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From: <gre...@un...> - 2005-11-02 06:45:27
|
Have you tried to simply use your mouse wheel? This will change the clipping view. |
|
From: Peter A. M. <pa...@co...> - 2005-11-01 17:37:42
|
Hi Marcus, > The surface rendering in PyMOL is quite nice, but I cannot separate the > "branches" of the surface. That is, I would like to view a large cavity > inside of a protein independently from the outer, solvent accessible > surface. Is anyone aware of a means to do this? The easiest way I'm aware of is to select the residues involved on the surface of your cavity, and then do show surface, [selection]. Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
|
From: Marcus C. <ma...@bi...> - 2005-11-01 16:10:16
|
Hello all,
The surface rendering in PyMOL is quite nice, but I cannot separate the
"branches" of the surface. That is, I would like to view a large cavity
inside of a protein independently from the outer, solvent accessible
surface. Is anyone aware of a means to do this?
Marcus Collins
*****************************************************************************
Marcus D. Collins
Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
(h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
"You have opened a new door, and I share this with you,
for I have been where you are now."
*****************************************************************************
|
|
From: Peter A. M. <pa...@co...> - 2005-10-31 23:09:26
|
Should anyone else ever need to try this, there turns out to be a very easy way to do it, assuming that your solvent mask is in ccp4 mask format. 1. use mapmask mskin $MASKFILE mapout $CONVERTED_FILE 2. load $CONVERTED_FILE into pymol, treating it as a normal map. Contouring at 1.0 will display the solvent mask correctly. Of course, it would be better if this had occured to me before spending a few hours in the depths of layer2/ObjectMask.c ; but that's Mondays for you. Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
|
From: Peter A. M. <pa...@co...> - 2005-10-31 15:47:22
|
Hi pymol users, Has anyone had any sucess in loading and displaying solvent masks in pymol? Checking the list archives and wiki didn't result in anything; neither did google. "help mask" within pymol seems to be talking about selection stuff. It seems like the best way would be to modify the ccp4 map loading/normalizing stuff so that it deals with the mask maptype; but if there's an easier way I'd greatly appreciate it if someone could let me know. Thanks, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
|
From: <gre...@un...> - 2005-10-31 08:02:11
|
Hi Jim, I am not aware of such functionality, but I posted some time ago a = script to generate cgo objects to render DNA molecules; maybe you can adapt this script for your needs... Have a look here: http://sourceforge.net/mailarchive/message.php?msg_id=3D12611100 Regards, Greg -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of James = Puckett Sent: lundi, 31. octobre 2005 00:27 To: pym...@li... Subject: [PyMOL] Selection of DNA backbone or base pairs I am trying to color the DNA backbone and DNA base pairs uniquely en =20 masse for several crystal / NMR structures. Is there a simple way to =20 select solely the DNA phosphate backbone or solely the DNA bases or =20 DNA bases + sugars, etc? I know how to select atoms individually, =20 but am wondering if there is either a) a script available for this =20 task or b) a selection logic that would render this task far easier. Thanks, Jim Puckett |
|
From: James P. <pu...@ca...> - 2005-10-30 23:27:29
|
I am trying to color the DNA backbone and DNA base pairs uniquely en masse for several crystal / NMR structures. Is there a simple way to select solely the DNA phosphate backbone or solely the DNA bases or DNA bases + sugars, etc? I know how to select atoms individually, but am wondering if there is either a) a script available for this task or b) a selection logic that would render this task far easier. Thanks, Jim Puckett |
|
From: Tsjerk W. <ts...@gm...> - 2005-10-30 22:39:12
|
Hi Indraneel, For this you want the operator "and"; look at the sections on selection in the manual. select newObj, (resi 2-4) and oldObj2 Cheers, Tsjerk On 10/28/05, Indraneel Majumdar <ind...@sm...> wrote: > > Hi, > > How can I select residues from a particular object? eg. > > select newObj, (resi 2-4) from-object-oldObj2 > > "in" does not work and I could not figure out how to use "byobj" or what > it means. > > TIA, > Indraneel > > -- > http://prodata.swmed.edu > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course > Free Certification Exam for All Training Attendees Through End of 2005 > Visit http://www.jboss.com/services/certification for more information > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 |
|
From: Warren D. <wa...@de...> - 2005-10-30 00:18:44
|
Folks, Everyone wants and needs this functionality (including myself), but it doesn't quite work right (yet). Although some instructions were posted awhile back using the "mview" command, there are bugs in the current releases that prevent this from working the way it should when it actually comes time to render and save the movie. =20 For the time being, you can either use scenes or programmatic movies, but not both together -- at least not reliably. Sorry! 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 > Nat Echols > Sent: Saturday, October 29, 2005 3:59 PM > To: pym...@li... > Subject: [PyMOL] scenes and movies >=20 >=20 > Apologies if this has been asked/answered already. My=20 > rotation student just showed me how PyMOL animates the=20 > transition between scenes, which makes for some beautiful=20 > zooming effects. Is it possible to capture these in a movie? >=20 > thanks, > Nat >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course=20 > Free Certification Exam for All Training Attendees Through=20 > End of 2005 Visit http://www.jboss.com/services/certification=20 > for more information _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
|
From: Nat E. <ec...@uc...> - 2005-10-29 22:52:38
|
Apologies if this has been asked/answered already. My rotation student just showed me how PyMOL animates the transition between scenes, which makes for some beautiful zooming effects. Is it possible to capture these in a movie? thanks, Nat |
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From: Warren D. <wa...@de...> - 2005-10-29 22:33:17
|
Folks, I am going to flip the sense of the mouse camera zoom actions in versions 0.99 and beyond. Going forward, right-click-and-drag will zoom out with upward motion and zoom in with downward motion. Why the switch? (1) It is more intuitive: pulling the mouse toward you move the molecule towards you; pushing the mouse away moves the molecule away. (2) It parallels the scroll-wheel behavior in PyMOL and other programs, where rolling the wheel towards you brings the molecule more near, and rolling the wheel away from you moves the molecule away. (3) It matches the expected behavior when dragging molecules relative to one another in the Z axis. (4) Coot, VIDA2, Chimera, Jmol, CCP4mg, and Dynamol already all follow this convention with their respective mouse zoom actions -- PyMOL was an outlier in this respect and for no good reason. Unfortunately this switch does take a bit of getting use too (especially for me!), but it will help everyone move between programs more easily. =20 To restore the old behavior: set legacy_mouse_zoom 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 |
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From: Indraneel M. <ind...@sm...> - 2005-10-28 19:15:40
|
Hi, How can I select residues from a particular object? eg. select newObj, (resi 2-4) from-object-oldObj2 "in" does not work and I could not figure out how to use "byobj" or what it means. TIA, Indraneel -- http://prodata.swmed.edu |
|
From: Peter A. M. <pa...@co...> - 2005-10-28 18:52:28
|
> hi, > In pymol how to increase the box size of electron density map. By default > it is opening with an square box of some value. I want to increase the > size. How to do that? > Thank you for your help in advance! > sidhu > By default, pymol shows the entire map range. The easiest way to increase this is to increase the range that your map covers (how you do this will depend on which programs you used to calculate your map. There may be a way to use your symmetry operators to expand the map range within pymol, but if so I'm not farmiliar with it. Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
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From: Dmitriy <br...@ma...> - 2005-10-28 05:08:06
|
Hello
I have a question about cmd.quit() behavior.
here goes simplest example:
-----------------------------------------------------
import __main__
__main__.pymol_argv = [ 'pymol', '-qx' ]
import pymol
pymol.finish_launching()
from pymol import cmd
raw_input("type something")
cmd.quit()
print "finfished"
----------------------------------------------------
cmd.quit() kills the whole program, not just PyMol's window.
i.e. "finished" is never printed.
Is it possible somehow to close only PyMol without interrupting the program?
What I want to be able to do in general is to launch PyMol from my program,
plot some data then close PyMol. Then launch PyMol again if I need to plot
some things again, plot, close, and so on. All these things related to PyMol
are separated in a class. Calling cmd.quit() simply ruins the whole program.
Pymol ver. 20beta I think (latest from CVS)
Help is really appreciated
Thanks
Dmitriy
|
|
From: Warren D. <wa...@de...> - 2005-10-27 18:16:52
|
Mirek, In recent versions (http://delsci.com/beta) , you can simply add measurements into a single object as you create them: dist my_measures, 14/ca, 16/ca dist my_measures, 17/ca, 16/ca dist my_measures, 19/ca, 16/ca angle my_measures, 14/n, 14/ca, 14/c dihedral my_measures, 10/n, 10/ca, 10/c, 11/n etc. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Mirek Cygler > Sent: Thursday, October 27, 2005 10:51 AM > To: pym...@li... > Subject: [PyMOL] Distnace objecs >=20 > Hi, > I have created several distance objects with the=20 > measurement wizard. > I would like to manipulate them together. Is there a way to=20 > create a new distance object that combines them all? Tried=20 > the CREATE command but it did not work. >=20 > Mirek >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course=20 > Free Certification Exam for All Training Attendees Through=20 > End of 2005 Visit http://www.jboss.com/services/certification=20 > for more information _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
|
From: Mirek C. <mi...@br...> - 2005-10-26 17:01:38
|
Hi,
I have created several distance objects with the measurement wizard.
I would like to manipulate them together. Is there a way to create a new
distance object that combines them all? Tried the CREATE command but it did
not work.
Mirek
|
|
From: Sebastien M. <seb...@ig...> - 2005-10-26 15:37:20
|
>> I looked into this a little. I think the apbs script (its apbs.py or=20
>> something -- if you can't find it search for it on google) calls a=20
>> function called cmd.ramp_new() with a bunch of arguements. Apparently=
=20
>> this 'ramp' is a built in c-level object. You maybe able to mimic the=
=20
>> code in apbs. What part of the color ramp are you trying to use in=20
>> your app ?
>>
>> ~Dan
>=20
>=20
> Hi Dan,
> I saw this function in "apbs_tools.py":
> ramp_name =3D 'e_lvl'
> map_name =3D self.map.getvalue()
> molecule_name =3D self.molecule.getvalue()
> low =3D float(self.mol_surf_low.getvalue())
> mid =3D float(self.mol_surf_middle.getvalue())
> high =3D float(self.mol_surf_high.getvalue())
> range =3D [low,mid,high]
> print "range is",range
> pymol.cmd.delete(ramp_name)
> pymol.cmd.ramp_new(ramp_name,map_name,range)
> pymol.cmd.set('surface_color',ramp_name,molecule_name)
> pymol.cmd.show('surface',molecule_name)
> pymol.cmd.sort()
>=20
> My range will be always the same, and the ramp_name too.
> But, how to set map_name and molecule_name ?
> With coordinates, or something else ?
I found a way to add a legend box:
load Legend.dx, map #with Legend.dx as an empty file
zoom PDB_ID #to view our structure again
ramp_new legend, map, [1.0,5.0,9.0], color=3D['C1',[1.0,1.0,1.0],'C9']
#legend is the object name for the names panel
#map is the fake map
#[1.0,5.0,9.0] is the legend range with
# [min,medium,max] values
#color C1 is the min color, and C9 the max color
cmd.delete("map") #delete the map object
I hope this will help someone.
>>> Hello,
>>> I try to make a legend box as apbs plugin does with colors it uses (t=
he
>>> box is set at the bottom of the visualization screen).
>>>
>>> Does someone know if a kind of tutorial exists for ?
>>>
>>> Thanks
--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex
|
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From: <sr...@mb...> - 2005-10-26 15:34:09
|
hi, In pymol how to increase the box size of electron density map. By default it is opening with an square box of some value. I want to increase the size. How to do that? Thank you for your help in advance! sidhu |
|
From: Warren D. <wa...@de...> - 2005-10-25 15:06:16
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Dmitriy, This is easily solved: PyMOL expects be imported at the global level as __main__.pymol, but you can spoof it by adding "__main__.pymol =3D pymol" as follows: def funct(): import __main__ __main__.pymol_argv =3D [ 'pymol', '-qx' ] import pymol __main__.pymol =3D pymol pymol.finish_launching() print "finished"=20 if __name__ =3D=3D '__main__': funct() 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 > Dmitriy Igor Bryndin > Sent: Tuesday, October 25, 2005 7:58 AM > To: pym...@li... > Subject: [PyMOL] launching PyMol from a python function >=20 > I'm trying to start PyMol from another python program. > After the 0_99beta17 it is possible to start it from the=20 > __main__ part of a code. But when I start PyMol from a=20 > function 'pymol.finish_launching()' goes in an endless loop.=20 >=20 > Here goes an example: > --------------------------------------------------------------- > def funct(): > import __main__ > __main__.pymol_argv =3D [ 'pymol', '-qx' ] > import pymol > pymol.finish_launching() > print "finished"=20 >=20 > if __name__ =3D=3D '__main__': > funct() > --------------------------------------------------------------- > In this case PyMol window starts, but program never reaches=20 > 'print "finished"'.=20 >=20 > The same time > --------------------------------------------------------------- > if __name__ =3D=3D '__main__': > import __main__ > __main__.pymol_argv =3D [ 'pymol', '-qx' ] > import pymol > pymol.finish_launching() > print "finished" > --------------------------------------------------------------- > works fineand prints "finshed"=20 >=20 > after getting into PyMol's finish_launching() (inside=20 > __init__.py) while not hasattr(__main__,'pymol'): > e.wait(0.01) > Goes in an endless loop. > I've tried print dir(__main__) just before this loop.=20 > When PyMol is=20 > launched not from a function, __main__ indeed have attributes=20 > '__main__' and 'pymol'. Launched from a function, there are=20 > no '__main__' or 'pymol', but 'funct'.=20 >=20 > I'll really appreciate any help or hints how make it possible=20 > to launch PyMol from a function or from a method of some class.=20 >=20 > Dmitriy >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. > Get Certified Today * Register for a JBoss Training Course=20 > Free Certification Exam for All Training Attendees Through=20 > End of 2005 Visit http://www.jboss.com/services/certification=20 > for more information _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
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From: D. J. A. <de...@ia...> - 2005-10-25 14:35:38
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On Mon, Oct 24, 2005 at 10:18:40AM -0500, Kristl Adams wrote: > I have several txt files of coordinates (mostly heme type compounds) > that I'd like to format correctly for pymol to be able to read. I've > tried several things looking at PDBs with hemes, but can't figure it out. > > Will someone with more experience please show me how this should be > formatted for pymol to read properly. You may have some luck doing a conversion using OpenBabel. http://openbabel.sourceforge.net http://packages.debian.org/openbabel For example, I took your file, saved it as TPP-NO.xyz and edited it to add the number of atoms as a first line (79) and then faked the last line by adding four zeros (0 0 0 0), then ran babel TPP-NO.xyz TPP-NO.pdb This generated a file that loaded the atoms into pymol, although the bonds are not depicted. That might be remedied by editing the CONECT records. What is the source of your coordinates? You may be able to save explicitly into a format that babel can convert to pdb without the need to edit it. -- Joe COMPND TPP-NO.xyz AUTHOR GENERATED BY OPEN BABEL 1.100.2 HETATM 1 Xx LIG 0 2.005 0.000 0.000 1.00 0.00 XX HETATM 2 Ca LIG 1 2.847 1.093 0.000 1.00 0.00 CA HETATM 3 Xx LIG 0 4.225 0.677 0.000 1.00 0.00 XX HETATM 4 Xx LIG 0 5.116 1.304 0.000 1.00 0.00 XX HETATM 5 Xx LIG 0 4.225 -0.679 -0.000 1.00 0.00 XX HETATM 6 Xx LIG 0 5.115 -1.307 -0.000 1.00 0.00 XX HETATM 7 Ca LIG 2 2.847 -1.094 -0.000 1.00 0.00 CA HETATM 8 Cm LIG 2 2.473 -2.475 -0.000 1.00 0.00 CM HETATM 9 Xx LIG 0 0.000 2.005 -0.000 1.00 0.00 XX HETATM 10 Ca LIG 3 -1.093 2.847 -0.000 1.00 0.00 CA HETATM 11 Xx LIG 0 -0.677 4.225 -0.000 1.00 0.00 XX HETATM 12 Xx LIG 0 -1.304 5.116 -0.000 1.00 0.00 XX HETATM 13 Xx LIG 0 0.679 4.225 0.000 1.00 0.00 XX HETATM 14 Xx LIG 0 1.307 5.115 0.000 1.00 0.00 XX HETATM 15 Ca LIG 1 1.093 2.848 0.000 1.00 0.00 CA HETATM 16 Cm LIG 1 2.473 2.474 0.000 1.00 0.00 CM HETATM 17 Xx LIG 0 -2.005 0.000 0.000 1.00 0.00 XX HETATM 18 Ca LIG 4 -2.847 -1.093 0.000 1.00 0.00 CA HETATM 19 Xx LIG 0 -4.225 -0.677 0.000 1.00 0.00 XX HETATM 20 Xx LIG 0 -5.116 -1.304 0.000 1.00 0.00 XX HETATM 21 Xx LIG 0 -4.225 0.679 -0.000 1.00 0.00 XX HETATM 22 Xx LIG 0 -5.115 1.307 -0.000 1.00 0.00 XX HETATM 23 Ca LIG 3 -2.847 1.093 -0.000 1.00 0.00 CA HETATM 24 Cm LIG 3 -2.472 2.474 -0.000 1.00 0.00 CM HETATM 25 Xx LIG 0 0.000 -2.005 -0.000 1.00 0.00 XX HETATM 26 Ca LIG 2 1.093 -2.849 -0.000 1.00 0.00 CA HETATM 27 Xx LIG 0 0.675 -4.226 -0.000 1.00 0.00 XX HETATM 28 Xx LIG 0 1.300 -5.119 -0.000 1.00 0.00 XX HETATM 29 Xx LIG 0 -0.681 -4.224 0.000 1.00 0.00 XX HETATM 30 Xx LIG 0 -1.311 -5.114 0.000 1.00 0.00 XX HETATM 31 Ca LIG 4 -1.093 -2.847 0.000 1.00 0.00 CA HETATM 32 Cm LIG 4 -2.473 -2.470 0.000 1.00 0.00 CM HETATM 33 Xx LIG 0 3.540 -3.542 0.000 1.00 0.00 XX HETATM 34 Xx LIG 0 4.028 -4.030 -1.195 1.00 0.00 XX HETATM 35 Xx LIG 0 3.643 -3.644 -2.139 1.00 0.00 XX HETATM 36 Xx LIG 0 5.004 -5.006 -1.195 1.00 0.00 XX HETATM 37 Xx LIG 0 5.389 -5.391 -2.139 1.00 0.00 XX HETATM 38 Xx LIG 0 5.492 -5.494 0.000 1.00 0.00 XX HETATM 39 Xx LIG 0 6.262 -6.264 0.000 1.00 0.00 XX HETATM 40 Xx LIG 0 5.004 -5.006 1.195 1.00 0.00 XX HETATM 41 Xx LIG 0 5.389 -5.391 2.139 1.00 0.00 XX HETATM 42 Xx LIG 0 4.028 -4.030 1.195 1.00 0.00 XX HETATM 43 Xx LIG 0 3.643 -3.644 2.139 1.00 0.00 XX HETATM 44 Xx LIG 0 3.540 3.541 0.000 1.00 0.00 XX HETATM 45 Xx LIG 0 4.028 4.029 -1.195 1.00 0.00 XX HETATM 46 Xx LIG 0 3.643 3.643 -2.139 1.00 0.00 XX HETATM 47 Xx LIG 0 5.004 5.005 -1.195 1.00 0.00 XX HETATM 48 Xx LIG 0 5.389 5.390 -2.139 1.00 0.00 XX HETATM 49 Xx LIG 0 5.492 5.492 0.000 1.00 0.00 XX HETATM 50 Xx LIG 0 6.262 6.263 0.000 1.00 0.00 XX HETATM 51 Xx LIG 0 5.004 5.005 1.195 1.00 0.00 XX HETATM 52 Xx LIG 0 5.389 5.390 2.139 1.00 0.00 XX HETATM 53 Xx LIG 0 4.028 4.029 1.195 1.00 0.00 XX HETATM 54 Xx LIG 0 3.643 3.643 2.139 1.00 0.00 XX HETATM 55 Xx LIG 0 -3.538 3.541 0.000 1.00 0.00 XX HETATM 56 Xx LIG 0 -4.026 4.030 -1.195 1.00 0.00 XX HETATM 57 Xx LIG 0 -3.641 3.644 -2.139 1.00 0.00 XX HETATM 58 Xx LIG 0 -5.001 5.006 -1.195 1.00 0.00 XX HETATM 59 Xx LIG 0 -5.386 5.392 -2.139 1.00 0.00 XX HETATM 60 Xx LIG 0 -5.488 5.494 0.000 1.00 0.00 XX HETATM 61 Xx LIG 0 -6.259 6.266 0.000 1.00 0.00 XX HETATM 62 Xx LIG 0 -5.001 5.006 1.195 1.00 0.00 XX HETATM 63 Xx LIG 0 -5.386 5.392 2.139 1.00 0.00 XX HETATM 64 Xx LIG 0 -4.026 4.030 1.195 1.00 0.00 XX HETATM 65 Xx LIG 0 -3.641 3.644 2.139 1.00 0.00 XX HETATM 66 Xx LIG 0 -3.542 -3.534 0.000 1.00 0.00 XX HETATM 67 Xx LIG 0 -4.032 -4.021 -1.195 1.00 0.00 XX HETATM 68 Xx LIG 0 -3.645 -3.637 -2.139 1.00 0.00 XX HETATM 69 Xx LIG 0 -5.010 -4.994 -1.195 1.00 0.00 XX HETATM 70 Xx LIG 0 -5.396 -5.379 -2.139 1.00 0.00 XX HETATM 71 Xx LIG 0 -5.499 -5.481 0.000 1.00 0.00 XX HETATM 72 Xx LIG 0 -6.271 -6.250 0.000 1.00 0.00 XX HETATM 73 Xx LIG 0 -5.010 -4.994 1.195 1.00 0.00 XX HETATM 74 Xx LIG 0 -5.396 -5.379 2.139 1.00 0.00 XX HETATM 75 Xx LIG 0 -4.032 -4.021 1.195 1.00 0.00 XX HETATM 76 Xx LIG 0 -3.645 -3.637 2.139 1.00 0.00 XX HETATM 77 N LIG 5 0.135 0.114 1.982 1.00 0.00 N HETATM 78 O LIG 5 0.661 0.554 2.899 1.00 0.00 O HETATM 79 Xx LIG 0 0.000 0.000 0.000 1.00 0.00 XX CONECT 1 CONECT 2 16 CONECT 3 CONECT 4 CONECT 5 CONECT 6 CONECT 7 8 CONECT 8 7 26 CONECT 9 CONECT 10 24 CONECT 11 CONECT 12 CONECT 13 CONECT 14 CONECT 15 16 CONECT 16 15 2 CONECT 17 CONECT 18 32 CONECT 19 CONECT 20 CONECT 21 CONECT 22 CONECT 23 24 CONECT 24 10 23 CONECT 25 CONECT 26 8 CONECT 27 CONECT 28 CONECT 29 CONECT 30 CONECT 31 32 CONECT 32 31 18 CONECT 33 CONECT 34 CONECT 35 CONECT 36 CONECT 37 CONECT 38 CONECT 39 CONECT 40 CONECT 41 CONECT 42 CONECT 43 CONECT 44 CONECT 45 CONECT 46 CONECT 47 CONECT 48 CONECT 49 CONECT 50 CONECT 51 CONECT 52 CONECT 53 CONECT 54 CONECT 55 CONECT 56 CONECT 57 CONECT 58 CONECT 59 CONECT 60 CONECT 61 CONECT 62 CONECT 63 CONECT 64 CONECT 65 CONECT 66 CONECT 67 CONECT 68 CONECT 69 CONECT 70 CONECT 71 CONECT 72 CONECT 73 CONECT 74 CONECT 75 CONECT 76 CONECT 77 78 CONECT 78 77 CONECT 79 MASTER 0 0 0 0 0 0 0 0 79 0 79 0 END |
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From: andrea s. <and...@gm...> - 2005-10-25 12:49:47
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Gilleain Torrance wrote: > Hi, > > I don't see how you can get rid of this loop actually. > > The thing that occurs to me is that you are loading structures, but > not deleting them! > > So, at the other end of the "for i in KeepStruc" loop, you should > have a "cmd.delete(i)". > > Other than that, you don't need to be opening the files "out" or > "full" inside the loop, or re-reading the data from "amb". > > Hth. > > gilleain torrance cmd.delete() did the job very well (now it takes few mins...rather than 7 hours..) The other suggestions did improve, but not too much. thanks a lot andrea |
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From: Gilleain T. <gil...@gm...> - 2005-10-25 11:51:33
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Hi,
Using the callbacks on the newest macpymol on tiger doesn't work:
run /Applications/MacPyMOL.app/pymol/examples/devel/gl01.py
Traceback (most recent call last):
File "/Users/delwarl/MacPyMOL/build/MacPyMOL.app/pymol/modules/
pymol/parser.py", line 273, in parse
File "/Users/delwarl/MacPyMOL/build/MacPyMOL.app/pymol/modules/
pymol/parsing.py", line 407, in run_file
File "/Applications/MacPyMOL.app/pymol/examples/devel/gl01.py",
line 1, in ?
from pymol.opengl.gl import *
File "/Applications/MacPyMOL.app/pymol/modules/pymol/opengl/gl/
__init__.py", line 21, in ?
import _opengl
ImportError: No module named _opengl
Not sure why, as there is a:
/System/Library/Frameworks/Python.Framework/Versions/Current/lib/
python2.3/site-packages/pymol/opengl/gl/_opengl.so
in existance.
gilleain torrance
On 14 Oct 2005, at 16:50, Warren DeLano wrote:
> For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
> integrates into a single window and links to the system Python instead
> of bringing its own copy (in part this is necessary preparation for
> Intel...).
>
> http://delsci.com/beta
>
> Please let me know how it works for you!
>
> Cheers,
> Warren
>
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From: Gilleain T. <gil...@gm...> - 2005-10-25 11:04:19
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Hi,
I don't see how you can get rid of this loop actually.
The thing that occurs to me is that you are loading structures, but
not deleting them!
So, at the other end of the "for i in KeepStruc" loop, you should
have a "cmd.delete(i)".
Other than that, you don't need to be opening the files "out" or
"full" inside the loop, or re-reading the data from "amb".
Hth.
gilleain torrance
On 25 Oct 2005, at 10:45, andrea spitaleri wrote:
> Hi again, reading my post I found the bottleneck....shame on me :)
>
> here it is:
> .......
> if (atomlig == "*"):
> ligand = cmd.select("ligand","segi B and "+i)
> atoms_lig = cmd.get_model('ligand')
> for atomsL in atoms_lig.atom:
> t = cmd.select("t","name "+atomsL.name)
> di = cmd.distance("di","t","p")
> .........
> I am running twice the same loop. removing "for atomsL in
> atoms_lig.atom" loop it goes faster. The problem is that now I am
> getting the "di" value as average over all atoms of the ligand. How
> I can get the different values in order to find the minimum
> distance between the ligand and the selected residue ??
>
> Thanks in advance
>
> andrea
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
|
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From: andrea s. <and...@gm...> - 2005-10-25 09:42:16
|
Hi again, reading my post I found the bottleneck....shame on me :)
here it is:
.......
if (atomlig == "*"):
ligand = cmd.select("ligand","segi B and "+i)
atoms_lig = cmd.get_model('ligand')
for atomsL in atoms_lig.atom:
t = cmd.select("t","name "+atomsL.name)
di = cmd.distance("di","t","p")
.........
I am running twice the same loop. removing "for atomsL in
atoms_lig.atom" loop it goes faster. The problem is that now I am
getting the "di" value as average over all atoms of the ligand. How I
can get the different values in order to find the minimum distance
between the ligand and the selected residue ??
Thanks in advance
andrea
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From: andrea s. <and...@gm...> - 2005-10-25 09:17:33
|
Jules Jacobsen wrote:
> Hi Andrea,
>
> It depends on how you've written it.... It does sound more than a
> little slow if you are just selecting a single residue. I had a script
> which ended up looping through several sets of atoms which took ages
> for larger models. I finally got fed-up with this and re-wrote it
> properly. Now it's practically instantaneous. If you post the script
> I'm sure someone will be able to offer you a pointer as to where you
> might be going wrong.
>
> Jules
Hi Jules, here it is:
-------------------------------------------------
from pymol import cmd
import string, sys, os
if ("dist.out"):
os.system("rm -f dist.out")
if ("full.out"):
os.system("rm -f full.out")
nam = open("file.nam",'r')
KeepStruc = []
readnam = nam.readlines()
deep = int(15)
for j in range(0,deep):
readnam[j] = string.strip(readnam[j])
KeepStruc.append(readnam[j])
for i in KeepStruc:
cmd.load(i,i)
print i
cmd.select("lig","segi B")
cmd.select("pro","all and not segi B")
amb = open("amb",'r')
out = open("dist.out","a")
full = open("full.out","a")
out.write("%4s\n"%(i))
full.write("%4s\n"%(i))
count = 0
for lines in amb.readlines():
lines = string.strip(lines)
tmp = string.split(lines,",")
resname = tmp[0]
atomtypes = tmp[1]
tmp1 =string.split(atomtypes,":")
atomlig = tmp1[0]
atompro = tmp1[1]
p = cmd.select("p","resi "+resname+" and name "+atompro+" and "+i)
if (atomlig == "*"):
ligand = cmd.select("ligand","segi B and "+i)
atoms_lig = cmd.get_model('ligand')
for atomsL in atoms_lig.atom:
t = cmd.select("t","name "+atomsL.name)
di = cmd.distance("di","t","p")
full.write("%4s%8s%8s%8.3f%12s\n"%(resname,atompro,atomsL.name,di,"DISTANCE"))
if (di < 4):
count = count + 1
# print resname,atompro,count
if (count == 0):
out.write("%4s%8s%8s%12s\n"%(resname,atompro,"*",">VIOLATED"))
count = 0
else:
l = cmd.select("l","name "+atomlig+" and segi B and "+i)
d = cmd.distance("dist_"+str(i),"p","l")
full.write("%4s%8s%8s%8.3f%12s\n"%(resname,atompro,atomlig,d,"DISTANCE"))
if (d > 5):
out.write("%4s%8s%8s%8.3f%10s\n"%(resname,atompro,atomlig,d,"VIOLATED"))
out.close()
--------------------------------------------------
At the beginning I thought that problem was the memory because when I
run it it starts fast and then aftr 4 structures it goes slowly slowly
per every molecule, but I see my free memory always 50% and the cpu
100%. I tried to empty the list in the script at end of each iteration
but it didn't work.
thanks
andrea
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