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From: Alan W. S. da S. <al...@la...> - 2003-09-30 14:40:39
|
Hi List! I'd like to know if I can use some character with cgo_text and how: '&', '=3D' are some that I didn't get on screen. BTW, where can I find more docs about it? In Python docs? Another question, which variable/parameter would return me the number of=20 frames/states of a trj file (MD)? Many thanks in advance. Cheers, -------------------------- Alan Wilter Sousa da Silva -------------------------- B.Sc. - Dep. F=EDsica - UFPA M.Sc. - Dep. F=EDsica - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE S=E3o Jos=E9 dos Campos (SP), Brasil www.lac.inpe.br/~alan |
|
From: Tina L. <th...@bi...> - 2003-09-29 19:16:33
|
Hello,
I have two questions:
1. I want to superpose object1 and object2 on top of each other, and have
derived a rotation matrix to transform object2 by. How do I apply this matrix
to all its atoms? Either I parse its PDB coordinates, multiply them by the
matrix, and load the object (which can be really slow), or, I specify the
(axis, angle) data via PyMOL's "rotate" command, which needs me to solve for
three angles from the matrix, and it's messy. Is there a better way to specify
a matrix to be multiplied to the atom coordinates?
(I saw set_view. But it rotates the viewing coordinates system (i.e. camera),
which would alter both object1 and object2.)
2. I have a series of commands in a python script to highlight secondary
structures:
cmd.do(" util.ss")
cmd.do(" color red, ss h")
cmd.do(" color yellow, ss s")
cmd.do(" color blue, ss l+''")
I found the "color" commands race ahead of util.ss and some odd color schemes
show up. I tried "cmd.sync(timeout=5.0, poll=2)" with numerous combinations of
timeout and poll after util.ss but it still happened. Now I'm using
time.sleep(1.5), which does block the main thread till util.ss finishes, but
it isn't nice for the program to "freeze" for the 1.5 seconds. My question is:
why does the sync command not work as expected? This race condition doesn't
occur if the commands are put in a PyMOL script or program (I guess there is
only one thread of execution in those cases?).
Thanks,
Tina
|
|
From: Alan W. S. da S. <al...@la...> - 2003-09-29 17:47:19
|
Hi List! I'm trying to make some movie script. I read a bit about in several places. By now I'm almost getting what I want, but I need help, follows my partial script: ----------------------------------- del all load c1/forcedin.pdb,c1 load c2/forcedin.pdb,c2 frame 1 hide all run Pymol/stride_ss.py stride2pymol c1 stride2pymol c2 show cartoon, all color red, c1 color blue, c2 reset zoom all,-10 set orthoscopic=3D1 viewport 640,480 set ray_trace_frames=3D1 set cache_frames=3D0 set antialias=3D1.0 mclear mset 1 x10 -28 28 x10 mpng test ----------------------------------- With it above, I get frame 1 by 10 steps, then do MD (28 frames) and frame= =20 28 stand for 10 steps. I started using the concept of loop (while etc) but I got nothing. mset=20 seems to be the solution, but I want to my molecule to turn around y axes= =20 (180 degree) and I don't know how to do it. =20 Could someone give some tip or even suggest me an improvement in my actual= =20 script? I would like to have a movie following that takes: frame 1 x10, a 180 rotation in 36 frames, MD in many frames, a 180 rotation in 36 frames again, last frame x10. Any help would be very welcome. Cheers, --=20 -------------------------- Alan Wilter Sousa da Silva -------------------------- B.Sc. - Dep. F=EDsica - UFPA M.Sc. - Dep. F=EDsica - PUC/RJ D.Sc. - IBCCF/UFRJ Bolsista Pesquisador LAC-INPE S=E3o Jos=E9 dos Campos (SP), Brasil www.lac.inpe.br/~alan |
|
From: Laurence P. <Lau...@ic...> - 2003-09-29 12:49:25
|
I'm having a problem with the routine described a few months ago for
rotating the direction of the light source when the picture is rotated
for making a stereo pair.
The problem is as follows :
PyMOL>run turn_y_light.py
Traceback (most recent call last):
File "/Applications/PyMOL/Darwin/modules/pymol/parser.py", line 186,
in pars
e
execfile(args[nest][0],pymol_names,pymol_names)
File "<string>", line 1
def turn_y_light(rot):
# assuming "rot" has angle in degrees
rot_rad = math.pi*rot/180.0
(X0,Y0,Z0)=cmd.get_setting_tuple("light")[1]
X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad)
Y1= Y0
Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad)
cmd.set("light",[X1,Y1,Z1])
^
SyntaxError: invalid syntax
Any suggestions as to what I'm doing wrong ?
---------------------------------------------------------------------------
Laurence H. Pearl
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road
London SW3 6JB, UK
Phone +44-207-970 6045 : Secretary +44-207-970 6046
FAX +44-207-970 6051 : E-Mail l....@ic...
---------------------------------------------------------------------------
" Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
---------------------------------------------------------------------------
|
|
From: Laurence P. <Lau...@ic...> - 2003-09-29 12:36:06
|
I'm trying to run the routine described a few months ago for rotating
the light source when rotating a picture to give stereo, and I keep
hitting an error that I do not understand, as follows :.
PyMOL>run turn_y_light.py
Traceback (most recent call last):
File "/Applications/PyMOL/Darwin/modules/pymol/parser.py", line 186,
in pars
e
execfile(args[nest][0],pymol_names,pymol_names)
File "<string>", line 1
def turn_y_light(rot):
# assuming "rot" has angle in degrees
rot_rad = math.pi*rot/180.0
(X0,Y0,Z0)=cmd.get_setting_tuple("light")[1]
X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad)
Y1= Y0
Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad)
cmd.set("light",[X1,Y1,Z1])
^
SyntaxError: invalid syntax
Any suggestions ?
---------------------------------------------------------------------------
Laurence H. Pearl
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road
London SW3 6JB, UK
Phone +44-207-970 6045 : Secretary +44-207-970 6046
FAX +44-207-970 6051 : E-Mail l....@ic...
---------------------------------------------------------------------------
" Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin
---------------------------------------------------------------------------
|
|
From: Bartholomeus K. <bku...@ep...> - 2003-09-27 22:10:45
|
> 1. color by b-factor (Smita Bhatia)
> --__--__--
> Message: 1
> Date: Thu, 25 Sep 2003 18:49:51 -0400 (EDT)
> From: Smita Bhatia <sm...@ma...>
> To: pym...@li...
> Subject: [PyMOL] color by b-factor
> Hello all,
> I have colored and rendered a pdb file in pymol according to the
> b-factor.
> What i would like to do is to also show a vertical/horizontal
> color bar indiacting the b-factor variation. is there a way to do this
> in pymol?
Hello Smita,
I had the same problem a while ago and worked out the following:
1. Create a pdb-file which contains CA positions only, whereas the numbers
correspond to your wanted increments of colors. Be sure that CA's are
separated by a contant value, say 5 Angstroem.
example (30 zones):
=======
ATOM 1 CA LYS C 1 0.000 0.000 0.000 1.00 20.00
C
ATOM 2 CA LYS C 2 5.000 0.000 0.000 1.00 20.00
C
ATOM 3 CA LYS C 3 10.000 0.000 0.000 1.00 20.00
C
ATOM 4 CA LYS C 4 15.000 0.000 0.000 1.00 20.00
C
ATOM 5 CA LYS C 5 20.000 0.000 0.000 1.00 20.00
C
ATOM 6 CA LYS C 6 25.000 0.000 0.000 1.00 20.00
C
ATOM 7 CA LYS C 7 30.000 0.000 0.000 1.00 20.00
C
ATOM 8 CA LYS C 8 35.000 0.000 0.000 1.00 20.00
C
ATOM 9 CA LYS C 9 40.000 0.000 0.000 1.00 20.00
C
ATOM 10 CA LYS C 10 45.000 0.000 0.000 1.00 20.00
C
ATOM 11 CA LYS C 11 50.000 0.000 0.000 1.00 20.00
C
ATOM 12 CA LYS C 12 55.000 0.000 0.000 1.00 20.00
C
ATOM 13 CA LYS C 13 60.000 0.000 0.000 1.00 20.00
C
ATOM 14 CA LYS C 14 65.000 0.000 0.000 1.00 20.00
C
ATOM 15 CA LYS C 15 70.000 0.000 0.000 1.00 20.00
C
ATOM 16 CA LYS C 16 75.000 0.000 0.000 1.00 20.00
C
ATOM 17 CA LYS C 17 80.000 0.000 0.000 1.00 20.00
C
ATOM 18 CA LYS C 18 85.000 0.000 0.000 1.00 20.00
C
ATOM 19 CA LYS C 19 90.000 0.000 0.000 1.00 20.00
C
ATOM 20 CA LYS C 20 95.000 0.000 0.000 1.00 20.00
C
ATOM 21 CA LYS C 21 100.000 0.000 0.000 1.00 20.00
C
ATOM 22 CA LYS C 22 105.000 0.000 0.000 1.00 20.00
C
ATOM 23 CA LYS C 23 110.000 0.000 0.000 1.00 20.00
C
ATOM 24 CA LYS C 24 115.000 0.000 0.000 1.00 20.00
C
ATOM 25 CA LYS C 25 120.000 0.000 0.000 1.00 20.00
C
ATOM 26 CA LYS C 26 125.000 0.000 0.000 1.00 20.00
C
ATOM 27 CA LYS C 27 130.000 0.000 0.000 1.00 20.00
C
ATOM 28 CA LYS C 28 135.000 0.000 0.000 1.00 20.00
C
ATOM 29 CA LYS C 29 140.000 0.000 0.000 1.00 20.00
C
ATOM 30 CA LYS C 30 145.000 0.000 0.000 1.00 20.00
C
ATOM 31 CA LYS C 31 150.000 0.000 0.000 1.00 20.00
C
- - - - - -
2. Load this new pseudobar-pdb file into PyMOL, make bonds between increment
1 and increment 2 [increment 2 and increment 3 and so on...], define/assign
a smooth color for each increment (copy colors definition from automatically
created colors made by b-factor script) and show the b-factor bar as lines:
example:
========
load pseudobar.pdb
create zone1, pseudobar and res 1:2
create zone2, pseudobar and res 2:3
create zone3, pseudobar and res 3:4
create zone4, pseudobar and res 4:5
create zone5, pseudobar and res 5:6
create zone6, pseudobar and res 6:7
create zone7, pseudobar and res 7:8
create zone8, pseudobar and res 8:9
create zone9, pseudobar and res 9:10
create zone10, pseudobar and res 10:11
create zone11, pseudobar and res 11:12
create zone12, pseudobar and res 12:13
create zone13, pseudobar and res 13:14
create zone14, pseudobar and res 14:15
create zone15, pseudobar and res 15:16
create zone16, pseudobar and res 16:17
create zone17, pseudobar and res 17:18
create zone18, pseudobar and res 18:19
create zone19, pseudobar and res 19:20
create zone20, pseudobar and res 20:21
create zone21, pseudobar and res 21:22
create zone22, pseudobar and res 22:23
create zone23, pseudobar and res 23:24
create zone24, pseudobar and res 24:25
create zone25, pseudobar and res 25:26
create zone26, pseudobar and res 26:27
create zone27, pseudobar and res 27:28
create zone28, pseudobar and res 28:29
create zone29, pseudobar and res 29:30
create zone30, pseudobar and res 30:31
hide nonbonded, pseudobar
bond (/zone1//C/1/CA),(/zone1//C/2/CA)
bond (/zone2//C/2/CA),(/zone2//C/3/CA)
bond (/zone3//C/3/CA),(/zone3//C/4/CA)
bond (/zone4//C/4/CA),(/zone4//C/5/CA)
bond (/zone5//C/5/CA),(/zone5//C/6/CA)
bond (/zone6//C/6/CA),(/zone6//C/7/CA)
bond (/zone7//C/7/CA),(/zone7//C/8/CA)
bond (/zone8//C/8/CA),(/zone8//C/9/CA)
bond (/zone9//C/9/CA),(/zone9//C/10/CA)
bond (/zone10//C/10/CA),(/zone10//C/11/CA)
bond (/zone11//C/11/CA),(/zone11//C/12/CA)
bond (/zone12//C/12/CA),(/zone12//C/13/CA)
bond (/zone13//C/13/CA),(/zone13//C/14/CA)
bond (/zone14//C/14/CA),(/zone14//C/15/CA)
bond (/zone15//C/15/CA),(/zone15//C/16/CA)
bond (/zone16//C/16/CA),(/zone16//C/17/CA)
bond (/zone17//C/17/CA),(/zone17//C/18/CA)
bond (/zone18//C/18/CA),(/zone18//C/19/CA)
bond (/zone19//C/19/CA),(/zone19//C/20/CA)
bond (/zone20//C/20/CA),(/zone20//C/21/CA)
bond (/zone21//C/21/CA),(/zone21//C/22/CA)
bond (/zone22//C/22/CA),(/zone22//C/23/CA)
bond (/zone23//C/23/CA),(/zone23//C/24/CA)
bond (/zone24//C/24/CA),(/zone24//C/25/CA)
bond (/zone25//C/25/CA),(/zone25//C/26/CA)
bond (/zone26//C/26/CA),(/zone26//C/27/CA)
bond (/zone27//C/27/CA),(/zone27//C/28/CA)
bond (/zone28//C/28/CA),(/zone28//C/29/CA)
bond (/zone29//C/29/CA),(/zone29//C/30/CA)
bond (/zone30//C/30/CA),(/zone30//C/31/CA)
show lines, pseudobar
set_color farbe1=[ 0.0, 0.0, 1.0 ]
set_color farbe2=[ 0.0, 0.1, 1.0 ]
set_color farbe3=[ 0.0, 0.3, 1.0 ]
set_color farbe4=[ 0.0, 0.4, 1.0 ]
set_color farbe5=[ 0.0, 0.6, 1.0 ]
set_color farbe6=[ 0.0, 0.7, 1.0 ]
set_color farbe7=[ 0.0, 0.8, 1.0 ]
set_color farbe8=[ 0.0, 1.0, 1.0 ]
set_color farbe9=[ 0.0, 1.0, 0.9 ]
set_color farbe10=[ 0.0, 1.0, 0.8 ]
set_color farbe11=[ 0.0, 1.0, 0.6 ]
set_color farbe12=[ 0.0, 1.0, 0.5 ]
set_color farbe13=[ 0.0, 1.0, 0.3 ]
set_color farbe14=[ 0.0, 1.0, 0.2 ]
set_color farbe15=[ 0.0, 1.0, 0.1 ]
set_color farbe16=[ 0.1, 1.0, 0.0 ]
set_color farbe17=[ 0.2, 1.0, 0.0 ]
set_color farbe18=[ 0.3, 1.0, 0.0 ]
set_color farbe19=[ 0.5, 1.0, 0.0 ]
set_color farbe20=[ 0.6, 1.0, 0.0 ]
set_color farbe21=[ 0.8, 1.0, 0.0 ]
set_color farbe22=[ 0.9, 1.0, 0.0 ]
set_color farbe23=[ 1.0, 1.0, 0.0 ]
set_color farbe24=[ 1.0, 0.8, 0.0 ]
set_color farbe25=[ 1.0, 0.7, 0.0 ]
set_color farbe26=[ 1.0, 0.6, 0.0 ]
set_color farbe27=[ 1.0, 0.4, 0.0 ]
set_color farbe28=[ 1.0, 0.3, 0.0 ]
set_color farbe29=[ 1.0, 0.1, 0.0 ]
set_color farbe30=[ 1.0, 0.0, 0.0 ]
color farbe1, zone1
color farbe2, zone2
color farbe3, zone3
color farbe4, zone4
color farbe5, zone5
color farbe6, zone6
color farbe7, zone7
color farbe8, zone8
color farbe9, zone9
color farbe10, zone10
color farbe11, zone11
color farbe12, zone12
color farbe13, zone13
color farbe14, zone14
color farbe15, zone15
color farbe16, zone16
color farbe17, zone17
color farbe18, zone18
color farbe19, zone19
color farbe20, zone20
color farbe21, zone21
color farbe22, zone22
color farbe23, zone23
color farbe24, zone24
color farbe25, zone25
color farbe26, zone26
color farbe27, zone27
color farbe28, zone28
color farbe29, zone29
color farbe30, zone30
set line_radius=2.5
set antialias=on
set direct=0.75
set orthoscopic=1
set spec_power=200
set spec_reflect=1.5
bg_color white
set_view (\
1.000000000, 0.000000000, 0.000000000,\
0.000000000, 1.000000000, 0.000000000,\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 0.000000000, -368.746154785,\
75.000000000, 0.000000000, 0.000000000,\
278.746154785, 484.996124268, 1.000000000 )
- - - - -
I hope this will fullfil your needs, Smita!
Cheers,
Bartholomeus
|
|
From: Jason P. <jp...@nc...> - 2003-09-26 22:52:02
|
Hello PyMOLers, Sorry for asking a GRASP question here, but is there a way to write out an rgb file in GRASP with a specified image resolution, e.g. 3000 x 3000? Also, what is the maximum surface resolution in GRASP? Is it 5000? Thanks, jp |
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From: Warren L. D. <wa...@de...> - 2003-09-26 20:24:50
|
Michael, PyMOL's PDB handling is an attempt to navigate a minefield of incompatible standards which exist in the conventions of various software packages. Amber in particular poses significant challenges, as its PDB files are unusual. Since version 0.90, PyMOL's behavior has changed. Nowadays, your input data: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O Would be returned as: HETATM 1 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 2 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 3 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END ...which does preserve atom names, but not the order. Note that white-space in the atom names is not preserved (an inherent limitation in PyMOL -- significant white-space within identifier is hell on users and parsers). Conventionally, atom names of length 3 or less are placed in the second column, not the first -- so your "LMN " atom may cause trouble. Also note that by some conventions, "2OA2" in a PDB file really means atom "OA22". PyMOL used to work this way (up to 0.90). Nowadays (v0.91+), "2OA2" is treated as "20A2" unless pdb_literal_names is on, in which case the old behavior returns. Note that in PyMOL, the PDB ATOM IDs are treated more as a property of the PDB file than of the atoms themselves since TER records also have unique IDs in that sequence and repeated MODELs sometimes do as well. Furthermore, in your example, they are not unique (a mistake?). However, I am trying to bend PyMOL around to meet your needs a bit better. Towards this end, I've created a new setting "pdb_retain_ids" which preserves the original PDB serial numbers in the output file. In future PyMOL versions, so long as set retain_order, 1 set pdb_retain_ids, 1 set pdb_no_end_record, 1 The following behavior will be obtainable: Assuming input of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 41.05 O You'll get an output of: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 1315 ABCD NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 1316 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O HETATM 1317 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O Which is as close as I think PyMOL is going to get... 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:pymol-users- > ad...@li...] On Behalf Of michael lerner > Sent: Friday, September 26, 2003 8:44 AM > To: pym...@li... > Subject: [PyMOL] why is PyMOL renaming my residues? > > Hi, > > If I load up a PDB file that looks like this: > > HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 > 31.54 O > HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 > 21.05 O > HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 > 11.05 O > HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 > 1.05 O > HETATM 1314 LMN NAP 164 32.554 68.174 20.275 > 41.05 O > > and then save it from PyMOL, the resulting PDB file looks like this: > > HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 > 31.54 O > HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 > 21.05 O > HETATM 3 DABC NAP 164 28.554 64.174 16.275 0.00 > 11.05 O > HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 > 41.05 O > HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 > 1.05 O > END > > You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to > 3OA2 and ABCD has been renamed to DABC. It looks to me like residue > with a four-letter name is getting renamed. > > No .. wait .. it's a little stranger than that .. if I open up the > second file (the one with DABC) and save *it*, I get this: > > HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 > 31.54 O > HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 > 21.05 O > HETATM 3 CDAB NAP 164 28.554 64.174 16.275 0.00 > 11.05 O > HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 > 41.05 O > HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 > 1.05 O > END > > Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 > and stayed there. LMN and XYZ weren't touched. > > Is there a way to supress this behavior? It causes me a bit of trouble > when, e.g., my AMBER parameter files expect residues to have certain > names. > > I'm not sure exactly when PyMOL decides to rename things .. if I > shift-left-click on one of the residues in the first file (either before > or after saving), PyMOL says "You clicked NAP: /test1///164/OA23" (i.e. > it gives me the original name). > > thanks, > > -michael > > -- > michael lerner > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
|
From: michael l. <ml...@um...> - 2003-09-26 17:44:18
|
oops .. two problems with my last message: 1) i said "residue" a few times when i meant "atom" .. it should be obvious from the context of the message. 2) my email program seems to have messed up some of the formatting in the last message .. the original PDB file should look like this (assuming i can format it correctly this time): HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O in case that's still not formatted correctly, each line should begin with HETATM, and the point is that the atoms are named "OA22", "OA23", "ABCD", "XYZ " and " LMN" respectively. also, i noticed that PyMOL is changing the atom ID (OA22 was 1313 in the first file, but 1 in the second). that's not actually causing me any trouble, but i'm curious: is there a way to make PyMOL leave the IDs alone? thanks, -michael michael lerner wrote: > Hi, > > If I load up a PDB file that looks like this: > > HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 > 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 > 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 > 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 > 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP > 164 32.554 68.174 20.275 41.05 O > and then save it from PyMOL, the resulting PDB file looks like this: > > HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 > 31.54 O > HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 > 21.05 O > HETATM 3 DABC NAP 164 28.554 64.174 16.275 0.00 > 11.05 O > HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 > 41.05 O > HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 > 1.05 O > END > > You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed > to 3OA2 and ABCD has been renamed to DABC. It looks to me like > residue with a four-letter name is getting renamed. > No .. wait .. it's a little stranger than that .. if I open up the > second file (the one with DABC) and save *it*, I get this: > > HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 > 31.54 O > HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 > 21.05 O > HETATM 3 CDAB NAP 164 28.554 64.174 16.275 0.00 > 11.05 O > HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 > 41.05 O > HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 > 1.05 O > END > > Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 > and stayed there. LMN and XYZ weren't touched. > > Is there a way to supress this behavior? It causes me a bit of > trouble when, e.g., my AMBER parameter files expect residues to have > certain names. > > I'm not sure exactly when PyMOL decides to rename things .. if I > shift-left-click on one of the residues in the first file (either > before or after saving), PyMOL says "You clicked NAP: > /test1///164/OA23" (i.e. it gives me the original name). > > thanks, > > -michael > > -- > michael lerner > |
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From: michael l. <ml...@um...> - 2003-09-26 17:19:31
|
Hi, If I load up a PDB file that looks like this: HETATM 1313 OA22 NAP 164 28.315 61.969 12.250 31.54 O HETATM 1314 OA23 NAP 164 26.554 62.174 14.275 21.05 O HETATM 1314 ABCD NAP 164 28.554 64.174 16.275 11.05 O HETATM 1314 XYZ NAP 164 30.554 66.174 18.275 1.05 O HETATM 1314 LMN NAP 164 32.554 68.174 20.275 41.05 O and then save it from PyMOL, the resulting PDB file looks like this: HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 3 DABC NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to 3OA2 and ABCD has been renamed to DABC. It looks to me like residue with a four-letter name is getting renamed. No .. wait .. it's a little stranger than that .. if I open up the second file (the one with DABC) and save *it*, I get this: HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00 31.54 O HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00 21.05 O HETATM 3 CDAB NAP 164 28.554 64.174 16.275 0.00 11.05 O HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00 41.05 O HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00 1.05 O END Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2 and stayed there. LMN and XYZ weren't touched. Is there a way to supress this behavior? It causes me a bit of trouble when, e.g., my AMBER parameter files expect residues to have certain names. I'm not sure exactly when PyMOL decides to rename things .. if I shift-left-click on one of the residues in the first file (either before or after saving), PyMOL says "You clicked NAP: /test1///164/OA23" (i.e. it gives me the original name). thanks, -michael -- michael lerner |
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From: Smita B. <sm...@ma...> - 2003-09-25 22:49:56
|
Hello all, I have colored and rendered a pdb file in pymol according to the b-factor. What i would like to do is to also show a vertical/horizontal color bar indiacting the b-factor variation. is there a way to do this in pymol? Thank you, Regards, Smita |
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From: Warren L. D. <wa...@de...> - 2003-09-24 19:48:48
|
Michael, Thanks for your question. flag ignore, atom-selection, set rebuild Will enable you to remove the surface from selected atoms. For example: show surface flag ignore, resn wat or resi 150, set rebuild 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:pymol-users- > ad...@li...] On Behalf Of michael lerner > Sent: Wednesday, September 24, 2003 11:03 AM > To: pym...@li... > Subject: [PyMOL] drawing the surface correctly > > Howdy, > > I have a pdb file that contains a protein, a ligand and two water > molecules. Everything in the protein is normal, and is listed with ATOM > cards. The ligand and waters are listed as HETATMs. When I show the > surface in PyMOL, I see the surface drawn around the protein only. This > is what I want. > > After I do some things to my protein in AMBER, I get a pdb file where > everything is listed as an ATOM (it's a pretty simple pdb file .. ATOM, > ATOM, ATOM, TER, ATOM, ATOM, TER, etc.). When I load this into PyMOL > and show the surface, the surface is drawn around the everything > (ligand, water, and protein), rather than just around the protein. > > If I open up the PDB file by hand and change all of the appropriate ATOM > cards into HETATM cards and then load it up in PyMOL, everything works > well (I see the surface drawn only around the protein). But I'd like to > be able to do this all within PyMOL. My ligand is named NAP, so I type > "alter resn NAP or resn WAT, type='HETATM'" followed by "sort" and > "rebuild" to fix things. Unfortunately, this doesn't work and I still > get the surface drawn around everything. The strange thing is that if I > alter the file, save it and reload it, PyMOL displays the surface > correctly. > > Can I get PyMOL to display the correct surface without saving and > reloading the file? > > If it helps, I'm running PyMOL 0.90 on a Mandrake 8.2 laptop with an > nVidia GeForce2Go graphics card. > > Thanks, > > -michael > > -- > michael lerner > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: michael l. <ml...@um...> - 2003-09-24 19:03:33
|
Howdy, I have a pdb file that contains a protein, a ligand and two water molecules. Everything in the protein is normal, and is listed with ATOM cards. The ligand and waters are listed as HETATMs. When I show the surface in PyMOL, I see the surface drawn around the protein only. This is what I want. After I do some things to my protein in AMBER, I get a pdb file where everything is listed as an ATOM (it's a pretty simple pdb file .. ATOM, ATOM, ATOM, TER, ATOM, ATOM, TER, etc.). When I load this into PyMOL and show the surface, the surface is drawn around the everything (ligand, water, and protein), rather than just around the protein. If I open up the PDB file by hand and change all of the appropriate ATOM cards into HETATM cards and then load it up in PyMOL, everything works well (I see the surface drawn only around the protein). But I'd like to be able to do this all within PyMOL. My ligand is named NAP, so I type "alter resn NAP or resn WAT, type='HETATM'" followed by "sort" and "rebuild" to fix things. Unfortunately, this doesn't work and I still get the surface drawn around everything. The strange thing is that if I alter the file, save it and reload it, PyMOL displays the surface correctly. Can I get PyMOL to display the correct surface without saving and reloading the file? If it helps, I'm running PyMOL 0.90 on a Mandrake 8.2 laptop with an nVidia GeForce2Go graphics card. Thanks, -michael -- michael lerner |
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From: Warren L. D. <wa...@de...> - 2003-09-24 17:26:34
|
Peter, The next version of PyMOL has a get_symmetry function which can be used to obtain the crystal symmetry of an object. As far as wizards go, both the name of the file and the name of the derived class should match. PyMOL expects the first letter of the class (only) to be capitalized, but the filename should be all lowercase. For example: pymol/modules/wizard/mywiz.py containing class Mywiz(Wizard): ... should work. 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:pymol-users- > ad...@li...] On Behalf Of Peter Haebel > Sent: Wednesday, September 24, 2003 5:31 AM > To: pym...@li... > Subject: [PyMOL] access space group and cell dimensions of stored > molecules > > i have started working on a space group class that can display symmetry > operators, etc... and i got stuck trying to obtain the space group > information from pymol molecule objects. > > - how can i get the space group and unit cell dimensions of an object? > > secondly, i am trying to write a wizard to easily access the new > functions. > > - but i dont fully understand how wizards work. if i simply rename the > density wizard it is no longer accessible in pymol, ie. 'wizard newname' > does not bring up the control panel. how can i rename/copy a wizard and > modify it? simply modifying the source code density wizard without > renaming > it seems to work. > > > cheers, > > peter > > > ________________________________________________________________________ __ > ____ > Bestes Testergebnis: Stiftung Warentest Doppelsieg fur WEB.DE FreeMail > und WEB.DE Club. Nur fuer unsere Nutzer! http://f.web.de/?mc=021182 > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Peter H. <pet...@we...> - 2003-09-24 13:31:16
|
i have started working on a space group class that can display symmetry operators, etc... and i got stuck trying to obtain the space group information from pymol molecule objects. - how can i get the space group and unit cell dimensions of an object? secondly, i am trying to write a wizard to easily access the new functions. - but i dont fully understand how wizards work. if i simply rename the density wizard it is no longer accessible in pymol, ie. 'wizard newname' does not bring up the control panel. how can i rename/copy a wizard and modify it? simply modifying the source code density wizard without renaming it seems to work. cheers, peter ______________________________________________________________________________ Bestes Testergebnis: Stiftung Warentest Doppelsieg fur WEB.DE FreeMail und WEB.DE Club. Nur fuer unsere Nutzer! http://f.web.de/?mc=021182 |
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From: Ezequiel P. <za...@SL...> - 2003-09-23 16:25:20
|
Hi Wataru, use the cartoon_smooth_loops setting: set cartoon_smooth_loops, 0 # through C-alpha set cartoon_smooth_loops, 1 # NOT through C-alpha cheers, Zac On Tue, 23 Sep 2003 wk...@jo... wrote: > How can we force cartoons through the alpha-carbon? I apologize if > this question was posted earlier. > > > Wataru Kagawa, Ph. D. > Special Postdoctoral Researcher > Protein Research Group > RIKEN (Physical and Chemical Research Institute) > > W221, West Research Bldg. > 1-7-22 Suehiro-cho, Tsurumi-ku > Yokohama, Japan 230-0045 > > tel. 045-503-9206 > fax. 045-503-9201 > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414 |
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From: <wk...@jo...> - 2003-09-23 13:22:02
|
How can we force cartoons through the alpha-carbon? I apologize if this question was posted earlier. Wataru Kagawa, Ph. D. Special Postdoctoral Researcher Protein Research Group RIKEN (Physical and Chemical Research Institute) W221, West Research Bldg. 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, Japan 230-0045 tel. 045-503-9206 fax. 045-503-9201 |
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From: Warren L. D. <wa...@de...> - 2003-09-22 22:06:31
|
> One quick question... how do I tell PyMOL to draw a cylinder (or bond) > of a given radius between two positions X,Y,Z and X', Y',Z'? (From Python...) from pymol.cgo import * from pymol import cmd obj = [] obj.extend( [ CUSTOM_CYLINDER, 1.0, 2.0, 3.0, # XYZ 1 4.0, 5.0, 6.0, # XYZ 2 2.0, # Radius 1.0, 1.0, 1.0, # RGB Color 1 1.0, 1.0, 1.0, # RGB Color 2 1, 1, # End caps (0=none, 1=flat, 2=round) ] ) cmd.load_cgo(obj,'my_cgo') Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 |
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From: Asam B. <a.b...@bi...> - 2003-09-22 19:54:32
|
>Dear All, > >Help, I don't know what I am doing wrong. I want to load a dimer >into pymol, 3GRS, the standard PDF file from the PDB bank only gives >co-ordinates for a monomer but if I download the PDB file for the >biological unit >http://www.rcsb.org/pdb/cgi/explore.cgi?job=download&pdbId=3GRS&page=0&pid=1521064246710 > >ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/gr/3grs.pdb1.gz > >If I load 3grs.pdb1 into pymol it still only shows a monomer. > >If I edit out "ENDMDL" after the co-ordinates for the first monomer >, pymol will then show a dimer with sidechains or sticks but if I >try to draw a cartoon it messes up and draws the ribbons ect all >wrong. > >I tried to also change all the A's in the second set of co-ordinates >to B's indicating subunit B but still it does not work. > >Is there a program I can use that will fix my pdb files downloaded >from pdb bank into correct format for pymol? > >Also, once I get the dimer loaded properly I want to colour each of >the four domains. How will I do that? > >Mac OS X 10.2.6 / x11 0.3 / pymol-0_90-bin-osx.dmg Well I managed to make it work after editiing out all the ENDMDL comments and making the second subunit with B's and duplicating the comments for Helix and Sheets then replacing A'S with B . Are these errors in the original biological unit file or a bug in pymol? Also still tring to work out how to label eg residues 1-124 red 125-250 blue ect, how do I do this? Asam.... |
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From: Warren L. D. <wa...@de...> - 2003-09-22 19:02:03
|
Meitian, Sorry, this is not possible. 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:pymol-users- > ad...@li...] On Behalf Of M Wang > Sent: Monday, September 22, 2003 9:49 AM > To: pym...@li... > Subject: [PyMOL] two_sided_lighting > > Hello everybody, > > For two_sided_lighting, is there a way to change the relative brightness > of the two lights? > > Thanks, > > Meitian Wang > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: M W. <me...@gp...> - 2003-09-22 17:49:02
|
Hello everybody, For two_sided_lighting, is there a way to change the relative brightness of the two lights? Thanks, Meitian Wang |
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From: Asam B. <a.b...@bi...> - 2003-09-22 16:19:28
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Dear All, Help, I don't know what I am doing wrong. I want to load a dimer into pymol, 3GRS, the standard PDF file from the PDB bank only gives co-ordinates for a monomer but if I download the PDB file for the biological unit http://www.rcsb.org/pdb/cgi/explore.cgi?job=download&pdbId=3GRS&page=0&pid=1521064246710 ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/gr/3grs.pdb1.gz If I load 3grs.pdb1 into pymol it still only shows a monomer. If I edit out "ENDMDL" after the co-ordinates for the first monomer , pymol will then show a dimer with sidechains or sticks but if I try to draw a cartoon it messes up and draws the ribbons ect all wrong. I tried to also change all the A's in the second set of co-ordinates to B's indicating subunit B but still it does not work. Is there a program I can use that will fix my pdb files downloaded from pdb bank into correct format for pymol? Also, once I get the dimer loaded properly I want to colour each of the four domains. How will I do that? Mac OS X 10.2.6 / x11 0.3 / pymol-0_90-bin-osx.dmg |
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From: Robert C. <rl...@po...> - 2003-09-22 13:32:24
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Craig, * Craig Smith <boi...@ma...> [2003-09-22 03:30] wrote: >=20 > I've done a structural alignment of 2 domains using your align command.= =20 > How do I write out the new coordinates? Look at "help save". USAGE save file [,(selection) [,state [,format]] ] This will save the modified coordinates generated by the alignment. So: align protein2 & n. ca, protein1 save protein2_align.pdb, protein2 will save the coordinates for protein2 after it has been aligned with protein1. Cheers, Rob --=20 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 |
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From: Craig S. <boi...@ma...> - 2003-09-22 08:30:38
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Hey Warren, I've done a structural alignment of 2 domains using your align command. How do I write out the new coordinates? Craig |
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From: Warren L. D. <wa...@de...> - 2003-09-19 23:33:53
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Edmund, No, this kind of technical information isn't documented... If I recall correctly, when PyMOL hooks fragments together, it replaces hydrogen with a bond along the existing vectors. In other words, one fragment is translated so as to fit onto another. Peptides are a special case because the phi-psi vectors are fairly well defined. Nevertheless, I wouldn't trust peptide geometries generated by PyMOL until they've passed through some external force-field, such as MMFF or Amber/OPLS. PyMOL is a reasonable builder for defining the covalent scaffold of peptides and arbitrary small molecules, but it knows nothing about forces and energies. 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:pymol-users- > ad...@li...] On Behalf Of Edmund Kump > Sent: Thursday, September 18, 2003 8:59 PM > To: pym...@li... > Subject: RE: [PyMOL] modifying atom coordinates > > Yes, but what happens when, for example, I take a lysine residue, and > connect a glutamine residue? Shouldn't all the atoms have different > coordinates from when they are stand alone, based on the forces from > nearby atoms? Does pymol account for this as residues are added, or is > there a command or wizard which accounts for nearby atomic forces that I > would execute after I build my chain? > > To give some background to what I'm trying to do, the end goal of my > project is to modify the forces involved in protien folding. I'm sorry if > I'm asking questions that are documented, but I haven't seen anything that > answers my question yet. > > Much Thanks, > Edmund > > > On Wed, 17 Sep 2003, Warren L. DeLano wrote: > > > Hi Edmund, > > > > Actually, PyMOL uses a set of stored coordinates for fragments > > and residues. They can be found in $PYMOL_PATH/data/chempy/fragments. > > The files have .pkl extensions, which stands for pickled chempy model. > > These files can be viewed directly in PyMOL, or can be introspected by > > unpickling them in a Python interpreter. > > > > 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:pymol-users- > > > ad...@li...] On Behalf Of Edmund Kump > > > Sent: Wednesday, September 17, 2003 3:49 AM > > > To: pym...@li... > > > Subject: [PyMOL] modifying atom coordinates > > > > > > Greetings, > > > > > > I am interested in modifying how pymol generates the coordinates of > > > atoms in a peptide chain as you add residues to it. I am an > > > undergraduate math student, so my knowledge in this area is in the > > > range of "nothing". I would assume that this would be in the bonding > > > or editor modules, but so far I haven't found what I'm looking for. In > > > what Chempy or Pymol module(s) can I find the code that determines > > > these coordinates? > > > > > > Thanks, > > > Edmund Kump > > > ek...@ma... > > > Applied Mathematics and Statistics > > > SUNY Stony Brook > > > > > > > > > > > > ------------------------------------------------------- > > > This sf.net email is sponsored by:ThinkGeek > > > Welcome to geek heaven. > > > http://thinkgeek.com/sf > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |