> Thanks,
>>
>> Matt
>>
>> --
>> Matthew Franklin                     phone:(917)606-4116
>> Senior Scientist, ImClone Systems      fax:(212)645-2054
>> 180 Varick Street, 6th floor
>> New York, NY 10014
>>
>>
>> Confidentiality Note:  This e-mail, and any attachment to it,
>> contains privileged and confidential information intended
>> only for the use of the
>> individual(s) or entity named on the e-mail.  If the reader
>> of this e-mail is not the intended recipient, or the employee
>> or agent responsible for delivering it to the intended
>> recipient, you are hereby notified that reading it is
>> strictly prohibited.  If you have received this e-mail in
>> error, please immediately return it to the sender and delete
>> it from your system.  Thank you.
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>> scripting language that extends applications into web and
>> mobile media. Attend the live webcast and join the prime
>> developer group breaking into this new coding territory!
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> dat=121642
>> _______________________________________________
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>

[PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue

[Seth H. <se...@gm...>]

Just to throw my 2 cents in following Warren's invitation, I think
Mark Gerstein's programs work well for this (calcsurf.exe or
something...they're on his web site)
ccp4's areaimol does something similar, though I can't recall whether
its output was atom by atom.
In either case, you may have to add up the component atom parts if you
want residue by residue.

Despite Warren's comment, I think last time I was doing this Pymol's
results compared well with the above methods, but that was for large
areas of a protein interface
and perhaps if you want very fine residue level resolution you'd heed
his caveat. I though, which is reiterated in the notes accompanying a
former post of his...

-Seth

if I may quote Warren:

For a solvent accessible PSA approximation:

 set dot_density, 3
 remove hydro
 remove solvent
 show dots
 set dot_solvent, on
 get_area elem N+O
 get_area elem C+S
 get_area all

 For molecular PSA approximation

 set dot_density, 3
 remove hydro
 remove solvent
 set dot_solvent, off
 get_area elem N+O
 get_area elem C+S
 get_area all

 Showing dots isn"t mandatory, but it"s a good idea to confirm that you"re
 getting the value for the atom dot surface you think you"re using.

 Please realize that the resulting numbers are only approximate, reflecting
 the sum of partial surface areas for all the dots you see.  To increase
 accuracy, set dot_density to 4, but be prepared to wait...
  Cheers,
  Warren





---------------------------------------------------------------------------=
--------------------
Melanie,

At present, PyMOL isn't the right tool for this, but perhaps someone
on the mailing list will know what is...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.
Principal Scientist

. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942  Tech:(650)-872-0834
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...


> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of
> Melanie Rogers
> Sent: Monday, April 03, 2006 10:36 AM
> To: pym...@li...
> Subject: [PyMOL] Angstrom-squared values for solvent/protein
> contact surface per residue
>
> Dear Pymol Users,
>
> Is it possible to extract numerical values, (i.e. Angstrom-squared per
> residue)
> for the solvent/protein contact surface for individual
> residues in a crystal structure using Pymol?
>
> Thank you,
>
> Melanie Rogers
> University of Leeds
>
>

Re: [PyMOL] B & W Molscript & David Goodsell look-alike modes

[Jacob C. <jc...@uc...>]

Hi Michael,
Try
set ray_trace_mode = 0/1/2/3
Check out the wiki for more info and some examples
http://www.pymolwiki.org/index.php/Ray#Ray-Tracing_modes

Jacob

Michael Sawaya wrote:
> Dear Pymol Users,
> 
> Can you tell me how to access the
> B & W Molscript & David Goodsell look-alike modes
> in PyMOL Release 0.99?  The "CHANGES" file suggests
> that these new modes are now offered by version 0.99, but
> I can find no documentation on how to use them.
> 
> Thanks for your help,
> Mike Sawaya
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live 
> webcast
> and join the prime developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

-- 
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
jc...@uc...
phone: 510-643-8893
fax: 510-643-9290

[PyMOL] RE: making a movie from saved scenes

[Seth H. <se...@gm...>]

Hi Sun,

Warren (and others?) has posted some text before about this. A simple
template for it is as follows with the key being that mview interpolate
command at the end. This works, but I haven't been through it recently to
remind myself of the nuances of the animate=3D0 options and the view=3D0 op=
tions
at their respective occurences, but if you play around with it I think
you'll find it a treat.  Don't forget that the mset 1 x180 should be
replaced by however many total frames you want in the movie, and repeat the
little blocks for however many scenes you have. If you don't mind equal
sized steps between scenes you can automate the whole thing in a little
python loop for X number of scenes. Also replace 001, 002, etc. with
whatever your scenes are stored as. Use the mview store, YY to pinpoint at
which frame you want that scene to be set.

mset 1 x180
scene 001, animate=3D0
mview store, 1
scene 002, animate=3D0
mview store, 60
mview interpolate
mdo 1: scene 001, view=3D0
mdo 2: scene 002, view=3D0

There are other non-scene based movie mechanisms that allow fancier fades
and things, but this way is certainly much easier to work with.

-Seth

[PyMOL] B & W Molscript & David Goodsell look-alike modes

[Michael S. <sa...@mb...>]

Dear Pymol Users,

Can you tell me how to access the
B & W Molscript & David Goodsell look-alike modes
in PyMOL Release 0.99?  The "CHANGES" file suggests
that these new modes are now offered by version 0.99, but
I can find no documentation on how to use them.

Thanks for your help,
Mike Sawaya

[PyMOL] CVS to Subversion Migration

[Warren D. <wa...@de...>]

NOTE: If you are not in the habit of compiling PyMOL straight from the
CVS archive, then you can ignore this message.

Developers,

SourceForge experienced a major system failure last week that has halted
development on all CVS-based SourceForge projects, with no resolution in
sight. =20

Fortunately, a backup of the current CVS archive was available, so this
morning I migrated PyMOL's source code to the Subversion version control
system.  The new source-code checkout procedure for the main PyMOL trunk
is thus:

svn checkout https://svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol

If you don't have Subversion installed, you may need to compile it from
source code, available at http://subversion.tigris.org=20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

[PyMOL] making a movie from saved scenes

[Sun H. <hu...@ms...>]

Hi

I'm wondering whether you can make a movie that smoothly connects 
between the saved scenes.
For example, a smooth change from scene 1 to scene 2 to ...etc.

I'll appreciate any help.
Thanks

Sun

Re: [PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

[Jacob C. <jc...@uc...>]

Hi Melanie,
In the past I have used AREAIMOL, which is part of ccp4, to do something 
similar. Check out the documentation here http://www.ccp4.ac.uk/html/areaimol.html

However, you may also want to look at SURFACE, which is also part of ccp4 and 
has some nice features, but is no longer being developed.
There is a nice comparison of the two programs here 
http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html

Jacob

Melanie Rogers wrote:
> Dear Pymol Users, 
> 
> Is it possible to extract numerical values, (i.e. Angstrom-squared per
> residue)
> for the solvent/protein contact surface for individual residues in a crystal
> structure using Pymol?  
> 
> Thank you,
> 
> Melanie Rogers 
> University of Leeds 
> 
> 
> 
>   
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live webcast
> and join the prime developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd_______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

-- 
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
jc...@uc...
phone: 510-643-8893
fax: 510-643-9290

RE: [PyMOL] Atom type selection with the *

[Warren D. <wa...@de...>]

Matt,

There isn't an escape sequence, but PyMOL will automatically disable the =
asterisk as a wildcard for atom names if any PDB file loaded contains an =
asterisk in that field.

To manually choose another wildcard for that field, issue something like

set atom_name_wildcard, %

As for coloring atoms by element, use of wildcards should be avoided -- =
use the "elem" operator instead.

color red, elem o
color blue, elem n
color green, elem c

etc.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mat...@im...
> Sent: Monday, April 03, 2006 8:37 AM
> To: Kerff Fr=E9d=E9ric
> Cc: pym...@li...; Warren DeLano
> Subject: Re: [PyMOL] Atom type selection with the *
>=20
>=20
> pym...@li... wrote on 04/03/2006=20
> 09:49:51 AM:
>=20
> > Hi Pymol users,
> >
> > I'm experiencing some trouble with the selection of atom type using=20
> > the "*". Sometimes it works and sometimes it doesn't...
> > I used for example:
> > color red, object////o*
> > 'color red, name o*' give the same result.
> > Any idea why it's happening and more interesting what=20
> should I do to=20
> > fix
> it.
> > Thank you very much.
> >
> > Fred
> >
>=20
> Hi Fred -
>=20
> I don't have the answer to your question, but I did want to=20
> point out that "*" is a perfectly valid part of the atom name=20
> in some PDB files - the PDB expects you to use it for atoms=20
> in the ribose ring of nucleotides.  For example, this is from=20
> a structure I did a while ago:
>=20
> HETATM 8021  O5* TTP     1       0.035  48.396  15.975  1.00 50.15
> O
> HETATM 8022  C5* TTP     1      -0.048  49.462  14.957  1.00 40.93
> C
> HETATM 8023  C4* TTP     1       0.565  50.743  15.416  1.00 38.78
> C
> HETATM 8024  O4* TTP     1      -0.194  51.219  16.565  1.00 36.44
> O
> HETATM 8025  C3* TTP     1       1.977  50.628  15.948  1.00 38.12
> C
> HETATM 8026  O3* TTP     1       2.988  50.525  14.996  1.00 44.69
> O
> HETATM 8027  C2* TTP     1       2.084  51.848  16.841  1.00 33.48
> C
> HETATM 8028  C1* TTP     1       0.693  51.871  17.477  1.00 33.26
> C
>=20
>=20
> So watch out!
>=20
>=20
>=20
> Warren - is there a way of escaping the "*" if you want to=20
> use it for selection?  Let's say I wanted atom C5* but not C5M.
>=20
> Thanks,
>=20
> Matt
>=20
> --
> Matthew Franklin                     phone:(917)606-4116
> Senior Scientist, ImClone Systems      fax:(212)645-2054
> 180 Varick Street, 6th floor
> New York, NY 10014
>=20
>=20
> Confidentiality Note:  This e-mail, and any attachment to it,=20
> contains privileged and confidential information intended=20
> only for the use of the
> individual(s) or entity named on the e-mail.  If the reader=20
> of this e-mail is not the intended recipient, or the employee=20
> or agent responsible for delivering it to the intended=20
> recipient, you are hereby notified that reading it is=20
> strictly prohibited.  If you have received this e-mail in=20
> error, please immediately return it to the sender and delete=20
> it from your system.  Thank you.
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

[Warren D. <wa...@de...>]

Melanie,

At present, PyMOL isn't the right tool for this, but perhaps someone on =
the mailing list will know what is...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Melanie Rogers=20
> Sent: Monday, April 03, 2006 10:36 AM
> To: pym...@li...
> Subject: [PyMOL] Angstrom-squared values for solvent/protein=20
> contact surface per residue
>=20
> Dear Pymol Users,=20
>=20
> Is it possible to extract numerical values, (i.e. Angstrom-squared per
> residue)
> for the solvent/protein contact surface for individual=20
> residues in a crystal structure using Pymol? =20
>=20
> Thank you,
>=20
> Melanie Rogers
> University of Leeds=20
>=20
>=20
>=20
>  =20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language
> that extends applications into web and mobile media. Attend=20
> the live webcast
> and join the prime developer group breaking into this new=20
> coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Atom type selection with the *

[<Mat...@im...>]

pym...@li... wrote on 04/03/2006 09:49:51 AM:

> Hi Pymol users,
>
> I'm experiencing some trouble with the selection of atom type using the
> "*". Sometimes it works and sometimes it doesn't...
> I used for example:
> color red, object////o*
> 'color red, name o*' give the same result.
> Any idea why it's happening and more interesting what should I do to fix
it.
> Thank you very much.
>
> Fred
>

Hi Fred -

I don't have the answer to your question, but I did want to point out that
"*" is a perfectly valid part of the atom name in some PDB files - the PDB
expects you to use it for atoms in the ribose ring of nucleotides.  For
example, this is from a structure I did a while ago:

HETATM 8021  O5* TTP     1       0.035  48.396  15.975  1.00 50.15
O
HETATM 8022  C5* TTP     1      -0.048  49.462  14.957  1.00 40.93
C
HETATM 8023  C4* TTP     1       0.565  50.743  15.416  1.00 38.78
C
HETATM 8024  O4* TTP     1      -0.194  51.219  16.565  1.00 36.44
O
HETATM 8025  C3* TTP     1       1.977  50.628  15.948  1.00 38.12
C
HETATM 8026  O3* TTP     1       2.988  50.525  14.996  1.00 44.69
O
HETATM 8027  C2* TTP     1       2.084  51.848  16.841  1.00 33.48
C
HETATM 8028  C1* TTP     1       0.693  51.871  17.477  1.00 33.26
C


So watch out!



Warren - is there a way of escaping the "*" if you want to use it for
selection?  Let's say I wanted atom C5* but not C5M.

Thanks,

Matt

--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

Re: [PyMOL] resize viewing window

[<Mat...@im...>]

pym...@li... wrote on 04/02/2006 06:00:42 PM:

> Is there a way to adjust the viewing window without dragging the mouse
> on a corner to do so? I need to resize the window for several files and
> want to make sure they are all the same.
>
> Thanks,
> James
>
>

Hi James -

The "viewport" command does this, e.g. 'viewport 800,600' gives you an
800x600 pixel viewing area.  The arguments apply to the drawing area, not
the total window size - that is, if you say

viewport 500,500
png foo.png

you'll get a 500x500 pixel image.  This command behaves erratically if you
try to draw the window larger than your screen will allow, and you can't
save (in OpenGL mode) the parts of the image that are offscreen, so don't
do that.  (If you need a big image for publication, type 'ray 2000,2000' or
something similar.)

- Matt

--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

[PyMOL] Atom type selection with the *

[Kerff <fk...@ul...>]

Hi Pymol users,

I'm experiencing some trouble with the selection of atom type using the
"*". Sometimes it works and sometimes it doesn't...
I used for example:
color red, object////o*
'color red, name o*' give the same result.
Any idea why it's happening and more interesting what should I do to fix it.
Thank you very much.

Fred

[PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

[Melanie R. <me...@bm...>]

Dear Pymol Users,=20

Is it possible to extract numerical values, (i.e. Angstrom-squared per
residue)
for the solvent/protein contact surface for individual residues in a =
crystal
structure using Pymol? =20

Thank you,

Melanie Rogers=20
University of Leeds=20



 =20

[PyMOL] resize viewing window

[James K. <kni...@gm...>]

Is there a way to adjust the viewing window without dragging the mouse
on a corner to do so? I need to resize the window for several files and
want to make sure they are all the same.

Thanks,
James

[PyMOL] RE: SF

[Warren D. <wa...@de...>]

> Did you change anything on SourceForge?  I lost CVS access=20
> somehow.  Is this due to the switch to SVN?  Did you import=20
> PyMol into SVN?
>=20

No.  It's not just you -- SourceForge has been experiencing a major CVS =
outage since early Thursday morning.

<http://sourceforge.net/docman/display_doc.php?docid=3D2352&group_id=3D1>=


No word yet on a fix, but their minimum estimate is 48 hours, which =
would mean restoration early Sat AM at the earliest. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20