Re: [PyMOL] How to see all models in PDB file?

Hi, try movie - show all states and 2007/6/6, Kristoffer Torbjørn Bæk k...@life.ku.dk: Hi everyone, I have a PDB file containing the coordinates for six monomers together forming a hexamer. Each monomer is separated by MODEL/ENDMDL in the PDB file, but when I load the file in PyMOL I only

Re: [PyMOL] colour by rms...

Hi, you may try to change the B-factor with the rmsd values normalised from 0 to 100 let' say .. and then colour by spectrum-b-factor. Probably there is another better way ... i dunno :P Regards, andrea 2007/4/4, David Briggs bassoph...@gmail.com: Hi everyone... I'm sure this has been

Re: [PyMOL] apbs plugin in pymol

Hi, at this purpose, what kind of range (positive - negative) should be used in order to visualize correctly the potential surface on a protein? Normally I used -10 to +10 but I am wondering how you behaves with this issue too. Thanks in advance andrea 2006/11/23, D. Eric Dollins

Re: [PyMOL] Show residues and sticks

1) I superimposed two protein structures. They are similar but have different numbering of residues, e.g residue 34 in structure A is equivalent to residue 38 in structure B. I want to show only the side chain of residue 34 for structure A and residue 38 for structure B. I selected only structure

Re: [PyMOL] align states

do this by split_states my_struct dele my_struct for the NMR ensemble, then I would use the action menu, align function and align them to state_1. This is in effect aligning the separate states as objects, unless I misunderstood you J Andrea Spitaleri wrote: Hi all, in pymol

[PyMOL] align and iterate residues

Hi all, I found very nice the align command in order to align domains within huge complex. However, I was wondering whether is it possible to iterate on the superimposed structure in order to know which with wich residues. Creating the object, I cannot iterate on it. Thanks for any suggestion

Re: [PyMOL] pymol on amd64?

Hi, few weeks ago I had a problem with pymol-32bit on my laptop 64bit using slamd Warren built a pymol for 64bit and you can download it from here: http://delsci.com/beta/ In my case it worked. Regards andrea 2006/4/11, Florian Haberl florian.hab...@chemie.uni-erlangen.de: hi, On Tuesday

Re: [PyMOL] pymol on amd64?

. praedor On Wednesday 12 April 2006 04:18 am, Andrea Spitaleri wrote: Hi, few weeks ago I had a problem with pymol-32bit on my laptop 64bit using slamd Warren built a pymol for 64bit and you can download it from here: http://delsci.com/beta/ In my case it worked. Regards andrea

[PyMOL] load *only one* state for NMR ensemble ..

Hi all, I have more then 200 pdb files and each file represents an ensemble of NMR calculated structure (ca. 30). If I try to load all together, my system goes terribly slowly and pymols seems crashing (the windows freeze). Is there any way to load only the first structure for each file rather

Re: [PyMOL] surfaces

Hi I think you should select the chain A and then create the object for this selection. Then you can manipulate as standalone object. select A, chain A create A_obj, A show A_obj,surface I hope this help Regards andrea 2006/3/28, Chandra chan...@bii.a-star.edu.sg: If I have two chains in a

Re: [PyMOL] (no subject)

Hi, for this purpose I have used caver program. You can download it free of charge from here http://loschmidt.chemi.muni.cz/caver/download.php I hope this help Regards andrea 2006/3/27, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com: dear sir iam a pymol user, do we

[PyMOL] pymol-099rc6 installation problem on am64bit

Hi all, I have downloaded pymol-099rc6 and followed the instructions to install it. Typing pymol I get back: pymol.exe not such file or dir even if the pymol exec is there. My laptop is an amd64bit hp pavillon thanks andrea -- La conoscenza libera il genere umano dalla superstizione J.

Re: [PyMOL] (no subject)

Hi try align or fit regards andrea 2006/3/3, srilath...@jubilantbiosys.com srilath...@jubilantbiosys.com: dear all can we superimpose structures in pymol Thanks Regards srilatha potlapelly MSc Biotechnology Drug discovery, #450,4th D Main, 12th cross, Mahalakshmipuram - 560086

Re: [PyMOL] Surface of cavity

Hi, you may try to use caver: http://viper.chemi.muni.cz/caver/concept.php or castp http://cast.engr.uic.edu/cast/oldindex.php regards andrea 2006/1/21, Paul Wilhelm Elsinghorst p...@uni-bonn.de: Hi, a little question regarding cavity surfaces :-) I have a set of active atoms (GOLD

Re: [PyMOL] display of multiple NMR structures stored in one PDB file

Hi,you can either with mouse clicking on the left-down on or on the menu display all frames. I hope this can help, Regards andrea 2006/1/13, Michael Weber web...@staff.uni-marburg.de: Hello, I have a short question concerning the display of multiple NMR structures stored in one PDB file.

Re: [PyMOL] combine align and rms_cur to calculate rms for complexes

Hi Warren, yes this is the case. My complexes are from a docking calculations with the same ligand. I was just quite doubtful about the procedure... to use align and then rms_cur. I compared the rms results with another software (vmd) and it seems to be consistents. Thanks, Regards, andrea

Re: [PyMOL] Viewing cavities?

what about Caver: http://loschmidt.chemi.muni.cz/caver/concept.php very nice and it works very well andrea 2005/11/7, Bingding Huang bhu...@biotec.tu-dresden.de: Dear all, I download CASTpyMOL.pyc and put it in the right folder. Now I want to use it for detecting cavity for 50 proteins. I

[PyMOL] very slow script for distance calculation

Hi all, is it normal that a script in pymol runs very very slow. In my case I am just selecting a residue of a protein and calculating the distance from the ligand atoms. I am doing this in a loop over 100 molecule. It took ca. 6 hours...! My memory is 50% free (1Gb total). I am using this

Re: [PyMOL] very slow script for distance calculation

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

Re: [PyMOL] very slow script for distance calculation

Hi again, reading my post I found the bottleneckshame 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

Re: [PyMOL] very slow script for distance calculation

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

[PyMOL] feed value to pymol -qrc script.py

Hi there, I made a script in pymol and I'd like to use it as pymol -qrc script.py argv[1] argv[2] ... but it seems not working properly. It says that it cannot open such file, even if the argument is a number... In fact, if I replace the sys.argv[] with the values into script.py, it woks. Any

[PyMOL] script feedback: how print out distance and not average

Hi all, this script below runs well in pymol. It loads pdb files and calculates the distance of some atoms contained in the fileAmb whose format is: 26,O11:HN 28,*:HE1 ... With * I select whole ligand (segi B) and pymol returns only one value, the average distance for all atoms to the

Re: [PyMOL] antialiasing and povray

try povray +A0.3 file.pov zero -^ regards Cameron Mura wrote: hi, Is there anything special I need to do/set to achieve antialiased images via pymol + POV-ray? To be more explicit, i'm using robert campbell's make_pov.py to have pymol dump the scene into a povray input file, and

Re: [PyMOL] [OT] alternative python module

://frowns.sourceforge.net/) MMTK (http://starship.python.net/crew/hinsen/MMTK/) All these software are free software. Regards, Jerome PANSANEL -- Jerome PANSANEL http://www.alchem.org Le Lundi 25 Juillet 2005 15:42, andrea spitaleri a crit: Hi all, I am using pymol also for python scripting

[PyMOL] script to write down distances ligand-protein: need feedback

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

Re: [PyMOL] script to write down distances ligand-protein: need feedback

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

Re: [PyMOL] Renumber protein segid

/scripts/pdb-mode.html Cheers Joel Andrea Spitaleri wrote: Hi all, I couldn't find any command in pymol to renumber the segid of a protein. Is there any way to do it? Regards andrea --- SF.Net email is sponsored by: Discover

Re: [PyMOL] run script

Hi, yes it worked. that mistake is so shameful ... :P thanks andrea 2005/6/30, lie...@ultr.vub.ac.be lie...@ultr.vub.ac.be: On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote: from pymol import cmd file=open(file.nam) for i in file.readlines(): cmd.load(i) You may have

[PyMOL] Renumber protein segid

Hi all, I couldn't find any command in pymol to renumber the segid of a protein. Is there any way to do it? Regards andrea

[PyMOL] fit command

Hi all, i have got two pdb files, ref.pdb and docked.pdb, where ref.pdb contains the protein A and docked.pdb the protein A + a docked ligand. when I try to run fit ref, docked I get: ExecutiveRMS-Error: No atoms selected. I tried to select the atoms or create a new object but i get the same

[PyMOL] still unresolved import pymol...

After any answer, I have been looking on this list and googling around (sorry if I didn't before...) there is: # set path in order to use pymol modules export PYMOL_PATH=/usr/local/pymol/ export PYTHONPATH=/usr/local/pymol/modules/ then type python to enter in the shell and: s...@darkstar:~

[PyMOL] import pymol

Hi guys/girls easy and quick question: how can i import pymol modules in my python scripts? ie. I want use translate... do i need to import what? thanks a lot andrea

[PyMOL] overlay ligands inside of protein

Hi everyone, I am quite new here (I have been reading your post in past...) and now I decide to post a question (easy maybe). I couldn't find any answer on Google. I have got two complexes of (protein+ligand)1 and (protein+ligand)2 where the only difference between the two is the different