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From: tree <jav...@ut...> - 2005-07-06 13:57:43
|
Sebastien, That doesn't sound normal. I have a Dell Latitude w/Radeon Mobility 9000 and I get 30+ FPS for larger proteins. I don't however use, FC4. If you need specs, I can get them for you when I'm near my laptop (later today) -- just let me know. -- Jason On Wed, 2005-07-06 at 06:29 -0700, pym...@li... wrote: > > Message: 1 > Date: Wed, 06 Jul 2005 14:32:46 +1000 > From: Sebastien Gerega <sge...@ma...> > To: "pym...@li..." > <pym...@li...> > Subject: [PyMOL] FPS on FC4 with ATI Mobility Radeio 9700 > > I have Pymol installed on my dual boot Asus M6Ne notebook and have > noticed that the performance is significantly better in windows than > it > is in linux. I am running FC4 and have installed the ati-fglrx > driver. > When rotating a 120 amino acid protein I get maximum 8 frames per > second > and the CPU usage goes up to about 90%. Is this normal? If not, are > there any known issues with ATi Drivers? or with FC4? > any help would be great, > Sebastien -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston jav...@ut... :: http://www.bscb.utmb.edu |
From: Michael G. L. <ml...@um...> - 2005-07-06 13:28:50
|
I asked a similar question a while ago, and Kristan Rother archived the answer at <http://www.rubor.de/bioinf/tips_python.html#insel>. Here it is: Using PyMOL commands: list=[] iterate (name ca),list.append((resi,resn)) print list [('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LEU', '6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', '11'), ('CYS', '12'), ('THR', '13')] or using a Python script (in PyMOL): from pymol import cmd,stored stored.list=[] cmd.iterate("(name ca)","stored.list.append((resi,resn))") print stored.list [('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), ('6', ' LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', 'TRP'), ('12', 'CYS'), ('13', 'THR')] -- www.umich.edu/~mlerner | _ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mlerner@umich On Wed, 6 Jul 2005, Sebastien Gerega wrote: > Is there a way to list the residues that are in a selection? For example if I > use the command "select near, sel01 around 6" how can I obtain a list of the > residues in the "near" selection? > thanks, > Sebastien > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
From: Andrea S. <and...@gm...> - 2005-07-06 09:06:03
|
Hi thanks for your reply. Yes it is the id. I found out also that it takes a lot time because is looping in all atoms and in the "active" site. So I fixed that. Anyway more in general, I saw that the manual is lacking of some information useful for who wants to program. I mean, sometimes it doesn't say if a command returns a tuple or a list or a dictionary. Ex: cmd.index("selection") is a list? thanks Regards, andrea 2005/7/6, Gilleain Torrance <gil...@ho...>: > Hi, >=20 > I suppose that these numbers are the atom_ids. It's probably the same > numbers returned by the cmd.index function. >=20 > I guess you could test this by typing "select atom260, id 260" and see if > that makes a selection with atom260... >=20 > As for the speed question, I have no idea. More of a question for Mr DeLa= no > :) Calculating pairwise like this is always going to be computationally > expensive, but I don't know ways to speed this up. >=20 > gilleain torrance >=20 >=20 > On 5/7/05 15:17, "Andrea Spitaleri" <and...@gm...> wrote: >=20 > >> HBA =3D cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) > > yes thanks for the trick. However, I edited my script to: > > DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd= ")) > > DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD)) > > but I cannot figure out the meaning of the output: > > complex_1 > > donor acceptor hba hbd > > 260 271 2.536 -1.000 > > complex_2 > > donor acceptor hba hbd > > 391 409 2.489 -1.000 > > complex_3 > > donor acceptor hba hbd > > 522 547 2.512 -1.000 > > complex_4 > > donor acceptor hba hbd > > 653 685 2.456 -1.000 > > what the numbers under donor and acceptor are? > > > >> > >> atoms_Don =3D cmd.index('don') > >> > > > > I tried also this option and it works fine (more or less) excet that > > it takes a lot time to calculate all the distance (quite weird on my > > dual-cpu 3Gz intel) > > this is the loop used: > > for donor in atoms_Don: > > for acceptor in atoms_Acc: > > di =3D cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor) > > DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di)) > > > > thanks > > > > Regards > > > > andrea > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclic= k > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Neil R. <n.a...@le...> - 2005-07-06 08:22:47
|
Hi there, Try an iiyama HM204DTA (at least in the UK) which will do >100Hz up to 1600x1200. I have one and at 1280x1024 @ 120Hz it works beautifully for me. Regards, Neil. ************************************* Neil Ranson PhD University Research Fellow, Astbury Centre for Structural Molecular Biology, School of Biochemistry & Microbiology, University of Leeds, Leeds, LS2 9JT. UK. Tel: +44 (0) 113 343 7065 Fax: +44 (0) 113 343 3167 n.a...@le... ************************************* |
From: Andrea S. <and...@gm...> - 2005-07-06 07:48:43
|
Hi Vanessa, try also pdb-mode.el (http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html) I have been using it for a while and I found very useful Regards, andrea |
From: <li...@ul...> - 2005-07-06 07:26:55
|
On Wednesday 06 July 2005 08:58, Sebastien Gerega wrote: > Is there a way to list the residues that are in a selection? For example > if I use the command "select near, sel01 around 6" how can I obtain a > list of the residues in the "near" selection? Using cmd.get_pdbstr("near") (after "import cmd" if required) you get a list of lines in PDB ATOM format for all the atoms in the selection. In principle, you can extract any information you want from these lines. Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel |
From: Sebastien G. <sge...@ma...> - 2005-07-06 06:58:20
|
Is there a way to list the residues that are in a selection? For example if I use the command "select near, sel01 around 6" how can I obtain a list of the residues in the "near" selection? thanks, Sebastien |
From: sankari t. <san...@ya...> - 2005-07-06 05:50:15
|
Dear All, I would like to know is there any possibility to determine the geometric location of amino acids in proteins using PYMOL. and visualize them.? (or) Please tell emt he softwares to do the same. With regards sankari __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: T.A.Wassenaar <T.A...@ru...> - 2005-07-06 05:11:49
|
Hi Vanessa, > (1) Are there commands that I can type such that I can >shift the coordinate for the entire PDB file without >using the mouse? Try: alter_state 1,selection,(x,y,z)=(newx,newy,newz) > > (2) If the mouse is the only way I can shift >coordinates, then how do I use the mouse so that I can >change the X-coordinate? Alternatively you can use the mouse in editing mode > > (3) What does the origin command do? origin sets the origin used in the pymol viewer to the centre of geometry of the selection (or of everything if no selection is given, or to a specified point). It does not change coordinates. > > Thanks, > Vanessa > Your welcome :) (Hope it helps) Cheers, Tsjerk > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux >Migration Strategies > from IBM. Find simple to follow Roadmaps, >straightforward articles, > informative Webcasts and more! Get everything you need >to get up to > speed, fast. >http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Sebastien G. <sge...@ma...> - 2005-07-06 04:32:44
|
I have Pymol installed on my dual boot Asus M6Ne notebook and have noticed that the performance is significantly better in windows than it is in linux. I am running FC4 and have installed the ati-fglrx driver. When rotating a 120 amino acid protein I get maximum 8 frames per second and the CPU usage goes up to about 90%. Is this normal? If not, are there any known issues with ATi Drivers? or with FC4? any help would be great, Sebastien |
From: Gilleain T. <gil...@ho...> - 2005-07-05 23:13:05
|
Hi, I suppose that these numbers are the atom_ids. It's probably the same numbers returned by the cmd.index function. I guess you could test this by typing "select atom260, id 260" and see if that makes a selection with atom260... As for the speed question, I have no idea. More of a question for Mr DeLano :) Calculating pairwise like this is always going to be computationally expensive, but I don't know ways to speed this up. gilleain torrance On 5/7/05 15:17, "Andrea Spitaleri" <and...@gm...> wrote: >> HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) > yes thanks for the trick. However, I edited my script to: > DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd")) > DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD)) > but I cannot figure out the meaning of the output: > complex_1 > donor acceptor hba hbd > 260 271 2.536 -1.000 > complex_2 > donor acceptor hba hbd > 391 409 2.489 -1.000 > complex_3 > donor acceptor hba hbd > 522 547 2.512 -1.000 > complex_4 > donor acceptor hba hbd > 653 685 2.456 -1.000 > what the numbers under donor and acceptor are? > >> >> atoms_Don = cmd.index('don') >> > > I tried also this option and it works fine (more or less) excet that > it takes a lot time to calculate all the distance (quite weird on my > dual-cpu 3Gz intel) > this is the loop used: > for donor in atoms_Don: > for acceptor in atoms_Acc: > di = cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor) > DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di)) > > thanks > > Regards > > andrea > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: <ji...@uc...> - 2005-07-05 22:54:19
|
I am a new user of pymol, I have learned a lot from the pymol list. Thank you all. Now I am trying to set up a hardware stereo viewing system on a PC running windows XP. I read the pymol list, and got some idea of installing hardware on window XP system, which is to get a nVidia graphic card FX3200 (which I already have now), and a CRT monitor with fast refresh rate (>100), like NEC -multisync FP2141SB-BK, as suggested by Pymol users. But I just found out that this model is discontinued now. I am wondering who can suggest another monitor(s) for this purpose? any suggestions, warnings, recommendations on this issue is highly appreciated. Thank you. Jie Yang |
From: Vanessa O. <vok...@st...> - 2005-07-05 22:54:11
|
Hi all, I'm a new user of MacPyMOL. I would like to modify the coordinates of my PDB file such that the origin (0,0,0) is centered at the mid-point of a molecular bond. I've found that I can make (and save) changes in the Z and Y coordinates (in 3 button editing mode moving the structure up/down (Z), left/right(Y)), but I cannot really reliably shift the X coordinate reliably using the mouse. So I have 3 questions: (1) Are there commands that I can type such that I can shift the coordinate for the entire PDB file without using the mouse? (2) If the mouse is the only way I can shift coordinates, then how do I use the mouse so that I can change the X-coordinate? (3) What does the origin command do? Thanks, Vanessa |
From: Andrea S. <and...@gm...> - 2005-07-05 14:17:13
|
> HBA =3D cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) yes thanks for the trick. However, I edited my script to: DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd")) DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD)) but I cannot figure out the meaning of the output: complex_1 donor acceptor hba hbd 260 271 2.536 -1.000 complex_2 donor acceptor hba hbd 391 409 2.489 -1.000 complex_3 donor acceptor hba hbd 522 547 2.512 -1.000 complex_4 donor acceptor hba hbd 653 685 2.456 -1.000 what the numbers under donor and acceptor are? >=20 > atoms_Don =3D cmd.index('don') >=20 I tried also this option and it works fine (more or less) excet that it takes a lot time to calculate all the distance (quite weird on my dual-cpu 3Gz intel) this is the loop used: for donor in atoms_Don: for acceptor in atoms_Acc: di =3D cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor) DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di)) thanks Regards andrea |
From: Warren D. <wa...@de...> - 2005-07-05 13:23:49
|
Akanksha, =20 The carve option to isomesh and isosurface uses a distance-based cutoff = for display around the selected atoms. To accomplish what you seek, you = should be able to simply reduce that cutoff. =20 =20 Cheers, Warren ________________________________ From: pym...@li... on behalf of Akanksha = Nagpal Sent: Mon 04/07/2005 13:27 To: pym...@li... Subject: [PyMOL] Electron density around selected residues Dear PyMol Users: I found a lot of e-mails in the archives discussing drawing electron = density around selected residue or ligand. The carve command works fine but I = also see density for other residues, which are adjacent to selected redidue. Is = there any way to just exclusively draw density around selected residues and = not show parts of density from the other surrounding residues? Any help is greatly appreciated. Regards, Akanksha -- Ph.D. Candidate, School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta, GA 30332 ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Gilleain T. <gil...@ho...> - 2005-07-05 12:59:29
|
Hi, Well, the cmd.distance method seems to take minimum 4 parameters, not three: cmd.distance( string name, string selection1, string selection2, string cutoff, string mode ) where 'mode' is not important. So, in the script you give, the line: HBA = cmd.distance('(lig and acc)','(active and don)',3.2) could become HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2) or, if you use the atom ids that you get from the (commented out) lines: atoms_Don = cmd.index('don') you could use cmd.get_distance in a loop: for donor in atoms_Don: for acceptor in atoms_Acc: DistOut.write("%s" % cmd.get_distance(donor, acceptor)) or something. gilleain torrance On 5/7/05 11:50, "Andrea Spitaleri" <and...@gm...> wrote: > Hi guys, > I am trying to make a script to automatize a procedure. I have got a > file where I can pick up the structure of protein-ligand complexes > cluster > The script below read the number of the cluster and then visualize > them align with a protein reference. Everything is fine except I'd > like write on a file the distances between some residues of each > structure with the ligand but I cannot figure out how do it. I read > different post but it seems that I missing something. > > thanks a lot > > Regards, > > andrea > > ##### CUT HERE ##### > from pymol import cmd > import string, sys, os > > def read_cluster(number): > cmd.reinitialize() > cmd.load('/home/pippo/ref.pdb','ref') > cmd.select('Refactive','resi 17+20+23+25+26+43+44 in ref') > HoL = {} > FileToOpen = 'Dist' + number > DistOutput = open(FileToOpen,'w') > DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n") > out = open('cluster.out','r') > pro_atoms = cmd.get_model("ref") > # read cluster file > for i in out.readlines(): > i=string.strip(i) > tmp = string.split(i," ") > index, elems = tmp[1], tmp[3:len(tmp)] > HoL[index] = elems > # visualize the structures of cluster number > for eachElem in HoL[number]: > newElem = eachElem + '.pdb' > cmd.load(newElem.strip(),eachElem) > cmd.select('active','resi 17+20+23+25+26+43+44') > cmd.select('lig','resn CBO') > cmd.select('ligDon','(elem n,o and (neighbor hydro) in lig)') > cmd.select('ligAcc','(elem o or (elem n and not (neighbor > hydro)) in lig)') > Don = cmd.select('don','(elem n,o and (neighbor hydro))') > Acc = cmd.select('acc','(elem o or (elem n and not (neighbor > hydro)))') > # atoms_Don = cmd.index('don') > # atoms_Acc = cmd.index('acc') > HBA = cmd.distance('(lig and acc)','(active and don)',3.2) > HBD = cmd.distance('(lig and don)','(active and acc)',3.2) > cmd.align('ref',eachElem) > DistOutput.write(" %14s %14s %8.3f\n"%(Don,Acc,HBA)) > > DistOutput.close() > > cmd.extend('read_cluster',read_cluster) > ########## CUT HERE ################ > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Andrea S. <and...@gm...> - 2005-07-05 10:50:31
|
Hi guys, I am trying to make a script to automatize a procedure. I have got a file where I can pick up the structure of protein-ligand complexes cluster The script below read the number of the cluster and then visualize them align with a protein reference. Everything is fine except I'd like write on a file the distances between some residues of each structure with the ligand but I cannot figure out how do it. I read different post but it seems that I missing something. thanks a lot Regards, andrea ##### CUT HERE ##### from pymol import cmd import string, sys, os def read_cluster(number): cmd.reinitialize() cmd.load('/home/pippo/ref.pdb','ref') cmd.select('Refactive','resi 17+20+23+25+26+43+44 in ref') HoL =3D {} FileToOpen =3D 'Dist' + number=20 DistOutput =3D open(FileToOpen,'w') DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n") out =3D open('cluster.out','r') pro_atoms =3D cmd.get_model("ref") # read cluster file for i in out.readlines(): i=3Dstring.strip(i) =20 tmp =3D string.split(i," ") index, elems =3D tmp[1], tmp[3:len(tmp)] =20 HoL[index] =3D elems # visualize the structures of cluster number for eachElem in HoL[number]: newElem =3D eachElem + '.pdb' cmd.load(newElem.strip(),eachElem) cmd.select('active','resi 17+20+23+25+26+43+44') cmd.select('lig','resn CBO') cmd.select('ligDon','(elem n,o and (neighbor hydro) in lig)') cmd.select('ligAcc','(elem o or (elem n and not (neighbor hydro)) in lig)') Don =3D cmd.select('don','(elem n,o and (neighbor hydro))') Acc =3D cmd.select('acc','(elem o or (elem n and not (neighbor hydr= o)))') # atoms_Don =3D cmd.index('don') # atoms_Acc =3D cmd.index('acc') HBA =3D cmd.distance('(lig and acc)','(active and don)',3.2) HBD =3D cmd.distance('(lig and don)','(active and acc)',3.2) cmd.align('ref',eachElem) DistOutput.write(" %14s %14s %8.3f\n"%(Don,Acc,HBA)) =20 DistOutput.close() =20 cmd.extend('read_cluster',read_cluster) ########## CUT HERE ################ |
From: Akanksha N. <gt...@ma...> - 2005-07-04 20:20:34
|
Dear PyMol Users: I found a lot of e-mails in the archives discussing drawing electron dens= ity around selected residue or ligand. The carve command works fine but I als= o see density for other residues, which are adjacent to selected redidue. Is th= ere any way to just exclusively draw density around selected residues and not= show parts of density from the other surrounding residues? Any help is greatly appreciated. Regards, Akanksha -- Ph.D. Candidate, School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta, GA 30332 |
From: <ag...@po...> - 2005-07-04 17:48:25
|
Hello, I would like to change the font and most importantly size of the labels of residues, or anything else that I want to show the label of. I'm using python to make a script for pymol. Is it possible? Does anyone know how to do that? Greetings, Aga |
From: Andrea S. <and...@gm...> - 2005-07-03 10:41:15
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Hi try Movie -> select all state it should work andrea |
From: bgbg bg <bg...@gm...> - 2005-07-03 10:34:21
|
Hello, list. When loading a mol2 file (or an SDF file) with multiple structures in it, I see only one structure displayed, although the following lines are printed in the external GUI window. ObjectMolReadMOL2Str: read molecule 1 ObjectMolReadMOL2Str: read molecule 2 ObjectMolReadMOL2Str: read molecule 3 ObjectMolReadMOL2Str: read molecule 4 ............... How can I display all the molecules ? Thanks a lot. |
From: Andrea S. <and...@gm...> - 2005-07-01 11:22:59
|
Hi I have been using apbs and the built-in generate electrostatic surface.=20 I'd like to know your impression on which tools is the best for MEP calcula= tion. thanks a lot Regards andrea |
From: Warren D. <wa...@de...> - 2005-06-30 16:31:07
|
Yusuf, alter selection, vdw=3Dradius eg. alter elem c, vdw=3D3.2 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 > tan...@st... > Sent: Thursday, June 30, 2005 8:41 AM > To: pym...@li... > Subject: [PyMOL] Radii in Angstrom >=20 > Hi, >=20 > if I show up a sphere around an picked atom, and want to=20 > change its radius, I always use the > set sphere_scale > method. But, to which value am I scaling to? Isn't it=20 > possible to change the radius of a sphere with something like=20 > 'set sphere_radius' in Angstroms? > I could not find any information in the manual and the reference. > My aim is to project a sphere (or another projection) with a=20 > certain radius like > 3.2 Angstrom around an atom. After I realized that I could=20 > not do this with the implemented spheres, I checked the > set dots_* methods, > where I did find a > set dots_radius. > But everytime I use this function, the dots stay at their=20 > position and PyMol does not change anything on screen (and=20 > raytracing leeds to a crash). >=20 > So, am I doing anything wrong or are these methods not=20 > available at the moment? >=20 > Regards >=20 > Yusuf Tanrikulu >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration=20 > Strategies from IBM. Find simple to follow Roadmaps,=20 > straightforward articles, informative Webcasts and more! Get=20 > everything you need to get up to speed, fast.=20 > http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: <tan...@st...> - 2005-06-30 15:32:44
|
Hi, if I show up a sphere around an picked atom, and want to change its radius, I always use the set sphere_scale method. But, to which value am I scaling to? Isn't it possible to change the radius of a sphere with something like 'set sphere_radius' in Angstroms? I could not find any information in the manual and the reference. My aim is to project a sphere (or another projection) with a certain radius like 3.2 Angstrom around an atom. After I realized that I could not do this with the implemented spheres, I checked the set dots_* methods, where I did find a set dots_radius. But everytime I use this function, the dots stay at their position and PyMol does not change anything on screen (and raytracing leeds to a crash). So, am I doing anything wrong or are these methods not available at the moment? Regards Yusuf Tanrikulu |
From: Andrea S. <and...@gm...> - 2005-06-30 12:21:30
|
Hi, yes it worked. that mistake is so shameful ... :P thanks andrea 2005/6/30, li...@ul... <li...@ul...>: > On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: > > from pymol import cmd > > file=3Dopen("file.nam") > > for i in file.readlines(): > > cmd.load(i) >=20 > You may have to strip the trailing newline ("\n") from each file name by = using > "cmd.load(i.strip())". >=20 > Hope this helps, > -- > Lieven Buts > Vrije Universiteit Brussel >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=3D7477&alloc_id=3D16492&op=3Dclic= k > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |