pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all:

I would like to make a simple movie of a structure ( a full rotation  
about the y axis) with a very strong fog effect. I have tried playing  
with depth_cue, ray_trace_fog settings as shown below  but I do not get  
as strong a fog effect as I would like. Adjusting the clip planes   
works nicely in the viewer window before the ray-tracing is executed,  
but when the movie images are written  out, Pymol seems to ignore the  
clip commands (?!).

######################################################################## 
#######
# Parameter Setup
######################################################################## 
#######
# don't use "fullscreen on" instead use viewport command later one in  
the script
full_screen on
clip near, 20
clip slab, 50
clip near, 30
set orthoscopic=0
set antialias=1
set spec_power=200
set depth_cue, 1
set ray_trace_fog = 1

Any suggestions?

Thank you very much in advance,
Alexandra

Hi,

I tried to open file in Tinker xyz format and something is wrong. I can see 
a lot of white points, regulary ordered and of course it does look like my 
protein. The format of my file is as follow:

 2458 my_compound_force_field
    1  S       -4.741101   14.540700    4.101900    1   238  239
    2  S        1.809200   -2.831001   10.350000    1   272  273
    3  S        4.400999    9.439899    3.958200    1   451
    4  S        0.294099   12.766001    6.539000    1   589  590
    5  O       -5.910101   15.293599   10.699300    1   232
    6  O       -5.774001   13.090999    7.783200    1   235
.......
 2456  H        7.374000   -7.408999   -1.064900    1  1834
 2457  H        8.559101   -7.826900    0.856000    1  1835
 2458  H        7.615100   -7.530000    2.910900    1  1836

Does anybody has idea why it does not work properly?
I used pylmol-0_98rc5-bin-win32.zip and rTools_0.7.2.zip files to install 
Pymol under Windows XP.

Thanks,
Paulina 

Hi Ramon,

* Ramon Crehuet <rc...@ii...> [2005-07-29 12:55] wrote:
> Hi all,
>    I have a problem with intra_fit. After reading two (or more) pdb 
> into the same molecule, it does not recognise atoms for other states. I 
> always get the message (this is for a short example):
> PyMOL>intra_fit name ca, 1
> Executive-Warning: Missing atoms in state 2 (0 instead of 2).
> Executive-Warning: No matches found for state 2.
> 
> even after executing:
> PyMOL>alter all, chain =''
> Alter: modified 24 atoms.
> 
> How can I know what is different in the two states or why the selection 
> doesn't work?

The problem is that the two states have different chain identifierss.  They must
be the same for intra_fit to work.

Here are your two example pdb files that do work now.


CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   GLY A   5      45.046  30.918  26.469  1.00 13.37      2CHT
ATOM      2  CA  GLY A   5      45.321  29.775  27.300  1.00  8.71      2CHT
ATOM      3  C   GLY A   5      45.834  28.644  26.444  1.00  4.68      2CHT
ATOM      4  O   GLY A   5      45.402  28.423  25.303  1.00  3.21      2CHT
ATOM      5  N   ILE A   6      46.763  27.874  26.979  1.00  5.74      2CHT
ATOM      6  CA  ILE A   6      47.318  26.743  26.260  1.00  3.53      2CHT
ATOM      7  CB  ILE A   6      48.842  26.828  26.098  1.00  4.24      2CHT
ATOM      8  CG1 ILE A   6      49.254  28.223  25.623  1.00  4.37      2CHT
ATOM      9  CG2 ILE A   6      49.258  25.732  25.115  1.00  2.06      2CHT
ATOM     10  CD1 ILE A   6      50.724  28.468  25.301  1.00  6.67      2CHT
ATOM     11  C   ILE A   6      46.981  25.563  27.127  1.00  4.66      2CHT
ATOM     12  O   ILE A   6      47.066  25.628  28.361  1.00  9.30      2CHT
END


CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   GLY A   5      45.044  31.002  26.859  1.00  7.52      2CHT
ATOM      2  CA  GLY A   5      45.492  29.807  27.582  1.00  2.01      2CHT
ATOM      3  C   GLY A   5      45.989  28.671  26.692  1.00  3.74      2CHT
ATOM      4  O   GLY A   5      45.500  28.434  25.576  1.00  2.36      2CHT
ATOM      5  N   ILE A   6      46.957  27.882  27.123  1.00  6.04      2CHT
ATOM      6  CA  ILE A   6      47.441  26.744  26.357  1.00 13.49      2CHT
ATOM      7  CB  ILE A   6      48.955  26.937  25.996  1.00 14.13      2CHT
ATOM      8  CG1 ILE A   6      49.190  28.322  25.354  1.00 19.71      2CHT
ATOM      9  CG2 ILE A   6      49.359  25.924  24.936  1.00 12.19      2CHT
ATOM     10  CD1 ILE A   6      50.665  28.738  25.151  1.00 20.45      2CHT
ATOM     11  C   ILE A   6      47.222  25.473  27.194  1.00 13.81      2CHT
ATOM     12  O   ILE A   6      47.782  25.283  28.269  1.00 13.60      2CHT
END

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 all,
    I have a problem with intra_fit. After reading two (or more) pdb 
into the same molecule, it does not recognise atoms for other states. I 
always get the message (this is for a short example):
PyMOL>intra_fit name ca, 1
Executive-Warning: Missing atoms in state 2 (0 instead of 2).
Executive-Warning: No matches found for state 2.

even after executing:
PyMOL>alter all, chain =''
Alter: modified 24 atoms.

How can I know what is different in the two states or why the selection 
doesn't work?
Thanks,
Ramon

I enclose two pdb files as examples that do not work.


CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   GLY B   5      45.046  30.918  26.469  1.00 13.37      2CHT
ATOM      2  CA  GLY B   5      45.321  29.775  27.300  1.00  8.71      2CHT
ATOM      3  C   GLY B   5      45.834  28.644  26.444  1.00  4.68      2CHT
ATOM      4  O   GLY B   5      45.402  28.423  25.303  1.00  3.21      2CHT
ATOM      5  N   ILE B   6      46.763  27.874  26.979  1.00  5.74      2CHT
ATOM      6  CA  ILE B   6      47.318  26.743  26.260  1.00  3.53      2CHT
ATOM      7  CB  ILE B   6      48.842  26.828  26.098  1.00  4.24      2CHT
ATOM      8  CG1 ILE B   6      49.254  28.223  25.623  1.00  4.37      2CHT
ATOM      9  CG2 ILE B   6      49.258  25.732  25.115  1.00  2.06      2CHT
ATOM     10  CD1 ILE B   6      50.724  28.468  25.301  1.00  6.67      2CHT
ATOM     11  C   ILE B   6      46.981  25.563  27.127  1.00  4.66      2CHT
ATOM     12  O   ILE B   6      47.066  25.628  28.361  1.00  9.30      2CHT
END


CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   GLY A   5      45.044  31.002  26.859  1.00  7.52      2CHT
ATOM      2  CA  GLY A   5      45.492  29.807  27.582  1.00  2.01      2CHT
ATOM      3  C   GLY A   5      45.989  28.671  26.692  1.00  3.74      2CHT
ATOM      4  O   GLY A   5      45.500  28.434  25.576  1.00  2.36      2CHT
ATOM      5  N   ILE A   6      46.957  27.882  27.123  1.00  6.04      2CHT
ATOM      6  CA  ILE A   6      47.441  26.744  26.357  1.00 13.49      2CHT
ATOM      7  CB  ILE A   6      48.955  26.937  25.996  1.00 14.13      2CHT
ATOM      8  CG1 ILE A   6      49.190  28.322  25.354  1.00 19.71      2CHT
ATOM      9  CG2 ILE A   6      49.359  25.924  24.936  1.00 12.19      2CHT
ATOM     10  CD1 ILE A   6      50.665  28.738  25.151  1.00 20.45      2CHT
ATOM     11  C   ILE A   6      47.222  25.473  27.194  1.00 13.81      2CHT
ATOM     12  O   ILE A   6      47.782  25.283  28.269  1.00 13.60      2CHT
END

Yi,

To stuff a bunch of identical object in one PDB file, you need to assign
a unique segment ID to each one.  For example:

load $PYMOL_PATH/test/dat/1tii.pdb

symexp s,1tii,1tii,5

names=3Dcmd.get_names()
for a in range(len(names)): cmd.alter(names[a],"segi=3D"+str(a))

save multi.pdb

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 yi zhang
> Sent: Sunday, July 24, 2005 8:43 PM
> To: pym...@li...
> Subject: [PyMOL] (no subject)
>=20
> Hi, everyone,
>=20
> I used symexp command in pymol to generate symmetry-related=20
> molecule, something like:
>=20
> cmd.symexp('sym', 'obj', 'obj',10 )
>=20
> of course, I can manually save each symmetry-related molecule=20
> to *.pdb file by clicking save molecule button, but how can I=20
> write a script to save all of them or part of them? the=20
> symmetry-related objects are not appendable.
>=20
> thanks!
>=20
> yi
>=20
> __________________________________________________
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>=20
>=20
>=20

Xavier,

A potentially confusing aspect of settings is that they only go down to
the object (and in some cases object-state) level.  Individual atoms
don't have their own settings. =20

So what you've doing is changing the stick_transparency for all objects
that include atoms in the "met" selection.

The workaround is to using the "create" command to create separate
objects.

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
> Xavier Deupi
> Sent: Wednesday, July 27, 2005 2:26 PM
> To: pym...@li...
> Subject: [PyMOL] transparent sticks
>=20
> Hi,
>=20
> I want to set some transparency in a selection, which is=20
> displayed as sticks. I'm using the following command:
>=20
> cmd.set("stick_transparency",0.5,"ret") # where ret is the selection
>=20
> But when I run the script, ALL the sticks are modified, and=20
> not only the selection "ret", as I was expecting.
>=20
> I've been trying a few variations in the syntax, but I can't=20
> figure out the correct way... any help?
>=20
> Thanks in advance,
>=20
> Xavier
>=20
> --
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology Beckman=20
> Center for Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine=20
> Stanford, CA 94305 (USA)
>=20
> E-mail: Xav...@st...
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

Hello Sebastien,

* Sebastien Moretti <seb...@ig...> [2005-07-28 08:47] wrote:
> Hello,
> Is there a way to expand the names panel to be able to read object and 
> selection names larger than 16 characters ?
 
At the bottom left corner of the panel, just to the left of the "VCR
controls" is a little vertical bar.  You can drag it to change the width
of the panel.

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

Hello,
Is there a way to expand the names panel to be able to read object and=20
selection names larger than 16 characters ?

Or, a way to show the full names when they are selected with the mouse ?

Thanks

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Hi,
  I can't comment about how the NVidia stereo works with other packages
but there are a few facts about the NVidia drivers that apply equally 
to all of us:
  -  Unlike classic graphics workstations like SGI and Sun, with NVidia 
     you can have _either_ stereo, or you can have multisample 
     antialiasing, but you can't have both at the same time (at least on the
     cards and drivers I've tested to date).  
     Since the vast majority of VMD users don't have stereo capable hardware, 
     the default VMD behavior is to acquire a window with antialiasing.  
     In order to get VMD to use stereo on an NVidia card, you need to do 
     this prior to running VMD: 
       setenv VMDPREFERSTEREO 1
     This environment variable tells VMD that you want stereo rather than
     antialiasing, and so it will request stereo only.  This is probably 
     functionally equivalent to the stereo settings described below for O.

  -  NVidia's cards exhibit a huge loss of performance if you acquire a 
     stereo window, but render to it in a monoscopically.
     It would seem that the NVidia drivers do some sort of software framebuffer
     copy to present the same image to both eyes, when drawing monoscopically
     to a stereo-capable window.  On SGI/Sun workstations and on PC video
     cards by 3DLabs, there isn't any performance penalty for this, 
     they run full speed regardless whether the window is stereo-capable 
     or not.  So, on the NVidia cards, you only want to run VMD with a 
     stereo window if you actually plan to use it.  I may consider adding
     some NVidia specific code to workaround this performance issue,
     but really this is due to the NVidia hardware/software implementation,
     and not the fault of O/PyMol/VMD, etc.

  John Stone
  vm...@ks...

On Wed, Jul 27, 2005 at 04:03:58PM -0700, Cameron Mura wrote:
> Demetres & Roger,
> 
> I've had the same problem w/ stereo on FC4 (tested only w/ an nVidia 
> Quadro 700 XGL card), and have been meaning to mail the list.  The 
> problem occurs even after taking the typical steps to set-up the nVidia 
> drivers on the system (as described by Roger), and also occurs w/ 
> hadrware quad-buffered stereo in other molecular graphics software 
> (e.g., PyMOL and VMD -- so I've cc'd this email to those lists too). I 
> haven't had time to really troubleshoot it yet (by fiddling around w/ X 
> and whatnot), so if anyone else sees this stereo/FC4 problem -- or, even 
> better, can explain it! -- it'd be great to hear about it...
> 
> Thanks,
> Cameron
> 
> 
> === o-i...@bi... wrote (on 07/27/2005 03:46 PM): ===
> 
> >Subject:
> >[o-info] Problems with stereo emitter
> >From:
> >"Demetres D. Leonidas" <dd...@ei...>
> >Date:
> >Wed, 27 Jul 2005 16:39:13 +0300
> >To:
> >o-...@o-...
> >
> >To:
> >o-...@o-...
> >
> >
> >Dear Ousers,
> >
> >We have just got a Celsius K330 workstation with an NVIDIA Quadro 
> >FX1300 128MB PCI-Ex stereo card and installed FC4. I did all the 
> >necessary modifications to the xorg.conf file to enable STEREO with O 
> >and when I hit F1 I get in the screen the stereoview. However, the 
> >emitter (NuVision 60GX) does not flash and hence the glasses do not 
> >work. The emitter is plugged on the 3-pin plug in the card. What do I 
> >do wrong ? Is there a special connector that I should use.
> >
> >
> >
> >Many thanks
> >
> >
> >
> >Demetres
> >
> >
> >------------------------------------------------------------------------
> >
> >Subject:
> >RE: [o-info] Problems with stereo emitter
> >From:
> >"Roger Rowlett" <RRo...@ma...>
> >Date:
> >Wed, 27 Jul 2005 11:05:55 -0400
> >To:
> >"Demetres D. Leonidas" <dd...@ei...>, <o-...@o-...>
> >
> >To:
> >"Demetres D. Leonidas" <dd...@ei...>, <o-...@o-...>
> >
> >
> >The following steps are typical for enabling stereo in O 9.0 with an
> >Nvidia card and NuVision 60GX emitter/glasses:
> >
> >1. Install the proprietary Nvidia graphics driver. In the XF86Config (or
> >its equivalent), the following settings should be included under the
> >Videocard0 device:
> >	Driver "nvidia"
> >	Option "Stereo" "3"
> >
> >2. Plug the NiVision emitter 3-pin mini-DIN connector to the appropriate
> >graphics card socket.
> >
> >3. Start O with stereo enabled, which will require setting the
> >environment variable STEREO to "on". I use a script, ono9-3d:
> >
> >#! /bin/tcsh
> >setenv STEREO on
> >setenv ODAT /usr/local/bin/ono9/data/
> >/usr/local/bin/ono9/lin_ono
> >
> >When O is started, you should see the red light on the stero emitter
> >immediately, whether or not you are using stereo.
> >
> >It's useful to have a script for both 3d-O and 2d-O as for some Nvidia
> >drivers, as graphics response can be slow when the environment variable
> >STEREO is set to "on" but stereo viewing is not enabled. I have a second
> >script, ono9, which is identical to ono9-3d except that the second line
> >(setting STEREO on) is omitted. This allows O to run quickly in 2d mode,
> >for those occasions when I don't want to use the glasses.
> >
> >I'm using RH9, an NVidia Quadro 980XGL, and the Nuvision 60GX and
> >everything works flawlessly, other than the "slow non-stereo response"
> >bug when stereo is "on". I'm still using version 4363 NVidia drivers, as
> >there are issues with some legacy software with the newer drivers. Works
> >fine anyway. Stereo also works flawlessly in VMD, PyMol, MolMol, and
> >DeepView.
> >
> >Cheers,
> >
> >____________________________________________
> >Roger S. Rowlett
> >Professor & Chair
> >Department of Chemistry
> >Colgate University
> >13 Oak Drive
> >Hamilton, NY 13346
> >
> >tel: 315-228-7245
> >ofc: 315-228-7395
> >fax: 315-228-7935
> >email: rro...@ma...
> >web: http://departments.colgate.edu/chemistry
> >
> >
> > 
> >
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: jo...@ks...                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

hi Cameron,

Geforce 6800GT and 6800Ultra come with PCI-E interfaces nowadays. =
Besides, the AGP8x vs PCI-E architecture does not have any significant =
performance difference for most people according to tests carried out by =
http://anantech.com, and many others. Your reported advantage in =
glxgears might not translate into any visible advantage in O or pymol.

The next issue is that XiG does not support Nvidia, whereas Rivatuner =
supports both ATI and Nvidia. XiG is a commerical product that emulates =
3D, whereas Rivatuner is an underground product that tricks the computer =
into thinking that a Quadro card was installed. Nowadays, chip makers =
tend to use the same chip across all their product lines to cut cost. =
Many people have found out that their Geforce GPU is actually an =
artifically disabled, yet fully functional Quadro GPU chip.

Don't be fooled by the marketing and external design, especially when =
electronics are involved. Electronic manufacturers like Nvidia, ATI, AMD =
and Intel almost always have higher profit margins for their premium =
products compared to their low-end products because the same core design =
is used across their product-lines.


-----Original Message-----
From:	Cameron Mura [mailto:cm...@uc...]
Sent:	Thu 7/28/2005 6:18 AM
To:	Wang Chern Hoe
Cc:	Philippe BENAS; ccp4bb; pymolbb; Obb
Subject:	Re: [PyMOL] nVidia Quadro FX 1400, FX 3400 and FX 4400 =
performances
part of this is also the hardware issue of AGP (8x) versus PCI and=20
PCI-express interfaces being used by newer cards on newer boards... so=20
the much higher bandwith of, e.g., using a Quadro FX1400 with a PCI-E=20
x16 makes it far superior (in my experiences, w/ linux) to the nVidia=20
GeForce 6800 GT... (talking >18k FPS versus ~13-14k FPS in glxgears!).=20
with regards to stereo capabilities, after having used things like the=20
XiG drivers to emulate QBS with cards that don't natively support it=20
(e.g., ATI Radeon 8500), i would definitely opt for the card that=20
provides hardware stereo (so i'd rather use the nVidia Quadro 700 XGL=20
rather than the technically superior (but stereo-less) GeForce 6800+XiG=20
summit drivers (or whatever).=20

cameron


=3D=3D=3D Wang Chern Hoe wrote (on 07/27/2005 08:55 AM): =3D=3D=3D

>Hi Philippe,
>
>If you are using the Windows platform, I suggest you get a Geforce =
6800Ultra, and use rivatuner from =
http://downloads.guru3d.com/download.php?det=3D163 to modify the driver =
to Quadro FX 4400 under Windows XP. Thereafter, substitute O with NOC =
from http://noc.ibp.ac.cn/ and you should have saved several thousand =
bucks, increased your graphics card performance, and enabled 3D stereo =
on a Geforce card! The same goes for enabling undocumented features on =
an ATI card.=20
>
>The only caveat is that this mod has not been ported over to Linux, and =
that your graphic card's warranty will be ineffectual in the event of =
damage to the GPU chip.
>
>best regards
>Wang Chern Hoe
>
>
>-----Original Message-----
>From:	own...@dl... on behalf of Philippe BENAS
>Sent:	Wed 7/27/2005 11:13 PM
>To:	ccp4bb; pymolbb; Obb
>Cc:=09
>Subject:	[ccp4bb]: nVidia Quadro FX 1400, FX 3400 and FX 4400 =
performances
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
>Hi Xtallographers, Oers and Pymolers,
>
>In late January, Warren wrote: "The Quadro FX 3000 is the fastest card=20
>I've ever seen PyMOL run on". Well since then half a year is gone.
>So, would any of you had a chance to compare the FX 1400, FX 3400 and=20
>FX 4400 performances for stereo under Linux, I mean for the usual=20
>stereo programs we're using like O, Pymol or Turbo ?
>
> From several tests I read it seems there is no serious gap between =
them=20
>at least when compared for various engineering software (Rightmark, 3D=20
>studio Max, AutoCAD, CATIA, Ensight, Maya, Patchwork 3D and=20
>SolidWorks). As for their price there are some huge gaps on the other=20
>hand...
>
>Which of those 3 Quadro would you recommend in terms of=20
>performance/price ratio for molecular graphics ?
>
>In his email, Warren also recommended the NEC-Mitsubishi FP2141SB-BK=20
>22" CRT. What do you Folks think about this monitor if you do use it ?=20
>What do you think about the Iiyama HM204 DT DiamondTron 22" CRT ? Any=20
>other good monitor for stereo around that you would recommended ?
>
>Any help will be greatly appreciated.
>Philippe
>
>------------------------------------------------------------------------=

>Philippe BENAS, Ph.D.
>X-ray diffraction facility manager
>Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
>Faculte de Pharmacie - Universite Paris 5
>4, Avenue de l'Observatoire - Case 48
>F-75270 Paris cedex 06
>---
>Office: +33.(0)1-5373-9831 (use ext. 9977 instead to leave a voice =
mail)
>Fax: +33.(0)1-5373-9925
>X-ray Room (rotating anode): +33.(0)1-5373-9977
>X-ray Room (small molecules): +33.(0)1-5373-9679
>---
>Url: http://lcrbw.pharmacie.univ-paris5.fr/
>------------------------------------------------------------------------=

>
>
>
>
>
>
>DISCLAIMER:
>This email is confidential and may be privileged. If you are not the =
intended recipient, please delete it and notify us immediately. Please =
do not copy or use it for any purpose, or disclose its contents to any =
other person as it may be an offence under the Official Secrets Act. =
Thank you.
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>from IBM. Find simple to follow Roadmaps, straightforward articles,
>informative Webcasts and more! Get everything you need to get up to
>speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick
>_______________________________________________
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>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> =20
>

--=20
Cameron Mura
UCSD







DISCLAIMER:
This email is confidential and may be privileged. If you are not the =
intended recipient, please delete it and notify us immediately. Please =
do not copy or use it for any purpose, or disclose its contents to any =
other person as it may be an offence under the Official Secrets Act. =
Thank you.

Demetres & Roger,

I've had the same problem w/ stereo on FC4 (tested only w/ an nVidia 
Quadro 700 XGL card), and have been meaning to mail the list.  The 
problem occurs even after taking the typical steps to set-up the nVidia 
drivers on the system (as described by Roger), and also occurs w/ 
hadrware quad-buffered stereo in other molecular graphics software 
(e.g., PyMOL and VMD -- so I've cc'd this email to those lists too). I 
haven't had time to really troubleshoot it yet (by fiddling around w/ X 
and whatnot), so if anyone else sees this stereo/FC4 problem -- or, even 
better, can explain it! -- it'd be great to hear about it...

Thanks,
Cameron


=== o-i...@bi... wrote (on 07/27/2005 03:46 PM): ===

> Subject:
> [o-info] Problems with stereo emitter
> From:
> "Demetres D. Leonidas" <dd...@ei...>
> Date:
> Wed, 27 Jul 2005 16:39:13 +0300
> To:
> o-...@o-...
>
> To:
> o-...@o-...
>
>
> Dear Ousers,
>
> We have just got a Celsius K330 workstation with an NVIDIA Quadro 
> FX1300 128MB PCI-Ex stereo card and installed FC4. I did all the 
> necessary modifications to the xorg.conf file to enable STEREO with O 
> and when I hit F1 I get in the screen the stereoview. However, the 
> emitter (NuVision 60GX) does not flash and hence the glasses do not 
> work. The emitter is plugged on the 3-pin plug in the card. What do I 
> do wrong ? Is there a special connector that I should use.
>
>
>
> Many thanks
>
>
>
> Demetres
>
>
> ------------------------------------------------------------------------
>
> Subject:
> RE: [o-info] Problems with stereo emitter
> From:
> "Roger Rowlett" <RRo...@ma...>
> Date:
> Wed, 27 Jul 2005 11:05:55 -0400
> To:
> "Demetres D. Leonidas" <dd...@ei...>, <o-...@o-...>
>
> To:
> "Demetres D. Leonidas" <dd...@ei...>, <o-...@o-...>
>
>
>The following steps are typical for enabling stereo in O 9.0 with an
>Nvidia card and NuVision 60GX emitter/glasses:
>
>1. Install the proprietary Nvidia graphics driver. In the XF86Config (or
>its equivalent), the following settings should be included under the
>Videocard0 device:
>	Driver "nvidia"
>	Option "Stereo" "3"
>
>2. Plug the NiVision emitter 3-pin mini-DIN connector to the appropriate
>graphics card socket.
>
>3. Start O with stereo enabled, which will require setting the
>environment variable STEREO to "on". I use a script, ono9-3d:
>
>#! /bin/tcsh
>setenv STEREO on
>setenv ODAT /usr/local/bin/ono9/data/
>/usr/local/bin/ono9/lin_ono
>
>When O is started, you should see the red light on the stero emitter
>immediately, whether or not you are using stereo.
>
>It's useful to have a script for both 3d-O and 2d-O as for some Nvidia
>drivers, as graphics response can be slow when the environment variable
>STEREO is set to "on" but stereo viewing is not enabled. I have a second
>script, ono9, which is identical to ono9-3d except that the second line
>(setting STEREO on) is omitted. This allows O to run quickly in 2d mode,
>for those occasions when I don't want to use the glasses.
>
>I'm using RH9, an NVidia Quadro 980XGL, and the Nuvision 60GX and
>everything works flawlessly, other than the "slow non-stereo response"
>bug when stereo is "on". I'm still using version 4363 NVidia drivers, as
>there are issues with some legacy software with the newer drivers. Works
>fine anyway. Stereo also works flawlessly in VMD, PyMol, MolMol, and
>DeepView.
>
>Cheers,
>
>____________________________________________
>Roger S. Rowlett
>Professor & Chair
>Department of Chemistry
>Colgate University
>13 Oak Drive
>Hamilton, NY 13346
>
>tel: 315-228-7245
>ofc: 315-228-7395
>fax: 315-228-7935
>email: rro...@ma...
>web: http://departments.colgate.edu/chemistry
>
>
>  
>

part of this is also the hardware issue of AGP (8x) versus PCI and=20
PCI-express interfaces being used by newer cards on newer boards... so=20
the much higher bandwith of, e.g., using a Quadro FX1400 with a PCI-E=20
x16 makes it far superior (in my experiences, w/ linux) to the nVidia=20
GeForce 6800 GT... (talking >18k FPS versus ~13-14k FPS in glxgears!).=20
with regards to stereo capabilities, after having used things like the=20
XiG drivers to emulate QBS with cards that don't natively support it=20
(e.g., ATI Radeon 8500), i would definitely opt for the card that=20
provides hardware stereo (so i'd rather use the nVidia Quadro 700 XGL=20
rather than the technically superior (but stereo-less) GeForce 6800+XiG=20
summit drivers (or whatever).=20

cameron


=3D=3D=3D Wang Chern Hoe wrote (on 07/27/2005 08:55 AM): =3D=3D=3D

>Hi Philippe,
>
>If you are using the Windows platform, I suggest you get a Geforce 6800U=
ltra, and use rivatuner from http://downloads.guru3d.com/download.php?det=
=3D163 to modify the driver to Quadro FX 4400 under Windows XP. Thereafte=
r, substitute O with NOC from http://noc.ibp.ac.cn/ and you should have s=
aved several thousand bucks, increased your graphics card performance, an=
d enabled 3D stereo on a Geforce card! The same goes for enabling undocum=
ented features on an ATI card.=20
>
>The only caveat is that this mod has not been ported over to Linux, and =
that your graphic card's warranty will be ineffectual in the event of dam=
age to the GPU chip.
>
>best regards
>Wang Chern Hoe
>
>
>-----Original Message-----
>From:	own...@dl... on behalf of Philippe BENAS
>Sent:	Wed 7/27/2005 11:13 PM
>To:	ccp4bb; pymolbb; Obb
>Cc:=09
>Subject:	[ccp4bb]: nVidia Quadro FX 1400, FX 3400 and FX 4400 performanc=
es
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
>Hi Xtallographers, Oers and Pymolers,
>
>In late January, Warren wrote: "The Quadro FX 3000 is the fastest card=20
>I've ever seen PyMOL run on". Well since then half a year is gone.
>So, would any of you had a chance to compare the FX 1400, FX 3400 and=20
>FX 4400 performances for stereo under Linux, I mean for the usual=20
>stereo programs we're using like O, Pymol or Turbo ?
>
> From several tests I read it seems there is no serious gap between them=
=20
>at least when compared for various engineering software (Rightmark, 3D=20
>studio Max, AutoCAD, CATIA, Ensight, Maya, Patchwork 3D and=20
>SolidWorks). As for their price there are some huge gaps on the other=20
>hand...
>
>Which of those 3 Quadro would you recommend in terms of=20
>performance/price ratio for molecular graphics ?
>
>In his email, Warren also recommended the NEC-Mitsubishi FP2141SB-BK=20
>22" CRT. What do you Folks think about this monitor if you do use it ?=20
>What do you think about the Iiyama HM204 DT DiamondTron 22" CRT ? Any=20
>other good monitor for stereo around that you would recommended ?
>
>Any help will be greatly appreciated.
>Philippe
>
>------------------------------------------------------------------------=

>Philippe BENAS, Ph.D.
>X-ray diffraction facility manager
>Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
>Faculte de Pharmacie - Universite Paris 5
>4, Avenue de l'Observatoire - Case 48
>F-75270 Paris cedex 06
>---
>Office: +33.(0)1-5373-9831 (use ext. 9977 instead to leave a voice mail)=

>Fax: +33.(0)1-5373-9925
>X-ray Room (rotating anode): +33.(0)1-5373-9977
>X-ray Room (small molecules): +33.(0)1-5373-9679
>---
>Url: http://lcrbw.pharmacie.univ-paris5.fr/
>------------------------------------------------------------------------=

>
>
>
>
>
>
>DISCLAIMER:
>This email is confidential and may be privileged. If you are not the int=
ended recipient, please delete it and notify us immediately. Please do no=
t copy or use it for any purpose, or disclose its contents to any other p=
erson as it may be an offence under the Official Secrets Act. Thank you.
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>from IBM. Find simple to follow Roadmaps, straightforward articles,
>informative Webcasts and more! Get everything you need to get up to
>speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> =20
>

--=20
Cameron Mura
UCSD

Marc,

If the pair of images at the bottom of 
"http://mccammon.ucsd.edu/~cmura/PyMOL/Sandbox/#variableloops" is what 
you'd like to do, then modify the "cartoon_loop_radius"... The default 
for this setting is 0.2, so typing "set cartoon_loop_radius, 0.4" should 
achieve the desired effect by doubling it (in order to successfully 
apply this setting to just a particular subset of atoms, you'd need to 
create a new object out of that selection of atoms -- see the "create" 
command in the manual). The sample PyMOL macro and PDB file that 
produced that pair of images are also on the website.

Good luck,
Cameron


=== Marc Vogt wrote (on 07/27/2005 01:16 PM): ===

>Hello all
>
>I want to increase loop/coil thickness while preserving the standard
>cartoon for alpha and beta regions.  I like the thickness that is a result
>of "cartoon tube, all", but it removes the regular cartoon depictions in
>the helical and beta regions.  Any ideas?
>
>thanks,
>
>Marc
>
>
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO September
>19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
>Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
>Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>  
>

-- 
Cameron Mura
UCSD

Hi,

I want to set some transparency in a selection, which is displayed as 
sticks. I'm using the following command:

cmd.set("stick_transparency",0.5,"ret") # where ret is the selection

But when I run the script, ALL the sticks are modified, and not only the 
selection "ret", as I was expecting.

I've been trying a few variations in the syntax, but I can't figure out 
the correct way... any help?

Thanks in advance,

Xavier

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

Hello all

I want to increase loop/coil thickness while preserving the standard
cartoon for alpha and beta regions.  I like the thickness that is a result
of "cartoon tube, all", but it removes the regular cartoon depictions in
the helical and beta regions.  Any ideas?

thanks,

Marc

PyMOL Users -- a New Product FYI:

For those in the market for a 3D stereo projecter, InFocus now makes a
portable active-stereo 3D projector called the DepthQ that works with
shutter-glasses and sells for just $3,995 USD.

http://depthq.com/index.html

We got a chance to try PyMOL on this device this last week and were
rather impressed.  The stereo image quality is great and it exhibits
noticably less ghosting than a CRT. =20

Though the native resolution is only 800x600, 1024x768 compression is
supported and graphics look just fine at that resolution.  Though text
at 1024x768 is not as crisp as one might like, it is still legible. =20

In my view, this projecter would be ideal for full-screen molecular
graphics presentations to small audiences in typical conference room
settings.  Since you may already have plenty of shutter-glasses for your
3D workstations, the DepthQ could be a zero-hassle, low-cost alternative
to a passive-stereo "geowall" setup for your project-group meetings.

Cheers,
Warren

PS. Special thanks to Lightspeed Design for loaning us a projector for
evaluation!  Please contact them directly regarding purchase or
evaluation ( mailto:sa...@de... ).

--
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

Hi Xtallographers, Oers and Pymolers,

In late January, Warren wrote: "The Quadro FX 3000 is the fastest card 
I've ever seen PyMOL run on". Well since then half a year is gone.
So, would any of you had a chance to compare the FX 1400, FX 3400 and 
FX 4400 performances for stereo under Linux, I mean for the usual 
stereo programs we're using like O, Pymol or Turbo ?

 From several tests I read it seems there is no serious gap between them 
at least when compared for various engineering software (Rightmark, 3D 
studio Max, AutoCAD, CATIA, Ensight, Maya, Patchwork 3D and 
SolidWorks). As for their price there are some huge gaps on the other 
hand...

Which of those 3 Quadro would you recommend in terms of 
performance/price ratio for molecular graphics ?

In his email, Warren also recommended the NEC-Mitsubishi FP2141SB-BK 
22" CRT. What do you Folks think about this monitor if you do use it ? 
What do you think about the Iiyama HM204 DT DiamondTron 22" CRT ? Any 
other good monitor for stereo around that you would recommended ?

Any help will be greatly appreciated.
Philippe

------------------------------------------------------------------------
Philippe BENAS, Ph.D.
X-ray diffraction facility manager
Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculte de Pharmacie - Universite Paris 5
4, Avenue de l'Observatoire - Case 48
F-75270 Paris cedex 06
---
Office: +33.(0)1-5373-9831 (use ext. 9977 instead to leave a voice mail)
Fax: +33.(0)1-5373-9925
X-ray Room (rotating anode): +33.(0)1-5373-9977
X-ray Room (small molecules): +33.(0)1-5373-9679
---
Url: http://lcrbw.pharmacie.univ-paris5.fr/
------------------------------------------------------------------------

I have been using a Tripp-Lite 2 port KVM switch now for about 3 years
with a whole different combination of platforms and have yet to run into
a problem.

Len


On Wed, 2005-07-27 at 08:48, D. Joe Anderson wrote:
> On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote:
> 
> > there may be many O and PyMOL users who use stereo with a monitor 
> > connected through a KVM switch? 
> 
> > >3) would be nice if the KVM, linux boxes, and USB mouse were all 
> > >interoperable.  Reason i point this out is that the logitech USB mouse 
> > >i had been using w/ the FC4 box freaked-out (at least on the FC4 box) 
> > >after being plugged-in (via USB<-->PS/2 adapter) to the PS/2 connector 
> > >of a Belkin KVM switch (the popular OmniView SOHO F1DS104T model)...
> 
> I've found that when switching amongst Linux boxes with a
> two-port Belkin OmniView PS/2-VGA KVM that I have to switch out
> of X Windows and into a virtual terminal and then back to X
> Windows before the pointer and mouse will work well again
> together.  So, in terms of specific keystrokes, that is for
> example Ctrl-Alt-F1 to switch from X to virtual terminal 1, and
> then Alt-F7 to switch back to X (though of course X is at Alt-F5
> on various live CDs like KNOPPIX).
> 
> I'm in the process now of deploying KVMs more widely for general
> use, using a mix of connectors, including USB-VGA KVMs with
> Dell-Dell combinations and Dell-Mac combinations with and
> without USB-to-PS/2 and PS/2-to-USB adapters , and in one case,
> using a (rather pricey, but seems to work OK) DVI-USB KVM to
> switch between a G4 and a G5 PowerMac.  
> 
> I have not run any quad-buffered stereo through any of the KVMs,
> yet, but hope to get the chance to do that (even if just in full
> screen mode, or in Linux if/when the drivers catch up) on the G5
> PowerMacs we're deploying now.  I'd also appreciate reading
> about experience with this that anyone has had.
-- 
Leonard M. Thomas Ph.D. 		Howard Hughes Medical Institute	
X-ray Laboratory Manager		California Institute of Technology 
tho...@ca...			Division of Biology, 114-96
626-395-2453				Pasadena, CA 91125
http://www.br.caltech.edu/cmclab

Yes. You can do this with pymol easily.First open both
PDB files in PYMOL. Now go to mounse menu option and
click on 3 Button editing mode. Next step double click
on any atom of the PDB file which you want to rotate
or translate wrt first. Press shift and use left mouse
button  to rotate or press shift and use middle mouse
button to translate(for three button mouse). 
best, surendra

> 
> --__--__--
> 
> Message: 2
> Date: Tue, 26 Jul 2005 08:32:23 -0700
> From: "S. Frank Yan" <SY...@gn...>
> To: <pym...@li...>
> Subject: [PyMOL] Manually move one molecule relative
> to another
> 
> Hi all,
> 
> I was wondering if there's a way to manually move a
> molecule relative to
> other molecules (such as in the case of manual
> docking) using the mouse.
> I searched the previous posts and found that
> MovF/RotF are the way to do
> that.  But, when using these mouse functions to move
> the molecule, one
> atom of the molecule moves erratically and the
> molecule is then
> distorted.  It appears to be a bug.
> 
> Thanks a lot,
> Frank
> 
>

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

On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote:

> there may be many O and PyMOL users who use stereo with a monitor 
> connected through a KVM switch? 

> >3) would be nice if the KVM, linux boxes, and USB mouse were all 
> >interoperable.  Reason i point this out is that the logitech USB mouse 
> >i had been using w/ the FC4 box freaked-out (at least on the FC4 box) 
> >after being plugged-in (via USB<-->PS/2 adapter) to the PS/2 connector 
> >of a Belkin KVM switch (the popular OmniView SOHO F1DS104T model)...

I've found that when switching amongst Linux boxes with a
two-port Belkin OmniView PS/2-VGA KVM that I have to switch out
of X Windows and into a virtual terminal and then back to X
Windows before the pointer and mouse will work well again
together.  So, in terms of specific keystrokes, that is for
example Ctrl-Alt-F1 to switch from X to virtual terminal 1, and
then Alt-F7 to switch back to X (though of course X is at Alt-F5
on various live CDs like KNOPPIX).

I'm in the process now of deploying KVMs more widely for general
use, using a mix of connectors, including USB-VGA KVMs with
Dell-Dell combinations and Dell-Mac combinations with and
without USB-to-PS/2 and PS/2-to-USB adapters , and in one case,
using a (rather pricey, but seems to work OK) DVI-USB KVM to
switch between a G4 and a G5 PowerMac.  

I have not run any quad-buffered stereo through any of the KVMs,
yet, but hope to get the chance to do that (even if just in full
screen mode, or in Linux if/when the drivers catch up) on the G5
PowerMacs we're deploying now.  I'd also appreciate reading
about experience with this that anyone has had.

-- 
D. Joe Anderson, Asst. Sci.    2252 Molecular Biology Bldg   
  Biochem, Biophys, & Mol Bio  Iowa State Univ, Ames, IA 50010
How to help someone use a computer
       http://polaris.gseis.ucla.edu/pagre/how-to-help.html

Hi Philippe,

If you are using the Windows platform, I suggest you get a Geforce =
6800Ultra, and use rivatuner from =
http://downloads.guru3d.com/download.php?det=3D163 to modify the driver =
to Quadro FX 4400 under Windows XP. Thereafter, substitute O with NOC =
from http://noc.ibp.ac.cn/ and you should have saved several thousand =
bucks, increased your graphics card performance, and enabled 3D stereo =
on a Geforce card! The same goes for enabling undocumented features on =
an ATI card.=20

The only caveat is that this mod has not been ported over to Linux, and =
that your graphic card's warranty will be ineffectual in the event of =
damage to the GPU chip.

best regards
Wang Chern Hoe


-----Original Message-----
From:	own...@dl... on behalf of Philippe BENAS
Sent:	Wed 7/27/2005 11:13 PM
To:	ccp4bb; pymolbb; Obb
Cc:=09
Subject:	[ccp4bb]: nVidia Quadro FX 1400, FX 3400 and FX 4400 =
performances
***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Hi Xtallographers, Oers and Pymolers,

In late January, Warren wrote: "The Quadro FX 3000 is the fastest card=20
I've ever seen PyMOL run on". Well since then half a year is gone.
So, would any of you had a chance to compare the FX 1400, FX 3400 and=20
FX 4400 performances for stereo under Linux, I mean for the usual=20
stereo programs we're using like O, Pymol or Turbo ?

 From several tests I read it seems there is no serious gap between them =

at least when compared for various engineering software (Rightmark, 3D=20
studio Max, AutoCAD, CATIA, Ensight, Maya, Patchwork 3D and=20
SolidWorks). As for their price there are some huge gaps on the other=20
hand...

Which of those 3 Quadro would you recommend in terms of=20
performance/price ratio for molecular graphics ?

In his email, Warren also recommended the NEC-Mitsubishi FP2141SB-BK=20
22" CRT. What do you Folks think about this monitor if you do use it ?=20
What do you think about the Iiyama HM204 DT DiamondTron 22" CRT ? Any=20
other good monitor for stereo around that you would recommended ?

Any help will be greatly appreciated.
Philippe

------------------------------------------------------------------------
Philippe BENAS, Ph.D.
X-ray diffraction facility manager
Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculte de Pharmacie - Universite Paris 5
4, Avenue de l'Observatoire - Case 48
F-75270 Paris cedex 06
---
Office: +33.(0)1-5373-9831 (use ext. 9977 instead to leave a voice mail)
Fax: +33.(0)1-5373-9925
X-ray Room (rotating anode): +33.(0)1-5373-9977
X-ray Room (small molecules): +33.(0)1-5373-9679
---
Url: http://lcrbw.pharmacie.univ-paris5.fr/
------------------------------------------------------------------------






DISCLAIMER:
This email is confidential and may be privileged. If you are not the =
intended recipient, please delete it and notify us immediately. Please =
do not copy or use it for any purpose, or disclose its contents to any =
other person as it may be an offence under the Official Secrets Act. =
Thank you.

S. Frank Yan wrote:
> Hi all,
> 
> I was wondering if there's a way to manually move a molecule relative to
> other molecules (such as in the case of manual docking) using the mouse.
> I searched the previous posts and found that MovF/RotF are the way to do
> that.  But, when using these mouse functions to move the molecule, one
> atom of the molecule moves erratically and the molecule is then
> distorted.  It appears to be a bug.

No.

Set the mouse in editing mode. Hold the shift key and put the mouse on 
any atom of the ligand. (While holding the shift key) Press the right 
key and move for rotation and Press the middle key and move for 
translation. Works like a charm. I do all manual dockings on pymol 
because bond rotation etc is so easy! And the best part is if you move 
the ligand into a bad conformation, just hit Ctrl-Z to regain the last 
conformation.

Make sure that the ligand is a separate object from the protein.

Hope this helps.

-- 
:-)
Ramesh K. Sistla

May the wicked become good, may the good attain peace
May the peaceful be freed from bonds, may the freed set others free
                                 -- Rig Veda

hi Doug & others who deal with bundles,

> Many thanks for the suggestion.  I worked something up using CNS/ 
> python scripts -- but if anyone comes up with an all PyMOL  
> alternative, please share with the list!
> Doug

i've written a quick-n-dirty python module to have pymol deal w/ 
multiple conformers of the same protein (NMR bundles, MD ensembles, etc) 
by calculating the average structure and two types of residue-specific 
RMSDs -- (i) RMSDs w/ respect to the average structure and (ii) a 
pairwise RMSD that's averaged over all unique pairs (it's my 
understanding that the first measure (which is <= the second measure for 
a given residue) is more frequently used in the NMR world?).  You can 
find the "average3d.py" module (and samples of its usage) on my pymol 
page by scrolling down to the "Averaging Structures!" row of the table 
in the "PyMOL Examples" section (http://mccammon.ucsd.edu/~cmura/PyMOL ; 
i should put it on pymolwiki soon).

> details), load that into pymol, and voila.  If the effect isn't  enough,
> you could always multiply your RMS values by some value (eg. 10).   Good
> luck!
> JP Cartailler 

This type of pre-processing of B-factors shouldn't be necessary -- you 
should be able to get the desired effect by tweaking putty cartoon 
settings (particularly 'cartoon_putty_scale_power').  you can see the 
relevant settings (and their default vals) via Zaq Panepucci's nifty 
grepset:

> PyMOL>import grepset
> PyMOL>grepset putty
> cartoon_putty_quality          11.00000
> cartoon_putty_radius           0.40000
> cartoon_putty_range            2.00000
> cartoon_putty_scale_max        4.00000
> cartoon_putty_scale_min        0.60000
> cartoon_putty_scale_power      1.50000


good luck,
cameron


=== pym...@li... wrote (on 07/21/2005 08:13 
PM): ===

> Subject:
> Re: [PyMOL] putty/sausage NMR figure
> From:
> Douglas Kojetin <djk...@un...>
> Date:
> Thu, 21 Jul 2005 10:49:21 -0400
> To:
> pymol <pym...@li...>
>
> To:
> pymol <pym...@li...>
> CC:
> "Cartailler, Jean-Philippe" <jp....@Va...>
>
>
> Many thanks for the suggestion.  I worked something up using CNS/ 
> python scripts -- but if anyone comes up with an all PyMOL  
> alternative, please share with the list!
>
> Doug
>
> On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote:
>
>
>
>>
>> One way to do this would be to calculate RMSD between your models  
>> (using
>> whatever package) and replace the B-factor column with those values
>> (make sure you respect the PDB format (B-factors are in columns 61  - 
>> 66,
>> with first column as "1" - see
>> http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for
>> details), load that into pymol, and voila.  If the effect isn't  enough,
>> you could always multiply your RMS values by some value (eg. 10).   Good
>> luck!
>>
>> JP Cartailler
>>
>>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of Douglas
>> Kojetin
>> Sent: Tuesday, July 19, 2005 3:48 PM
>> To: pymol
>> Subject: [PyMOL] putty/sausage NMR figure
>>
>> Hello All-
>>
>>  From what I've read, the 'cartoon putty' command uses the PDB B-  
>> factor
>> value to determine the appearance of the sausage diagram.  How can  I 
>> use
>> the 'cartoon putty' command with NMR structures in a way that  
>> represents
>> the structure ensemble, similar to that as the MOLMOL sausage diagram?
>>
>> Thanks,
>> Doug
>

-- 
Cameron Mura
UCSD

Hi all,

I was wondering if there's a way to manually move a molecule relative to
other molecules (such as in the case of manual docking) using the mouse.
I searched the previous posts and found that MovF/RotF are the way to do
that.  But, when using these mouse functions to move the molecule, one
atom of the molecule moves erratically and the molecule is then
distorted.  It appears to be a bug.

Thanks a lot,
Frank

If you just type=20

povray

you'll get all command line options.

Tsjerk

On 7/25/05, andrea spitaleri <and...@gm...> wrote:
> try povray +A0.3 file.pov
>    zero ---------^
>=20
> regards
>=20
>=20
>=20
> Cameron Mura wrote:
>=20
> > hi,
> > Is there anything special I need to do/set to achieve antialiased
> > images via pymol + POV-ray?
> > To be more explicit, i'm using robert campbell's make_pov.py to have
> > pymol dump the scene into a povray input file, and then ray-tracing w/
> > a minimalistic command-line (e.g., "povray +Iwhatever_pov.inp +W640
> > +H480")... all of this is w/ "antialias" set 'on' in pymol..  i'm
> > unfamiliar w/ povray, so any tips or advice would be greatly appreciate=
d.
> > thanks,
> > cameron
> >
> >
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>=20
>=20
>=20
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