pymol-users Mailing List for PyMOL Molecular Graphics System

On Tue, 28 Sep 2004 pym...@li... wrote:

> From: Jacob Corn <jc...@uc...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] reiterating a ccp4 map problem
>
> I have several CCP4 maps that have been calculated over the entire unit
> cell (using ccp4's "extend") that can be read in, but only displayed in
> a rectangle covering ~1/3 of the unit cell. Unfortunately, my molecule
> does not lie within that 1/3. Converting the ccp4 maps to other formats
> (xplor, omap, etc.) does not solve the problem.


Coot reads a map asymmetric unit, or an mtz file, and generates the map
over the required space on the fly using the symmetry operators of the
space group.

Would it be possible for pymol to do something similar, or at least to
permit generation of symmetry related maps?

Andreas

>  ExecutiveAlign: 2889 atoms aligned.
>  ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=3D6.10).
>  ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=3D2.98).

means:

2889 atoms were aligned intially, then after looking at the quality of =
the
alignment, 95 atoms were rejected as outliers and the alignment was run
again with 2794 atoms.  On cycle two, 152 more atoms were rejected and =
the
fit was performed with the remaining 2642 atoms with a final RMS of =
2.98.

align (protein1 and name ca), (protein2 and name ca), object=3Dalignment

will show you visually the atoms used in the final fit.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
400 Oyster Pt. Blvd., Ste 213
South San Francisco, CA 94080
(650)-346-1154  Fax:(650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Andreas F=F6rster
> Sent: Wednesday, September 29, 2004 8:23 AM
> To: pymol
> Subject: [PyMOL] align output
>=20
> Hey Warren, world,
>=20
> I want to make sure that I understand the output from the=20
> align command correctly.  Here is an example:
>=20
>=20
> align (protein1 and name ca), (protein2 and name ca)
>  Match: read scoring matrix.
>  Match: assigning 3194 x 3010 pairwise scores.
>  MatchAlign: aligning residues (3194 vs 3010)...
>  ExecutiveAlign: 2889 atoms aligned.
>  ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=3D6.10).
>  ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=3D2.98).
>=20
>=20
> Does this mean that in the end, 2642 atoms (2889 - 95 - 152)=20
> are aligned?  Or are 2889 atoms aligned?
>=20
>=20
> Thanks
>=20
>=20
> Andreas
>=20
>=20
>=20
> --=20
>                     Andreas F=F6rster
> Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
> Salt Lake City, UT 84132, phone: 001.801.585.3919
> home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
>         http://www.biochem.utah.edu/~andreas
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on=20
> ITManagersJournal Use IT products in your business? Tell us=20
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hey Warren, world,

I want to make sure that I understand the output from the align command
correctly.  Here is an example:


align (protein1 and name ca), (protein2 and name ca)
 Match: read scoring matrix.
 Match: assigning 3194 x 3010 pairwise scores.
 MatchAlign: aligning residues (3194 vs 3010)...
 ExecutiveAlign: 2889 atoms aligned.
 ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=3D6.10).
 ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=3D2.98).


Does this mean that in the end, 2642 atoms (2889 - 95 - 152) are
aligned?  Or are 2889 atoms aligned?


Thanks


Andreas



--=20
                    Andreas F=F6rster
Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
Salt Lake City, UT 84132, phone: 001.801.585.3919
home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
        http://www.biochem.utah.edu/~andreas

Jamie,

# first, just show sticks

hide all
show sticks

# for uniform-radius balls, use the stick_ball settings

set stick_ball, on
set stick_ball_ratio, 2.5
set stick_radius, 0.12

# for variable radius balls, use scaled spheres

show spheres
set sphere_scale, 0.2
set stick_radius, 0.12

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
400 Oyster Pt. Blvd., Ste 213
South San Francisco, CA 94080
(650)-346-1154  Fax:(650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> jw...@cs...
> Sent: Tuesday, September 28, 2004 2:37 PM
> To: pym...@li...
> Subject: [PyMOL] Trouble with rendering in ball and stick
> 
> Hi,
> 
> I am having issues with rendering in pymol, and I'm hoping 
> someone out there can help. I am trying to render an image 
> with everything in ball and stick. The problem is that some 
> of the residues/cofactors are rendering as spheres, while 
> others remain in ball and stick. Despite what I try, they 
> still continue to render as spheres. Any advice?
> 
> Jamie Wallen
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on 
> ITManagersJournal Use IT products in your business? Tell us 
> what you think of them. Give us Your Opinions, Get Free 
> ThinkGeek Gift Certificates! Click to find out more 
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Jacob Corn wrote:

> This question was posted by someone else in January, but no solution was 
> ever described. I'm currently running up against the same problem and 
> would very much like to know if there is a solution, or if I'm stuck in 
> bug-land.
> 
> I have several CCP4 maps that have been calculated over the entire unit 
> cell (using ccp4's "extend") that can be read in, but only displayed in 
> a rectangle covering ~1/3 of the unit cell. Unfortunately, my molecule 
> does not lie within that 1/3. Converting the ccp4 maps to other formats 
> (xplor, omap, etc.) does not solve the problem.
> 
> Is there a way to get pymol to re-center the contouring around my 
> molecule? Trying to use isomesh or the density wizard to carve around 
> selections only results in "Surface generated using 0 lines". Putting up 
> the entire map shows the aforementioned rectangle.
> Why are unit-cell-wide maps only displayed over part of the unit cell?
> 
> Jacob
> 


Hi Jacob -

Here's my jiffy for making a CCP4-format map covering the molecule. 
There are three steps (repeated for the 2Fo-Fc and Fo-Fc maps): using 
fft to calculate the maps in an asymmetric unit, using mapmask to move 
the map to cover the molecule (with a 6 A cushion), and using mapman (an 
Uppsala Software Factory program - thanks Gerard!) to normalize the 
maps.  Skip any step that seems superfluous...



#!/bin/csh -f

set outmtz='mlsg_refmac_cycle4e.mtz'
set crdout='mlsg_refmac_cycle4e.pdb'
set fftspc=1
set maproot1='map_cycle4e_2fofc'
set maproot2='map_cycle4e_fofc'
set reso='20 1.3'
#  Sigmaa style 2mfo-dfc map
#
fft hklin $outmtz mapout $CCP4_SCR/map_2fofcwt.map << eof
title Sigmaa style 2mfo-dfc map calculated with refmac coefficients
labi F1=2FOFCWT PHI=PHWT
resolution $reso
fftspg $fftspc
binmapout
end
eof
#
mapmask \
MAPIN $CCP4_SCR/map_2fofcwt.map MAPOUT $maproot1.dn6 \
   xyzin $crdout << eof
border 6.0
end
eof
#
#   Sigmaa style mfo-dfc map
#
fft hklin $outmtz mapout $CCP4_SCR/map_fofcwt.map <<eof
title Sigmaa style mfo-dfc map calculated with refmac coefficients
labi F1=FOFCWT PHI=PHDELWT
resolution $reso
fftspg $fftspc
binmapout
end
eof
#
mapmask \
MAPIN $CCP4_SCR/map_fofcwt.map MAPOUT $maproot2.dn6 \
   xyzin $crdout << eof
border 6.0
end
eof
#
6d_mapman << eof
read m1 $maproot1.dn6 ccp4
norm m1
write m1 $maproot1.ccp4 ccp4
read m2 $maproot2.dn6 ccp4
norm m2
write m2 $maproot2.ccp4 ccp4
quit
eof



Hope this helps!

- Matt


-- 
Matthew Franklin            Phone:(650)225-4596
Postdoctoral Researcher       Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080

Hi,

I am having issues with rendering in pymol, and I'm hoping someone out
there can help. I am trying to render an image with everything in ball and
stick. The problem is that some of the residues/cofactors are rendering as
spheres, while others remain in ball and stick. Despite what I try, they
still continue to render as spheres. Any advice?

Jamie Wallen

Oops. I actually used mapmask to extend the map over the unit cell. 
Apologies.

Jacob Corn wrote:
> This question was posted by someone else in January, but no solution was 
> ever described. I'm currently running up against the same problem and 
> would very much like to know if there is a solution, or if I'm stuck in 
> bug-land.
> 
> I have several CCP4 maps that have been calculated over the entire unit 
> cell (using ccp4's "extend") that can be read in, but only displayed in 
> a rectangle covering ~1/3 of the unit cell. Unfortunately, my molecule 
> does not lie within that 1/3. Converting the ccp4 maps to other formats 
> (xplor, omap, etc.) does not solve the problem.
> 
> Is there a way to get pymol to re-center the contouring around my 
> molecule? Trying to use isomesh or the density wizard to carve around 
> selections only results in "Surface generated using 0 lines". Putting up 
> the entire map shows the aforementioned rectangle.
> Why are unit-cell-wide maps only displayed over part of the unit cell?
> 
> Jacob
> 

-- 
Jacob Corn
UC Berkeley - Berger Lab
Lab: 510-643-8893
Fax: 510-643-9290
jc...@uc...

This question was posted by someone else in January, but no solution was 
ever described. I'm currently running up against the same problem and 
would very much like to know if there is a solution, or if I'm stuck in 
bug-land.

I have several CCP4 maps that have been calculated over the entire unit 
cell (using ccp4's "extend") that can be read in, but only displayed in 
a rectangle covering ~1/3 of the unit cell. Unfortunately, my molecule 
does not lie within that 1/3. Converting the ccp4 maps to other formats 
(xplor, omap, etc.) does not solve the problem.

Is there a way to get pymol to re-center the contouring around my 
molecule? Trying to use isomesh or the density wizard to carve around 
selections only results in "Surface generated using 0 lines". Putting up 
the entire map shows the aforementioned rectangle.
Why are unit-cell-wide maps only displayed over part of the unit cell?

Jacob

-- 
Jacob Corn
UC Berkeley - Berger Lab
Lab: 510-643-8893
Fax: 510-643-9290
jc...@uc...

Tassos,

> 1. How do I make a cartoon passing through Ca's ? It refuses 
> to do that with default values like for a 'full' PDB file !

set cartoon_flat_sheets, off
set cartoon_smooth_loops, off

Also, the following command will reduce cartoon "jitter" during animations

set cartoon_refine_normals, off

> 2. I want to include another single molecule and have frames 
> where the second molecules 'stays the same'

This is actually the default behavior if you load a second PDB file that
contains only one state.  If it has multiple states, then you'll need to
specifically set a state for that object.  For example:

load animation1.pdb
load animation2.pdb
set state, 1, animation2
mplay

would freeze animation2 at state 1, while playing through animation 2

To change the default freezing behavior for single-state object, set
static_singletons, off

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Anastassis Perrakis (NKI)
> Sent: Monday, September 27, 2004 2:05 AM
> To: pym...@li...
> Cc: wa...@de...
> Subject: [PyMOL] Ca-only and multi-mol PDB
> 
> Dear Warren et al,
> 
> A couple of questions about PyMol:
> 
> When I open a multi-molecule PDB file, it nicely stores every 
> 'instance' of the PDB in a frame.
> This file is coming from the 'Dynamite' server of Martin 
> Noble and has only Ca's.
> 
> I have two problems:
> 1. How do I make a cartoon passing through Ca's ? It refuses 
> to do that with default values like for a 'full' PDB file !
> 2. I want to include another single molecule and have frames 
> where the second molecules 'stays the same'
> while the first one changes in each frame. Is that easy to do 
> ? Anyone has a script ?
> 
> Thanks in advance,
> 
> Tassos
> 
> 
> 
> -------------------------------------------------------
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> _______________________________________________
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> PyM...@li...
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> 

Dear Warren et al,

A couple of questions about PyMol:

When I open a multi-molecule PDB file, it nicely stores every 
'instance' of the PDB in a frame.
This file is coming from the 'Dynamite' server of Martin Noble and has 
only Ca's.

I have two problems:
1. How do I make a cartoon passing through Ca's ? It refuses to do that 
with default values like for a 'full' PDB file !
2. I want to include another single molecule and have frames where the 
second molecules 'stays the same'
while the first one changes in each frame. Is that easy to do ? Anyone 
has a script ?

Thanks in advance,

Tassos

A new development release of MMTK is available for download. See

	http://dirac.cnrs-orleans.fr/MMTK/download.html

for details. The major new experimental feature is the PyMOL interface=20=

module. If Python scripts using MMTK are run from inside PyMOL, then=20
all visualization routines will automatically use PyMOL. Animations of=20=

all kind are supported.

The PyMOL interface module also permits to obtain molecular data from=20
PyMOL and work on it. This is illustrated by two plugins, which can be=20=

downloaded as well:

- normal_mode_plugin.py
   Computes normal modes using a simplified model for the protein that =
is
   loaded into PyMOL. The normal modes are shown using animations.

- deformation_plugin.py
   Performs a normal-mode based deformation analysis that identifies=20
rigid
   and flexible regions in a protein. The result is shown by=20
colour-coding.

A third plugin, trajectory_plugin.py, loads MMTK trajectories into=20
PyMOL for visualization.

As always, feedback is welcome!
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hi...@ll...
---------------------------------------------------------------------

Steve,

Yes, in fact that's currently the only way it can save them.  Just use the
save command.


You also might think about selections and loops:

cnt=22

for a in range(1,cnt+1): \
   cmd.load("FINALCNS_%d"%a,"MOL%d"%a)

select region,
(102-106,112-116,122-135,137-139,141-145,148-149,156-160,166,171/CA,N,C,O)

for a in range(2,cnt+1): \
   cmd.align("region & MOL%d"%a,"region & MOL1")

for a in range(1,cnt+1): \
   cmd.save("fit%d"%a,"MOL%d"%a)

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> steve Alam
> Sent: Friday, September 24, 2004 8:52 AM
> To: pym...@li...
> Subject: [PyMOL] saving transformed PDB files
> 
> Dear Pymolers,
> 
> I've been using pymol to superimpose NMR ensembles. The Align 
> FXN works great and would look something like:
> 
> 
> load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_1.pdb, 
> MOL1 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_2.pdb, MOL2 
> load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_3.pdb, 
> MOL3 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_4.pdb, MOL4 
> load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_5.pdb, 
> MOL5 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_6.pdb, MOL6 
> load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_7.pdb, 
> MOL7 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_8.pdb, MOL8 
> load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_9.pdb, 
> MOL9 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_10.pdb, 
> MOL10 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_11.pdb, 
> MOL11 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_12.pdb, 
> MOL12 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_13.pdb, 
> MOL13 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_14.pdb, 
> MOL14 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_15.pdb, 
> MOL15 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_16.pdb, 
> MOL16 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_17.pdb, 
> MOL17 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_18.pdb, 
> MOL18 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_19.pdb, 
> MOL19 load 
> /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_20.pdb, MOL20
> 
> 
> align 
> (MOL2///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL3///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL4///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL5///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL6///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL7///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL8///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL9///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL10///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL11///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL12///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL13///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL14///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL15///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL16///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL17///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL18///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL19///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O)
> align 
> (MOL20///102-106,112-116,122-135,137-139,141-145,148-149,156-1
> 60,166,171/CA,N,C,O), 
> (MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156-16
> 0,166,171/CA,N,C,O) 
> 
> 
> 
> My question is how (and IF) can I get pymol to save each file 
> in the newly transformed coordinates. Is this possible?
> 
> THNX in advance!
> 
> Steve
> 
> Steven L. Alam, Assistant Professor
> School of Molecular Biosciences
> Washington State University
> PO BOX 644660
> Pullman, WA 99164-4660
> al...@ws...
> 
> ******office*************
> Rm 539 Fulmer Hall
> Office: (509)335-2765
> Lab: (509)335-2762
> NMR Center: (509)335-3005
> FAX: (509)335-9688
> 
> FEDEX Address********
> Rm 630 Fulmer Hall
> Washington State University
> Pullman, WA 99164-4660
> 
> 

Dear Pymolers,

I've been using pymol to superimpose NMR ensembles.  The Align FXN  
works great and would look something like:


load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_1.pdb, MOL1
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_2.pdb, MOL2
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_3.pdb, MOL3
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_4.pdb, MOL4
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_5.pdb, MOL5
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_6.pdb, MOL6
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_7.pdb, MOL7
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_8.pdb, MOL8
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_9.pdb, MOL9
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_10.pdb, MOL10
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_11.pdb, MOL11
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_12.pdb, MOL12
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_13.pdb, MOL13
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_14.pdb, MOL14
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_15.pdb, MOL15
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_16.pdb, MOL16
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_17.pdb, MOL17
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_18.pdb, MOL18
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_19.pdb, MOL19
load /Users/alam/Documents/nzfcomplex/cnspdbs/FINALCNS_20.pdb, MOL20


align  
(MOL2///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL3///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL4///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL5///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL6///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL7///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL8///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL9///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL10///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL11///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL12///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL13///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL14///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL15///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL16///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL17///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL18///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL19///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)
align  
(MOL20///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O),  
(MOL1///102-106,112-116,122-135,137-139,141-145,148-149,156 
-160,166,171/CA,N,C,O)



My question is how (and IF) can I get pymol to save each file in the  
newly transformed coordinates.  Is this possible?

THNX in advance!

Steve

Steven L. Alam, Assistant Professor
School of Molecular Biosciences
Washington State University
PO BOX 644660
Pullman, WA 99164-4660
al...@ws...

******office*************
Rm 539 Fulmer Hall
Office: (509)335-2765
Lab: (509)335-2762
NMR Center: (509)335-3005
FAX: (509)335-9688

FEDEX Address********
Rm 630 Fulmer Hall
Washington State University
Pullman, WA 99164-4660

Frank,

Yes, PyMOL has molecular editing functions, but it doesn't yet have a
clean-up ability.

To rotate bonds, put the mouse into Editing Node and then
control-right-click-and-drag on the end of the bond you wish to move.  To
delete bonds, control right-click and release on the bond, then type Ctrl-D.
To add a new bond, ctrl-middle-click on the first atom, ctrl-middle-click on
the second, and then type Ctrl-T to add the new bond.  If a bond is
selected, Ctrl-W will cycle through possible valences.

PyMOL does normally connect based on distance if your file does not include
connectivity information.  If atoms are too close together, then you'll get
extra bonds.  We don't yet have a pure pattern-based connectivity mode.
What kind of files are you finding this problem with most often?  Is there
an example you can share?

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> S. Frank Yan
> Sent: Wednesday, September 22, 2004 10:47 AM
> To: pym...@li...
> Subject: [PyMOL] modeling in pymol
> 
> Hi,
> 
> I was wondering if PyMOL has some simple modeling 
> functionalities, such as rotate through a particular bond 
> (change the dihedral angle), delete/form bonds, superimpose, 
> etc., via mouse.  These functions will be particularly useful 
> for molecular modeling besides the wonderful graphics.  
> 
> Also, when I load certain PDB files, PyMOL automatically 
> assign many bonds which are not supposed to be there.  I 
> understand it may base on distance rule for assigning 
> molecular bonds; however, is there any way I can change the 
> behavior of this?
> 
> Thanks,
> Frank
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one 
> of 170 Project Admins to receive an Apple iPod Mini FREE for 
> your judgement on who ports your project to Linux PPC the 
> best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Uwe,

Yes:

   label 23/ca, "This is the CA of residue 23"

Right now, the only way to modify the distance at present is to insert
spaces in the label:

   label 23/ca, "   This is the CA of residue 23"

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Uwe Mueller
> Sent: Wednesday, September 22, 2004 11:29 PM
> To: pym...@li...
> Subject: [PyMOL] Free text labels
>=20
> Dear pymol experts,
> Is there a way to attach a user defined text as a label to a=20
> particular atom ?
> Furthermore, how can I modify the distance between the atom=20
> center and label?
>=20
> Thanks a lot,
> Uwe
>=20
> --
> _______________________________
>=20
>   Dr. Uwe M=FCller
>   Freie Universit=E4t Berlin
>   Proteinstrukturfabrik
>   c/o Bessy GmbH
>   Albert-Einstein-Stra=DFe-15
>   D-12489 Berlin
> =20
>   phone: +49-(0)30-6392 4974
>   fax  : +49-(0)30-6392 4975
>   mailto:um...@be...
>   http://www.psf.bessy.de
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be 
> of 170 Project Admins to receive an Apple iPod Mini FREE for=20
> your judgement on who ports your project to Linux PPC the=20
> best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

> i) Is there any guarantee that atoms are stored internally in 
> the same order that they appear in the PDB file?

set retain_order
sort

However, that's not really necessary:

> ii) If so, is there any way to directly construct a selection 
> containing e.g. atoms 1,3,8,10,11... of a given object?

select my_sel, my_object and id 1+3+8+10+11

> ... and of course any other comments or advice are most welcome!

In addition to "id" there is a new operator "rank" (0.98beta+) which gives
the literal order in the input source.  "id" actually uses the PDB atom
ids...which can be a problem with PDB files that don't have IDs.

Cheers,
Warren

Hey Gil,

One way to do this is to manually color the cartoon representation in
the settings panel. For example if you have a particular residue selected
with its side chain displayed, you can color it whatever color you want,
then change the color of 'cartoons' in the settings panel to another color.
From then on you may change the color of the residue, without affecting the
color of the back bone.

Pete D.
UCLA Chemistry

----- Original Message ----- 
From: "Gil amiati" <gil...@we...>
To: <pym...@li...>
Sent: Thursday, September 23, 2004 7:05 AM
Subject: [PyMOL] Coloring residues without the N-C-C backbone


> Dear all,
>
> I would be happy to know how to color my specific residues while leaving 
> the
> NH-C_alpha-CO backbone with another color that marks the type of secondary
> structure.
> For example:
> If I color a specific residue in blue, I want its base (NH-Calpha-CO) to 
> be
> in another color according to the secondary structure it is found in.
>
>
> Thanks,
>
> Gil Amitai
> Biological Chemistry Dept.
> Weizmann Institute of Science
> Rehovot, 76100
> Israel
> gil...@we...
> 972-8-9344427
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users 

Eric,

PyMOL loads multi-model PDB, SDF, or MOL2 files as movies.  You can use the
VCR conrols/arrow keys to iterate through them.  Alternatively, you can use
the split_states command to create single objects out of each state.

load multimod.mol2
split_states multimod

I'm not sure if 0.97 will get the ligand names right from the MOL2, but the
latest windows beta should:

http://delsci.com/beta

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Peterson, Eric C
> Sent: Thursday, September 23, 2004 6:59 AM
> To: pym...@li...
> Subject: [PyMOL] Opening FlexX multi files
> 
> Pymolers,
> 
>  
> 
> I am using Sybyl/Flexx to do some theoretical docking of a 
> small molecule into an antibody binding site.  FlexX 
> generates a single .mol2 file with all of the docking 
> configurations that were generated, called a multi file.  In 
> Sybyl, all of these configurations appear when the file is 
> opened. However, when I open this file in Pymol only the 
> first configuration appears.  Is there any way for Pymol to 
> read this multi file, or do I have to separate all of the 
> configurations into individual files?  Thanks.
> 
>  
> 
> Eric
> 
>  
> 
> __________________________________
> 
> Eric Peterson, Ph.D
> 
> Department of Pharmacology
> 
> University of Arkansas for Medical Sciences
> 
> 4301 W. Markham Rd. #611
> 
> Little Rock, AR 72205
> 
> Phone: (501) 686-5513
> 
> Fax: (501) 686-5521
> 
>  
> 
> ---------------------------------
> 
> Confidentiality Notice: This e-mail message, including any 
> attachments, is for the sole use of the intended recipient(s) 
> and may contain confidential and privileged information.  Any 
> unauthorized review, use, disclosure or distribution is 
> prohibited.  If you are not the intended recipient, please 
> contact the sender by reply e-mail and destroy all copies of 
> the original message.
> 
> 

Hey Gil,

just make the appropriate selections:

color blue, residue
color anotherColor, (residue & name c,o,n,ca)

or, if you want more flexibility, create a separate object with the
sidechain part of the residue.


Andreas



On Thu, 2004-09-23 at 08:05, Gil amiati wrote:
> Dear all,
>=20
> I would be happy to know how to color my specific residues while leavin=
g the
> NH-C_alpha-CO backbone with another color that marks the type of second=
ary
> structure.
> For example:
> If I color a specific residue in blue, I want its base (NH-Calpha-CO) t=
o be
> in another color according to the secondary structure it is found in.
>=20
>=20
> Thanks,=20
>=20
> Gil Amitai
> Biological Chemistry Dept.
> Weizmann Institute of Science
> Rehovot, 76100
> Israel
> gil...@we...
> 972-8-9344427
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
--=20
                    Andreas F=F6rster
Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg.
Salt Lake City, UT 84132, phone: 001.801.585.3919
home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529
        http://www.biochem.utah.edu/~andreas

Dear all,

I would be happy to know how to color my specific residues while leaving the
NH-C_alpha-CO backbone with another color that marks the type of secondary
structure.
For example:
If I color a specific residue in blue, I want its base (NH-Calpha-CO) to be
in another color according to the secondary structure it is found in.


Thanks, 

Gil Amitai
Biological Chemistry Dept.
Weizmann Institute of Science
Rehovot, 76100
Israel
gil...@we...
972-8-9344427

Pymolers,

=20

I am using Sybyl/Flexx to do some theoretical docking of a small
molecule into an antibody binding site.  FlexX generates a single .mol2
file with all of the docking configurations that were generated, called
a multi file.  In Sybyl, all of these configurations appear when the
file is opened. However, when I open this file in Pymol only the first
configuration appears.  Is there any way for Pymol to read this multi
file, or do I have to separate all of the configurations into individual
files?  Thanks.

=20

Eric

=20

__________________________________

Eric Peterson, Ph.D

Department of Pharmacology

University of Arkansas for Medical Sciences

4301 W. Markham Rd. #611

Little Rock, AR 72205

Phone: (501) 686-5513

Fax: (501) 686-5521

=20


------------------------------------

Confidentiality Notice: This e-mail message, including any attachments, =
is for the sole use of the intended recipient(s) and may contain =
confidential and privileged information.  Any unauthorized review, use, =
disclosure or distribution is prohibited.  If you are not the intended =
recipient, please contact the sender by reply e-mail and destroy all =
copies of the original message.

Dear pymol experts,
Is there a way to attach a user defined text as a label to a particular 
atom ?
Furthermore, how can I modify the distance between the atom center and 
label?

Thanks a lot,
Uwe

-- 
_______________________________

  Dr. Uwe Müller
  Freie Universität Berlin
  Proteinstrukturfabrik 
  c/o Bessy GmbH
  Albert-Einstein-Straße-15
  D-12489 Berlin
 
  phone: +49-(0)30-6392 4974
  fax  : +49-(0)30-6392 4975
  mailto:um...@be...
  http://www.psf.bessy.de

Hello,

I have three protein chains represented as cartoons.  I have one black=20=

chain and two white chains.  I'd like to emphasize the black chain over=20=

the white chains (i.e. have the black chain as an intense black and the=20=

white chains as very faint).  I've played with various settings such as=20=

direct, ray_trace_fog and gamma before ray-tracing, but none seem to do=20=

a good job of increasing the contrast between these two colours.

Does anyone have any suggestions?

Thanks in advance!

~
Peter J Stogios
Ph.D. candidate, Priv=E9 Lab
Dept. of Medical Biophysics, University of Toronto
e: pst...@uh...
w: http://xtal.uhnres.utoronto.ca/prive
p: (416) 946-4501x3280=

Hi,

I was wondering if PyMOL has some simple modeling functionalities, such
as rotate through a particular bond (change the dihedral angle),
delete/form bonds, superimpose, etc., via mouse.  These functions will
be particularly useful for molecular modeling besides the wonderful
graphics. =20

Also, when I load certain PDB files, PyMOL automatically assign many
bonds which are not supposed to be there.  I understand it may base on
distance rule for assigning molecular bonds; however, is there any way I
can change the behavior of this?

Thanks,
Frank

Mary,

You can write a Python loop like the following:

f=open("distance.txt","w")

pairs = ( \
( "45/ca", "47/ca"), \
( "45/ca", "49/ca"), \
( "45/ca", "51/ca"), \
)

for a in pairs:\
  f.write("%-10s %-10s %8.3f\n"%(a[0],a[1],cmd.get_distance(a[0],a[1])))
f.close()

will create a file like:

45/ca      47/ca         6.737
45/ca      49/ca        11.982
45/ca      51/ca        16.304

Note: PyMOL 0.97 or above may be required for the get_distance command (I
think).

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Mary C. Corbett
> Sent: Tuesday, September 21, 2004 10:27 AM
> To: pym...@li...
> Subject: [PyMOL] logging distances in a dist object
> 
> Is there a way to print the distances generated in a "dist" 
> object by the dist command or by a mouse selection into a log 
> file.  I can see them on the screen but I'd like to be able 
> to write them to a separate file.
> 
> Thanks
> Mary
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one 
> of 170 Project Admins to receive an Apple iPod Mini FREE for 
> your judgement on who ports your project to Linux PPC the 
> best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>