pymol-users Mailing List for PyMOL Molecular Graphics System

Noel,

I think you will need make a copy first and mutate the copy for =
something like this to work.  That is essentially what the mutagenesis =
wizard does, if I recall correctly.

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
> Noel Faux
> Sent: Friday, April 28, 2006 12:31 AM
> To: pym...@li...
> Subject: [PyMOL] mutagenesis via python?
>=20
> Hi all,
>=20
> I'm in the process of creating a plugin for pymol, however=20
> I've hit a small wall.  Is there a series of python calls I=20
> can make in my code to perform a mutation without the loss of=20
> the original residue?  I've tried to follow the commands the=20
> wizard returns but I'm unable to follow what is being done.
>=20
> Cheers
> Noel
>=20
>=20

Hi Orla,

* Orla O'Sullivan <Orl...@te...> [2006-04-28 11:37] wrote:
> 
> Is there any way to change an L-alanine to a D-alanine in pymol

Sure.  In the "build" menu there is an entry:

  Invert (pk2)-(pk1)-(pk3) [Ctrl-E]

pk1 is the atom whose configuration is to be inverted.  pk2 and pk3 are
the two atoms attached to pk1 whose position will remain the same.  The
other two atoms attached to pk1 (assuming in the general case that it is
tetrahedral) will swap places.

So in the specific case of converting an L-amino acid to a D-amino acid:

Using the mouse, pick first the Calpha and then the N and C atoms of the
main chain of the residue you wish to convert to the "D" configuration.
These atoms will not move.

Then use that menu item (or type "Ctrl-E") and the Cbeta will flip to
the other configuration.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Mikko Huhtala writes:
 >  > If so, I guess it must be a bug in the new driver? If not, here's a wild
 >  > shot: I tried to connect some older Stereographics emitters to our
 >  > Quadro FX3000 cards, and that didn't work. After some investigation, I
 >  > found out that the old emitters required 12V output from the stereo
 >  > connector, whereas the Nvidia card uses the 5V VESA standard. Could this
 >  > be a hint?
 > 
 > I do not think it is a hardware problem, since the hardware did work
 > with Fedora 3 and the newest cards we have (NV36 chips) work with the
 > latest driver and kernel, too. As far as I know, all of the emitters
 > are the same model, Stereographics E2 for PCs.
 > 

I tested the recent versions of the nvidia driver on Fedora 3, and the
one that still works is 7676. All the 8xxx versions after that are
broken. Version 7676 cannot be installed on Fedora 5, because it does
not compile against kernels 2.6.15 and 2.6.16. The solution turned out
to a patch to the driver found here

http://www.nvnews.net/vbulletin/showthread.php?t=66750

After patching, the driver compiles/links against kernel version
2.6.16.

So, for the record: Quadro stereo sync on NV25 and NV28 chips is
broken in driver versions 8174, 8178 and 8756.

Mikko

Hi=20

=20

Is there any way to change an L-alanine to a D-alanine in pymol

=20

Orla

=20

Dr.Orla O'Sullivan

=20

Research Officer

=20

Biotechnology

=20

=20

=20

=20

=20

Moorepark Food Research Centre
Teagasc

=20

Moorepark
Fermoy, Co. Cork
Ireland

=20

=20

=20

Tel:       +353 - (0)25 - 42344

=20

Hi all,

I'm in the process of creating a plugin for pymol, however I've hit a 
small wall.  Is there a series of python calls I can make in my code to 
perform a mutation without the loss of the original residue?  I've tried 
to follow the commands the wizard returns but I'm unable to follow what 
is being done.

Cheers
Noel

 Hi everybody,
I'm working on multiple sequence alignments and I'm looking for co-evolving
residues (positions/columns in the alignment).
I performed a statistical analysis (clustering) and obtain a tree in which
leaves are positions. I use a tree viewer (written in tcl/tk) to manipulate
the tree, and i'd like to link this tree viewer to PyMOL in order to be abl=
e
to select residues or cluster of residues in the tree and color them in the
pdb structure displayed in Pymol.
In the PyMOL user manual, it's said that to link PyMOL with an other
program, we have to use a separate external GUI window to control the
interaction, rather than changing internal PyMOL code.
Is someone could tell me more about this idea? how can this work ?
Thanks in advance!

pierre.

Thanks for your reply!

EPF (Esben Peter Friis) writes:
 > 
 > Does it work with older drivers / FC installations?

Yes, we have used these emitters and cards with Fedora 1 and 3 for
several years with no problems. I haven't tested the latest driver on
FC3 (which is still around on some harddrive partitions), but I guess
I should do that, too.


 > If so, I guess it must be a bug in the new driver? If not, here's a wild
 > shot: I tried to connect some older Stereographics emitters to our
 > Quadro FX3000 cards, and that didn't work. After some investigation, I
 > found out that the old emitters required 12V output from the stereo
 > connector, whereas the Nvidia card uses the 5V VESA standard. Could this
 > be a hint?

I do not think it is a hardware problem, since the hardware did work
with Fedora 3 and the newest cards we have (NV36 chips) work with the
latest driver and kernel, too. As far as I know, all of the emitters
are the same model, Stereographics E2 for PCs.

Mikko

If the Mac version has the option "hash_max", try to decrease it. The
rendering will take longer, but the memory usage will be lower. For
example:

set hash_max, 50

Try with different values. I think the default is 100.


Best wishes

Esben

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mat...@im...
> Sent: 27. april 2006 03:03
> To: XIE, DONGLU
> Cc: pym...@li...
> Subject: Re: [PyMOL] run out of memory problem
>=20
>=20
> pym...@li... wrote on 04/26/2006=20
> 08:03:40 PM:
>=20
> > Hi all,
> >
> > The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was=20
> > installed in Mac 10.4.6. This Mac has 1.5G memory. When=20
> doing ray, it=20
> > was using about 1.2G memory, it stopped in  the middle and
> > at last it died. The error message is about running out of memory.
> >
> > Did anybody meet the same problem? Thanks.
> >
> > -Donglu
> >
>=20
> Hi Donglu -
>=20
> We need more information to figure out what happened.  How=20
> much memory was Pymol using when you first launched it?  What=20
> about right before you started the raytracing?  Are you=20
> rendering an unusually large or complex image?
>=20
> You can try adjusting the memory settings for raytracing: in=20
> the "Setting" menu, go to "Rendering" then "Memory".  Try the=20
> various options and see if you still run out of memory.
>=20
> If your image is complex, try reducing the quality.  In the=20
> "Display" menu, go to "Quality".  You may be able to reduce=20
> the quality a bit without noticeably affecting the image and=20
> it should reduce memory usage.  Reducing the size of the=20
> raytraced image will also reduce memory usage, but of course=20
> your image will be smaller...
>=20
> Hope these suggestions help,
>=20
> Matt
>=20
>=20
>=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
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web=20
> services, security? Get stuff done quickly with=20
> pre-integrated technology to make your job easier Download=20
> IBM WebSphere Application Server v.1.0.1 based on Apache=20
> Geronimo=20
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
dat=3D121642
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Does it work with older drivers / FC installations?

If so, I guess it must be a bug in the new driver? If not, here's a wild
shot: I tried to connect some older Stereographics emitters to our
Quadro FX3000 cards, and that didn't work. After some investigation, I
found out that the old emitters required 12V output from the stereo
connector, whereas the Nvidia card uses the 5V VESA standard. Could this
be a hint?

best wishes

Esben

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> mhu...@ab...
> Sent: 27. april 2006 06:58
> To: pym...@li...
> Subject: [PyMOL] Nvidia Quadro/stereo emitter sync problem on Fedora 5
>=20
>=20
>=20
> This is off-topic on this list, but I figured someone among=20
> the subscribers might have an idea about what is going on. I=20
> posted a question on the Nvidia nVnews forum, but got no=20
> replies so far.
>=20
> We are using version 8756 of the Nvidia driver on Fedora Core=20
> 5. There are several machines with various versions of the=20
> Quadro chip. The driver seems to work, except for=20
> Stereographics emitter sync on older NV25 and NV28 cards. On=20
> NV25 the emitter led does not light at all, and on NV28 it=20
> lights, but the synchronization is off (the picture flickers=20
> badly and there is no proper stereo effect when looking=20
> through the glasses). Newer NV36 cards work as advertised.
>=20
> This happens with the 8756 and 8178 (requires patching to=20
> work at all on
> FC5) drivers when using the latest kernels, 2.6.16-1.2096_FC5=20
> or 2.6.16-1.2080_FC5. The machines have x86 Pentium 4 processors.
>=20
> Has anyone else seen this? Does stereo work using these=20
> drivers on older kernels/distributions and this is just=20
> kernel/compiler incompatibility on Fedora 5?
>=20
> Mikko Huhtala
> =20
>=20
>=20
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web=20
> services, security? Get stuff done quickly with=20
> pre-integrated technology to make your job easier Download=20
> IBM WebSphere Application Server v.1.0.1 based on Apache=20
> Geronimo=20
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
dat=3D121642
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

This is off-topic on this list, but I figured someone among the
subscribers might have an idea about what is going on. I posted a
question on the Nvidia nVnews forum, but got no replies so far.

We are using version 8756 of the Nvidia driver on Fedora Core 5. There
are several machines with various versions of the Quadro chip. The
driver seems to work, except for Stereographics emitter sync on older
NV25 and NV28 cards. On NV25 the emitter led does not light at all, and
on NV28 it lights, but the synchronization is off (the picture flickers
badly and there is no proper stereo effect when looking through the
glasses). Newer NV36 cards work as advertised.

This happens with the 8756 and 8178 (requires patching to work at all on
FC5) drivers when using the latest kernels, 2.6.16-1.2096_FC5 or
2.6.16-1.2080_FC5. The machines have x86 Pentium 4 processors.

Has anyone else seen this? Does stereo work using these drivers on older
kernels/distributions and this is just kernel/compiler incompatibility
on Fedora 5?

Mikko Huhtala
 

pym...@li... wrote on 04/26/2006 08:03:40 PM:

> Hi all,
>
> The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was
> installed in Mac 10.4.6. This
> Mac has 1.5G memory. When doing ray, it was using about 1.2G memory,
> it stopped in  the middle and
> at last it died. The error message is about running out of memory.
>
> Did anybody meet the same problem? Thanks.
>
> -Donglu
>

Hi Donglu -

We need more information to figure out what happened.  How much memory was
Pymol using when you first launched it?  What about right before you
started the raytracing?  Are you rendering an unusually large or complex
image?

You can try adjusting the memory settings for raytracing: in the "Setting"
menu, go to "Rendering" then "Memory".  Try the various options and see if
you still run out of memory.

If your image is complex, try reducing the quality.  In the "Display" menu,
go to "Quality".  You may be able to reduce the quality a bit without
noticeably affecting the image and it should reduce memory usage.  Reducing
the size of the raytraced image will also reduce memory usage, but of
course your image will be smaller...

Hope these suggestions help,

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.

Hi all,

The binary distribution (macpymol-0_99rc6.tar.gz) of PyMol 0.99 was installed in Mac 10.4.6. This
Mac has 1.5G memory. When doing ray, it was using about 1.2G memory, it stopped in  the middle and
at last it died. The error message is about running out of memory.

Did anybody meet the same problem? Thanks.

-Donglu

Pete,

Thanks -- I ran some tests too and wasn't able to find any convincing =
memory leaks either. =20

Instead, it appears that Python simply caching memory previously used, =
all of which appears to remain available to Python for loading of =
subsequent session.  As it turns out, this inefficiency in Python is =
something people are aware of and thinking about:  =
http://evanjones.ca/memoryallocator

Since we are currently dependent upon Python for our =
platform-independent session save & restore capability, we are stuck =
with this behavior until Python itself is fixed.

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
> Peter Adrian Meyer
> Sent: Wednesday, April 26, 2006 9:02 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: RE: [PyMOL] pse/session files increase memory usage?
>=20
> Warren,
>=20
> I did a bit of testing (memory figures from top VIRT column,=20
> after pymol
> had finished executing commands and was responsive to input):
>=20
> >pymol set.pml (316MB)
> save test.pse (537MB)
> reinitialize ; load test.pse (539MB after load)
> reinitialize ; load test.pse (540MB after load)
> reinitialize ; load test.pse (542MB after load)
> quit
>=20
> > pymol test.pse (532MB)
>=20
> It looks to me like there's a small memory leak when=20
> reloading the same
> session file, but that this is fairly minor compared to the difference
> between loading objects from a script and loading from a session file.
>=20
>=20
> Pete
>=20
> > Pete,
> >
> > It is a PyMOL fact of life that session files take more=20
> memory, because
> > all state information must transient exist in both Python=20
> and C while the
> > session is being loading.  However, we should get that=20
> memory back after
> > the session is fully loaded.  If not, then you may be right=20
> about a memory
> > leak.  A good way to test this is to see what happens if=20
> you load the same
> > session over and over again without restarting PyMOL.  Does=20
> memory usage
> > consistently increase or does it level off?
> >
> > The most likely cause of this would be PyMOL failing to=20
> decrement the
> > reference counts on certain session data.
> >
> > 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
> >> Peter Adrian Meyer
> >> Sent: Tuesday, April 25, 2006 3:15 PM
> >> To: pym...@li...
> >> Subject: [PyMOL] pse/session files increase memory usage?
> >>
> >> Hi all,
> >>
> >> For complex scenes, I've noticed that pymol 0.99rc6 (with
> >> ext0.99rc1) on linux appears to use more memory when started
> >> from a pse file than it does when loading the models/maps
> >> manually or from a pml script (based on the fact that I get
> >> out of memory errors during ray-tracing after starting from a
> >> pse, but not after starting from pml scripts).
> >>
> >> The easy work-around is to use pml scripts instead of pse
> >> files, but I was curious if anyone else had run into this
> >> (or, for that matter if it's a known issue...my best guess
> >> would be that there's a memory leak somewhere, or that the
> >> configuration flags I used to build python were causing problems).
> >>
> >> Pete
> >>
> >>
> >> Pete Meyer
> >> Fu Lab
> >> BMCB grad student
> >> Cornell University
> >>
> >>
> >>
> >> -------------------------------------------------------
> >> Using Tomcat but need to do more? Need to support web
> >> services, security?
> >> Get stuff done quickly with pre-integrated technology to make
> >> your job easier Download IBM WebSphere Application Server
> >> v.1.0.1 based on Apache Geronimo
> >> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> > dat=3D121642
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>
> >>
> >>
> >
>=20
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on=20
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

Warren,

I did a bit of testing (memory figures from top VIRT column, after pymol
had finished executing commands and was responsive to input):

>pymol set.pml (316MB)
save test.pse (537MB)
reinitialize ; load test.pse (539MB after load)
reinitialize ; load test.pse (540MB after load)
reinitialize ; load test.pse (542MB after load)
quit

> pymol test.pse (532MB)

It looks to me like there's a small memory leak when reloading the same
session file, but that this is fairly minor compared to the difference
between loading objects from a script and loading from a session file.


Pete

> Pete,
>
> It is a PyMOL fact of life that session files take more memory, because
> all state information must transient exist in both Python and C while the
> session is being loading.  However, we should get that memory back after
> the session is fully loaded.  If not, then you may be right about a memory
> leak.  A good way to test this is to see what happens if you load the same
> session over and over again without restarting PyMOL.  Does memory usage
> consistently increase or does it level off?
>
> The most likely cause of this would be PyMOL failing to decrement the
> reference counts on certain session data.
>
> 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
>> Peter Adrian Meyer
>> Sent: Tuesday, April 25, 2006 3:15 PM
>> To: pym...@li...
>> Subject: [PyMOL] pse/session files increase memory usage?
>>
>> Hi all,
>>
>> For complex scenes, I've noticed that pymol 0.99rc6 (with
>> ext0.99rc1) on linux appears to use more memory when started
>> from a pse file than it does when loading the models/maps
>> manually or from a pml script (based on the fact that I get
>> out of memory errors during ray-tracing after starting from a
>> pse, but not after starting from pml scripts).
>>
>> The easy work-around is to use pml scripts instead of pse
>> files, but I was curious if anyone else had run into this
>> (or, for that matter if it's a known issue...my best guess
>> would be that there's a memory leak somewhere, or that the
>> configuration flags I used to build python were causing problems).
>>
>> Pete
>>
>>
>> Pete Meyer
>> Fu Lab
>> BMCB grad student
>> Cornell University
>>
>>
>>
>> -------------------------------------------------------
>> Using Tomcat but need to do more? Need to support web
>> services, security?
>> Get stuff done quickly with pre-integrated technology to make
>> your job easier Download IBM WebSphere Application Server
>> v.1.0.1 based on Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&
> dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Pete,

It is a PyMOL fact of life that session files take more memory, because =
all state information must transient exist in both Python and C while =
the session is being loading.  However, we should get that memory back =
after the session is fully loaded.  If not, then you may be right about =
a memory leak.  A good way to test this is to see what happens if you =
load the same session over and over again without restarting PyMOL.  =
Does memory usage consistently increase or does it level off?

The most likely cause of this would be PyMOL failing to decrement the =
reference counts on certain session data.=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
> Peter Adrian Meyer
> Sent: Tuesday, April 25, 2006 3:15 PM
> To: pym...@li...
> Subject: [PyMOL] pse/session files increase memory usage?
>=20
> Hi all,
>=20
> For complex scenes, I've noticed that pymol 0.99rc6 (with=20
> ext0.99rc1) on linux appears to use more memory when started=20
> from a pse file than it does when loading the models/maps=20
> manually or from a pml script (based on the fact that I get=20
> out of memory errors during ray-tracing after starting from a=20
> pse, but not after starting from pml scripts).
>=20
> The easy work-around is to use pml scripts instead of pse=20
> files, but I was curious if anyone else had run into this=20
> (or, for that matter if it's a known issue...my best guess=20
> would be that there's a memory leak somewhere, or that the=20
> configuration flags I used to build python were causing problems).
>=20
> Pete
>=20
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
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dat=3D121642
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>=20
>=20
>=20
>=20

Hi Tsjerk

>>>>> "Tsjerk" == Tsjerk Wassenaar <ts...@gm...> writes:
Tsjerk> There's a bit more to it. In the pymol view, the camera is located
Tsjerk> at the origin, so to rotate your coordinates you first have to move
Tsjerk> the center to the origin, do the rotation and move the thing
Tsjerk> back. I've scripted this in Povray. If you're interested, I can
Tsjerk> send you the script.

Yes, that sounds great, thanks.

Tsjerk> You can then rescript it in python or you can
Tsjerk> output your scene to povray and do the rest there.

If it's not too complex, I'll rewrite for python so I can run it
interactively.

Tsjerk> In addition (although you may already know this), the meaning of
Tsjerk> all elements of the result of get_view (python index) is

Yes, thanks a lot.

Terry

Hi Terry,

There's a bit more to it. In the pymol view, the camera is located at the
origin, so to rotate your coordinates you first have to move the center to
the origin, do the rotation and move the thing back. I've scripted this in
Povray. If you're interested, I can send you the script. You can then
rescript it in python or you can output your scene to povray and do the res=
t
there.

In addition (although you may already know this), the meaning of all
elements of the result of get_view (python index) is

0:9 - rotation matrix
9:12 - camera position
12:15 - origin of rotation
15:17 - slab near and far
17 - orthoscopic flag

Cheers,

Tsjerk


On 4/25/06, Terry Jones <tc...@ca...> wrote:
>
> I wrote a pymol plugin that produces a bunch of cgo. The images I generat=
e
> have a cube drawn around them.
>
> I've been asked if it's possible to allow the user to initially rotate th=
e
> image to their heart's content and then have the plugin draw the
> surrounding cube. I.e., once the image is rotated, the cube will be drawn
> in a way that always looks good to the viewer, not at some random angle.
> In
> other words, the cube will always have the same orientation, no matter ho=
w
> much the image has been rotated before the cube is drawn.
>
> OK, having said the same thing 3 times, and hopefully made sense at least
> once, I'll say something new...
>
> I imagine this can be done easily enough. I guess I should be able to cal=
l
> get_view and get the current rotation matrix (elements 0-8 of the returne=
d
> list) and apply this to all points that I plan to draw between when makin=
g
> the cube.
>
> My questions: Is this right? Do I need to do anything more than just
> multiply the old point by the rotation matrix? What's the easiest way to
> do
> this in Pymol or Python, or should I just code it (it's very simple after
> all).  And, of course, is there a better way to do what I want?
>
> Thanks for any help. Don't assume I know what I'm doing, because I
> probably
> don't. So the more details, the better.
>
> Regards,
> Terry
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi all,

For complex scenes, I've noticed that pymol 0.99rc6 (with ext0.99rc1) on
linux appears to use more memory when started from a pse file than it does
when loading the models/maps manually or from a pml script (based on the
fact that I get out of memory errors during ray-tracing after starting
from a pse, but not after starting from pml scripts).

The easy work-around is to use pml scripts instead of pse files, but I was
curious if anyone else had run into this (or, for that matter if it's a
known issue...my best guess would be that there's a memory leak somewhere,
or that the configuration flags I used to build python were causing
problems).

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

I wrote a pymol plugin that produces a bunch of cgo. The images I generate
have a cube drawn around them.

I've been asked if it's possible to allow the user to initially rotate the
image to their heart's content and then have the plugin draw the
surrounding cube. I.e., once the image is rotated, the cube will be drawn
in a way that always looks good to the viewer, not at some random angle. In
other words, the cube will always have the same orientation, no matter how
much the image has been rotated before the cube is drawn.

OK, having said the same thing 3 times, and hopefully made sense at least
once, I'll say something new...

I imagine this can be done easily enough. I guess I should be able to call
get_view and get the current rotation matrix (elements 0-8 of the returned
list) and apply this to all points that I plan to draw between when making
the cube.

My questions: Is this right? Do I need to do anything more than just
multiply the old point by the rotation matrix? What's the easiest way to do
this in Pymol or Python, or should I just code it (it's very simple after
all).  And, of course, is there a better way to do what I want?

Thanks for any help. Don't assume I know what I'm doing, because I probably
don't. So the more details, the better.

Regards,
Terry

Adi,

I have forwarded you some previous discussions on mutations.  You will find 
your answer below.  If you need anything further, please let me know.

Best of Luck!


Cheers,
Nick

---------------------------------------------------
Hi,

I would like to ask how to change (modify or replace)
the amino acid residue? I'm using MacPymol and my
computer is iBookG4.

Thank you very much
Adi
----------------------------------------------------


----- Original Message ----- 
From: "Andrew Colasanti" <aco...@gm...>
To: <pym...@li...>
Sent: Thursday, April 20, 2006 9:36 AM
Subject: Re: [PyMOL] mutations


I follow the method outlined by Nick with one additional step, after
selecting the new residue you can run through a sidechain rotamer
library using the forward arrows at the bottom of the window.  You
also have a choice to use backbone dependant or backbone independant
rotamers.

Andrew

On 4/18/06, Noinaj <no...@uk...> wrote:
>
> Orla,
>
> This is simply, for the most part.  Here is what I do.
>
> Load your *.pdb file.  Then under WIZARD in the menu bar, select
> MUTAGENESIS.  Then pretty much, follow directions.  In the PyMOL VIEWER
> window, it will ask you to ' pick a residue.'  Once you pick a residue,
> select the type of residue you want to mutate to by left clicking on [No
> Mutation] button and holding down (under Mutagenesis).  This brings up a
> list of residues that you can then select from.  Once you select the 
> residue
> you want, hit APPLY, then DONE.  If everything was done correctly, you
> should see your mutated residue.
>
> There are probably other ways to do this, but I hope this helps.  If you
> would like screenshots of the steps, just let me know.
>
>
>
> Cheers,
> Nick
>
>
>
>
> ----- Original Message -----
> From: Orla O'Sullivan
> To: pym...@li...
> Sent: Tuesday, April 18, 2006 11:31 AM
> Subject: [PyMOL] mutations
>
>
>
>
> Hi all
>
> I'm a newbie to Pymol and so far have been very impressed. However I have
> tried to mutate some residues in my structure and have hit a brick wall.
>
> Has anyone done this with pymol and let me know how to do it?
>
>
>
> Regards
>
>
>
> Orla
>
>
>
> Dr.Orla O'Sullivan
>
> Research Officer
>
> Biotechnology
>
>
>
>
>
> Moorepark Food Research Centre
> Teagasc
>
> Moorepark
> Fermoy, Co. Cork
> Ireland
>
>
>
>
> Tel:       +353 - (0)25 - 42344
>
>


-------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job 
easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
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_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi Miguel,

This seems like a big in the program. Save the file as per usual (.pse) 
Change the suffix of the file to .psw and that works fine

J

Miguel Alejandro Pabon Sanclemente wrote:

>PyMOL community,
>
>I want to assemble a short animation using the PyMOL movie-making 
>capabilities.  I tried to save several scenes  as a .psw file (as previously 
>suggested) but by default PyMOL saves the file as .pse.  How can I make PyMOL  
>save the file as .psw? I'm working with PyMOL version 0.99.
>
>Thanks beforehand!!
>
>
>
>
>-------------------------------------------------------
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>  
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

Hi,

I would like to ask how to change (modify or replace)
the amino acid residue? I'm using MacPymol and my
computer is iBookG4. 

Thank you very much 
Adi 

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

PyMOL community,

I want to assemble a short animation using the PyMOL movie-making 
capabilities.  I tried to save several scenes  as a .psw file (as previously 
suggested) but by default PyMOL saves the file as .pse.  How can I make PyMOL  
save the file as .psw? I'm working with PyMOL version 0.99.

Thanks beforehand!!

Hi Fei,

* Fei Xu <fe...@ru...> [2006-04-19 11:55] wrote:
> Hi!:
> I met a scaling problem.
> I created many pdb files along one trajectory of DNA movement. I loaded
> each pdb file in pymol to create a picture, that is, one frame of the
> trajectory. Pymol shows each molecule in an optimal size automatically
> according the general shape of the molecular. The shape of the molecule
> along trajectory kept changing so that the size of the molecule also kept
> changing. When I connected all the time frames together, I saw the funny
> effect that the molecule was jumping back and forth.
> How can I put the molecule in the different time frames in exactly the
> same size?

What you are experiencing is the "auto_zoom" feature of pymol.  I have
this turned off in my .pymolrc file.  You can type:

  set auto_zoom, 0

to disable this feature.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Hi Eva,

If you save your scenes (conformations) as a psw file (under save as) 
you can then use a hyperlink in powerpoint and this will launch pymol in 
presentation mode and you can just use page down to scroll through the 
scenes. Pymol is still active so you can rotate the molecules in the 
presentation.

Hope this helps

J

Eva Vanamee wrote:

> I regularly use the F function keys in PyMol to store
> conformations and call them back in a presentation.
> I really like the transition effects. Is it possible to record those
> transitions as a movie and use them in a Powerpoint presentation?
> Thanks in advance,
> - Eva
>
>
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job 
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
> Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034