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 see one of the monomers. What do I have to do in order to see the whole hexamer? Sincerely, Kristoffer - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- WAR IS PEACE FREEDOM IS SLAVERY IGNORANCE IS STRENGTH 2+2=5
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 covered in the pymol mailing list previously, but I've looked back 12months and I can't find it. Can I colour a structure by its rmsd from another strucutre. Thanks in advance Dave -- --- David Briggs, PhD. Father Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile --- Anyone who is capable of getting themselves made President should on no account be allowed to do the job. - Douglas Adams - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- WAR IS PEACE FREEDOM IS SLAVERY IGNORANCE IS STRENGTH 2+2=5
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 d.e.doll...@gmail.com: Florian, I had the same problem and I couldnt get everything to work internally in pymol. I never got pymol to write the *.pqr files. I couldn't figure it out. However, you can give your pdb to the PDB2PQR server: http://agave.wustl.edu/pdb2pqr/server.html Strip the waters/ligands and load in your pdb. Choose that you want to create an APBS input file. You get 2 files: *.pqr and *.in. Rename without .txt extension (if the output has them. My mac put them on). You can load input pdb (the one with waters/ligands stripped). Change the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't change the pymol generated dx. Under main, choose use another pqr. Choose externally generated pqr and browse for your x.pqr. Click set grid. Click run APBS. That will spit out a pymol-generated.dx. In pymol type load_dx [file].dx. In APBS window, go to the visualization tab and choose show mol. surface. Change levels and update. Perhaps not the best way to get this to work, but it will give you a surface to look at. Good luck, Eric On 11/22/06, Florian Schmitzberger florian.schmitzber...@ki.se wrote: Dear All, I am having a small problem using the apbs plugin in pymol on my pdb (I am using fink installed pymol and apbs versions on Mac OSX 10.4.8). When I try to run apbs I received the following message: Unable to assign parameters for 100 atoms in the selection unassigned. Please either remove these unassigned atoms and re-start ... In principle, I think I understand the problem is that pdb2pqr cannot assign charges to certain atoms, in my case posttranslationally modified cysteine residues. My question would be what the best way to fare with those atoms is. Since the modification introduces an acidic patch, if possible I would like to leave the atoms in (rather than remove them) when calculating surface charge representation, as this could be informative. So perhaps my question boils down to what the optimal way to manually assign reasonable charges (in the pqr-file) for this oxidised cysteine (sulfinic acid; O-S=O) is. I also noticed that I get the same error message with residues where side-chain atoms have been removed (such as surface lysines), while leaving the original residue name. But then I suppose there is no way around this. Thank you very much in advance for any comments! Best regards, Florian Florian Schmitzberger Medical Biochemistry and Biophysics Karolinska Institute Scheeles vaeg 2 SE-171 77 Stockholm, Sweden Tel: +46-8-524-86875 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- D. Eric Dollins C266 LSRC, Box 3813 Duke University Medical Center Durham, NC 27710 (919)681-1668 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- The last one to die please turn out the light…(children of men)
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 A, and type the command: show sticks, resi 34; and select only structure B and: show sticks, resi 38. But the residue 34 in structure B and residue 38 in structure A were also shown. Could anyone teach me how to show residue 34 in structure A and 38 in structure B only? select 34A, resi 34 and structureA select 38B, resi 38 and structureB then show sticks 34A and show sticks 38B 2) Related to the same molecules. I want to show sticks for the R-group of residue 34 only. I typed the command: show sticks, resi 34. But the backbone atoms were shown also. Could anyone teach me how to show sticks for the R-group only?? select 34AR, resi 34 and structure and not (name c,n,ca) show sticks, 34AR ciao andrea Thanks in advance Phoebe Graduate student - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- che spacchiu tali? a faccia di minchia ca gl'hai staiu taliannu salutami emma emmasucasti (Valerio)
Re: [PyMOL] align states
Hi, the command intra_fit was the one! However, if I'd like to visualize the first, let's say, 20 structures of my bundle? thanks again andrea 2006/7/19, Robert Campbell r...@post.queensu.ca: Hi, * Joel Tyndall joel.tynd...@otago.ac.nz [2006-07-15 14:29] wrote: Hi andrea, you can easily 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 is it possible to align states rather than object. I mean, I have loaded a pdb file with n-structures and I'd like to align each of them on the first one of the bundle. If in fact the n-structures contain all the same atoms, then you can use the intra_fit command instead: PyMOL help intra_fit intra_fit DESCRIPTION intra_fit fits all states of an object to an atom selection in the specified state. It returns the rms values to python as an array. USAGE intra_fit (selection),state PYMOL API cmd.intra_fit( string selection, int state ) EXAMPLES intra_fit ( name ca ) PYTHON EXAMPLE from pymol import cmd rms = cmd.intra_fit((name ca),1) SEE ALSO fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3N6 Canada r...@post.queensu.ca http://adelie.biochem.queensu.ca/~rlc phone: 613-533-6821fax: 613-533-2497 PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Why stand on a silent platform? Fight the war, fuck the norm (RATM)
[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 Regards andrea -- La conoscenza libera il genere umano dalla superstizione J. Watson
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 11 April 2006 19:59, Praedor Atrebates wrote: Is anyone running pymol on an AMD64 system? If so, did you find a prebuilt binary or did you build it yourself? If you built it yourself...HOW DID YOU DO IT? I'd greatly appreciate help in this regard. also the normal 32 bit standalone executebale works for me on em64t cpu. You can find it at http://delsci.com/rel/099/ don`t know if a special 64bit version is necessary if 32 bit version is running without problems. Os is Suse 10 for x86_64. Thank you, praedor Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- -- La conoscenza libera il genere umano dalla superstizione J. Watson
Re: [PyMOL] pymol on amd64?
Hi, this should be a binary, so just installing it should work ... try also to export the lib path (export or setenv LD_LIBRARY_PATH) Regards Andrea 2006/4/12, Praedor Atrebates prae...@yahoo.com: Great! Thank you. I've just finished trying and failing to get pymol to build again on my AMD64 Mandriva system. It invariably fails quickly with: layer0/Crystal.c:314:1: error: unterminated argument list invoking macro sprintf layer0/Crystal.c: In function 'CrystalDump': layer0/Crystal.c:201: error: syntax error at end of input layer0/Crystal.c:201: warning: unused variable '_FBstr' layer0/Crystal.c:199: warning: unused variable 'i' layer0/Crystal.c:198: warning: unused variable 'G' error: command 'gcc' failed with exit status 1 There must be a lib difference or gcc difference between the Mandriva 2006 system and SuSE that apparently allows a 64 bit build to proceed. 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 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
[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 than all the ensemble?? Thanks to all Regards andrea -- La conoscenza libera il genere umano dalla superstizione J. Watson
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 structure how can i draw a surface on each chain separately (as though the other chain did not exist). currently i have to separate the structure file into two different files with a chain each and read them both and draw teh surface on each. thanks chandra --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
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 can find area volume of active site in pymol if we can, just tell me how to do it thanking you srilatha Thanks Regards srilatha potlapelly MSc Biotechnology --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmdlnkkid0944bid$1720dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
[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. Watson
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 Bangalore Office: +9180-23495461-64 Extn.-1029 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmdlnkkid0944bid$1720dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
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 output) that surround a cavity. Now I want to dipslay the surface only for the cavity wall, not on the outside. Any ideas? Paul -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.0 (GNU/Linux) iD8DBQBD0eKigFneuXxhreARAnFLAJ9Z3o6zMiphEzzKpVzMXtdXxh6dBwCeMp9u ZIoavXwL2DE+hMObJhTiD8o= =uZkv -END PGP SIGNATURE- -- La conoscenza libera il genere umano dalla superstizione J. Watson
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. When loading NMR .PDB files with SWISS-PDB-VIEWER, the number of NMR structures present in that file is initially displayed during the loading process and one can select how many and which of the structures are going to be loaded. In pyMOL, when trying to load for example 1JOX.pdb (which contains 4 NMR models), only one single structure is displayed. How can I visualize the remaining three? Thanks for your help, ;-) Michael. -- La conoscenza libera il genere umano dalla superstizione J. Watson
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 don't want to do that one after one by hand. Is it possible to write a python (pymol) script to do that automatically? Thanks a lot! Regards Bingding Sebastien Moretti wrote: Dear Bingding, CASTp cavities are pre-computed for most of PDB entries. So, you could create a PyMOL script (.pml) which could look like that: call the CASTp plugin for ? save .pdb reinitialize call the CASTp plugin for ? ... With this kind of script you could be able to get the cavities for your 50 proteins with only one PyMOL execution. Nevertheless, I don't know how to call the CASTp plugin from a PyMOL script. And how to save all cavities as distinct pdb files. But I know that that is possible. Only the PyMOL mailing list or Wiki are able to help you now. Hi Marcus, You can install the CASTp plugin for PyMOL : http://cast.engr.uic.edu/cast/?mode=CASTpyMOL CASTp (http://cast.engr.uic.edu/cast/) is Computed Atlas of Surface Topography of proteins and analyzes the Anatomy of Protein Pockets and Cavities. So, with the plugin, you can get every cavities (pockets), CASTp has predicted, automatically. I hope this will help you. 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. * -- Bingding Huang PhD student Bioinformatics group Biotec Department of Computing Tazberg 47, 01307 TU Dresden, Germany Tel:0049 351 46340064 (Office) Tel:0049 351 4403368 (Home) Fax:0049 351 46340061 Web:http://www.biotec.tu-dresden.de/~bhuang E-mail: bhu...@biotec.tu-dresden.de --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- La conoscenza libera il genere umano dalla superstizione J. Watson
[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 script in shell without gui. thanks in advance Regards, andrea
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 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
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 +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
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 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
[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 help? Regards andrea
[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 HE1 atoms. I need to
print out all the distances, atom by atom.
any helps??
thanks a lot
andrea
--
from pymol import cmd
import string, sys, os
def viol(fileAmb,deep):
cmd.reinitialize()
if (dist.out):
os.system(rm -f dist.out)
nam = open(file.nam,'r')
KeepStruc = []
readnam = nam.readlines()
deep = int(deep)
for j in range(0,deep):
readnam[j] = string.strip(readnam[j])
KeepStruc.append(readnam[j])
for i in KeepStruc:
cmd.load(i,i)
cmd.select(lig,segi B)
cmd.select(pro,all and not segi B)
amb = open(fileAmb,'r')
out = open(dist.out,a)
out.write(%4s\n%(i))
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)
l = cmd.select(l,name +atomlig+ and segi B and +i)
d = cmd.distance(dist_+str(i),p,l)
if (d 5):
print resname,:,atompro,-,atomlig,d
out.write(%4s%8s%8s%8.3f\n%(resname,atompro,atomlig,d))
out.close()
cmd.extend('viol',viol)
--
La conoscenza libera il genere umano dalla superstizione
J. Watson
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 then ray-tracing w/ a minimalistic command-line (e.g., povray +Iwhatever_pov.inp +W640 +H480)... all of this is w/ antialias set 'on' in pymol.. i'm unfamiliar w/ povray, so any tips or advice would be greatly appreciated. thanks, cameron --- 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=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] [OT] alternative python module
Hi thanks to all for the links. and something a bit closer to pymol? more focused on biological files... thanks again Regards andrea Jerome PANSANEL wrote: Hello, You can find modules inside some software package, like: PyQuante (http://pyquante.sourceforge.net/) FROWNS (http://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 and perlmol for perl scripting. They are both very nice. I am just wondering if there are some other useful python modules around for chemistry. Sorry for the OT. 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_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- 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_idt77alloc_id492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[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 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
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 output:
complex_1
donoracceptor hba hbd
260 2712.536 -1.000
complex_2
donoracceptor hba hbd
391 4092.489 -1.000
complex_3
donoracceptor hba hbd
522 5472.512 -1.000
complex_4
donoracceptor hba hbd
653 6852.456 -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
Re: [PyMOL] Renumber protein segid
Hi Joel, thanks a lot for the tip! excellent stuff using my loved editor! andr 2005/6/29, Joel Tyndall joel.tynd...@otago.ac.nz: Hi andrea, I have found an excellent add on tool for emacs which does a lot of renumbering stuff (on unix/linux) http://stein.bioch.dundee.ac.uk/~charlie/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 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_idt77alloc_id492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
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 to strip the trailing newline (\n) from each file name by using cmd.load(i.strip()). Hope this helps, -- Lieven Buts Vrije Universiteit Brussel --- 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=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[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 results thanks for any help Regards andrea
[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:~ python Python 2.3.3 (#1, Feb 5 2005, 16:22:10) [GCC 3.3.3 (SuSE Linux)] on linux2 Type help, copyright, credits or license for more information. import pymol Traceback (most recent call last): File stdin, line 1, in ? File /usr/local/pymol/modules/pymol/__init__.py, line 306, in ? import _cmd ImportError: No module named _cmd I found already that someone got the same error but none helps him, so I tought that this is a pymol bug, isn't ? thanks again for any help regards andrea
[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 orientation of the ligand. My purpose is to overlay the protein (or maybe better the binding site) and to calculate the rms of the ligand's mismatch. The pdb file contains the protein+ligand. Do I need to create the ligand object for doing that? I aware that is a common task...sorry for the silly start :P andrea
