Re: [PyMOL] some help
Hi Thomas, > To address your question, it is not possible to my knowledge to upload > a sequence only to PyMOL. Keep in mind that PyMOL is a molecular > viewer, not a sequence viewer. If you want to see your sequence, you > probably would have to create a 3D model of your sequence (e.g. using > MODELLER). You can load FASTA files into PyMOL. Good luck understanding the results though. For example: # fetch a protein and save its sequence fetch 1cll, async=0 save 1cll.fasta, 1cll # delete everything & load the FASTA file dele * load 1cll.fasta Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] some help
A multiple sequence viewer incorporating structural information would be incredibly helpful, as then I wouldn't have to generate models for everything I want to compare substitutions in. It might be too much to ask of PyMOL to be good at everything, however. Perhaps adding the ability to read in alignments from an external program (e.g. in aligned fasta format) containing the sequence of the structure (or model) to be aligned to would be sufficient? Jed Thomas Juettemann wrote: > Hi Ashok, > > there are several ways to visualise alignments. Here is a nice overview: > > Visualization of multiple alignments, phylogenies and gene family evolution > James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice > Jossinet & Geoffrey J Barton > Nature Methods 7, S16 - S25 (2010) > http://dx.doi.org/doi:10.1038/nmeth.1434 > > To address your question, it is not possible to my knowledge to upload > a sequence only to PyMOL. Keep in mind that PyMOL is a molecular > viewer, not a sequence viewer. If you want to see your sequence, you > probably would have to create a 3D model of your sequence (e.g. using > MODELLER). > > However, I think you have an interesting idea. It would be handy to > sometimes see a given sequence aligned to the structure I am looking > at. > > Question to Jason (and the community for feedback): > Would it be possible to write a module that takes one or more > sequences, aligns them to a given structure (or set) that is opened > in PyMOL and shows the aligned sequences in the sequence viewer? This > feature would be very handy for me when evaluating alignments before I > run MODELLER. > > Cheers, > Thomas > > On Tue, May 25, 2010 at 23:13, Ashok Adhikari > wrote: > >> hi, >> >> do u know how to upload a sequence which is not in PDB. we dnt know the name >> of the sequence and we have only 250 residues we can align with the >> other file. we did that and we can upload those sequences from PDB but now >> we need to upload the original sequence. >> >> thanks...in advance. >> >> ashok >> from UNSW >> >> -- >> >> >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> > > -- > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] some help
Hi Ashok, there are several ways to visualise alignments. Here is a nice overview: Visualization of multiple alignments, phylogenies and gene family evolution James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet & Geoffrey J Barton Nature Methods 7, S16 - S25 (2010) http://dx.doi.org/doi:10.1038/nmeth.1434 To address your question, it is not possible to my knowledge to upload a sequence only to PyMOL. Keep in mind that PyMOL is a molecular viewer, not a sequence viewer. If you want to see your sequence, you probably would have to create a 3D model of your sequence (e.g. using MODELLER). However, I think you have an interesting idea. It would be handy to sometimes see a given sequence aligned to the structure I am looking at. Question to Jason (and the community for feedback): Would it be possible to write a module that takes one or more sequences, aligns them to a given structure (or set) that is opened in PyMOL and shows the aligned sequences in the sequence viewer? This feature would be very handy for me when evaluating alignments before I run MODELLER. Cheers, Thomas On Tue, May 25, 2010 at 23:13, Ashok Adhikari wrote: > hi, > > do u know how to upload a sequence which is not in PDB. we dnt know the name > of the sequence and we have only 250 residues we can align with the > other file. we did that and we can upload those sequences from PDB but now > we need to upload the original sequence. > > thanks...in advance. > > ashok > from UNSW > > -- > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] some help
hi, do u know how to upload a sequence which is not in PDB. we dnt know the name of the sequence and we have only 250 residues we can align with the other file. we did that and we can upload those sequences from PDB but now we need to upload the original sequence. thanks...in advance. ashok from UNSW -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Problem with display on Intel graphics card
Hi Timothy, Can you please send me the screenshots. Adaptation to the vagaries of vendor-specific hardware is always an issue. I'm happy to look into the problem. Thanks, -- Jason On Tue, May 25, 2010 at 6:31 PM, Tim Travers wrote: > > Good afternoon, > > Sorry for posting twice, just in case the previous one with attached > screenshots > is too large to be posted. > I've been having problems with color rendering when using PyMOL on a laptop > with an Intel graphics card. This only occurs when used with linux (I've > tested > Fedora 11, Fedora 12, and Ubuntu 10.04), but not when using Windows Vista > on the same laptop. The main problem is that the color rendering for the > stick > drawing method does not work right. > > I can send screenshots if needed. These screenshots use the stick drawing > with > coloring supposed to be by element. But the coloring is not at all done by > element, > instead some regions get clustered by different colors. Just to note, the > coloring > for drawing by line does seem to work fine. > I've googled this for some time now, and couldn't find any resolution. Just > to note, > I also have this problem with VMD's licorice rendering (its version of > stick). Again, > both work fine on Windows but not on the linux distros I've tested so far. > I'm not sure > if this'll be helpful, but here's the output of glxinfo | grep -i opengl: > > OpenGL vendor string: Tungsten Graphics, Inc > OpenGL renderer string: Mesa DRI Intel(R) 965GM GEM 20091221 2009Q4 > OpenGL version string: 2.1 Mesa 7.7.1 > OpenGL shading language version string: 1.20 > > As an aside, I used to have a problem with a flickering display, but this > was fixed by > turning off desktop effects like compiz. For this coloring problem, is there > some > X setting that needs to be maybe tweaked for Intel graphics cards? > > Thanks for any help on this. > > Thanks again, > Timothy > > > > -- > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] PyMOL Print Limitation
Hi All,
I noticed that when I write a script that prints something in PyMOL that there
appears to be a limitation to the continuous length that can be printed to the
external GUI. Here is an example script:
#
from pymol import cmd
def testing ():
out=""
for i in range (300):
out+=str(i)+" "
print out
return
cmd.extend("testing", testing)
##
In this example, my GUI is only able to print the value of "281" before it
inserts a newline character and continues printing. I should note that the
terminal (from where I opened PyMOL) prints everything out correctly.
Anybody know how to resolve this?
Thanks.
Sean
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