Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color
Hi Adam, this seems to be not yet fully implemented with the new shader rendering. So you may turn shaders off for now: PyMOL unset use_shaders Ray tracing is not affected, so you still can generate high quality figures with correct colors: PyMOL ray Hope that helps. Cheers, Thomas H. Adam Steinberg wrote, On 11/20/12 03:40: Hi all, If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? --- set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapA - Thanks in advance for the help! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Peptide location mapping onto protein 3D structure
Hi Sri,
if you have your structure loaded into PyMOL, you can make named
selections for your peptide sequences like this:
select pep1, pepseq RMFLS
select pep2, pepseq KGHGK
select pep3, pepseq ALSDL
There are also scripts available for pattern matching, for example:
http://pymolwiki.org/index.php/FindSeq
Highlighting the selections with colors:
color white
color red, pep1
color blue, pep2
color green, pep3
You can query these selections on various properties:
# (approximate) surface area
set dot_solvent
get_area pep1
# secondary structure
print [a.ss for a in cmd.get_model('pep1 and name CA').atom]
Doing this on a large number of structures is possible if you write a
python script, which requires general programming skills. All the
commands shown above are accessible from the PyMOL python API. Examples:
from pymol import cmd
cmd.select('pep1', 'pepseq RMFLS')
cmd.color('red', 'pep1')
print cmd.get_area('pep1')
Hope that helps.
Cheers,
Thomas
Sri Ramarathinam wrote, On 11/22/12 08:16:
Hi All
I am very new to using Pymol. I am wondering if anyone can point me towards
the right direction with the following:
1) I have a list of peptides and would like to know what their location is on
their respective proteins which already have structures in PDB (surface
exposed, buried, helix, loop or beta sheet?)
I guess I could do it manually but the peptide list could go into
hundreds and would be nice to see if there a command line or a script I could
use.
2) Can i ask Pymol to show the peptide's location on the 3d structure of the
protein? perhaps in a different colour to highlight location?
Manually I would select on the sequence and show as whatever I want but
is there a command to automate a huge list?
Is it possible to do these tasks with Pymol or is there any other software I
could be using?
Thanks very much for your help,
Cheers
Sri
--
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PyMOL Developer
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Re: [PyMOL] Controlling colors in volume object
Hi Per, you may check the volume_esp function here: https://github.com/speleo3/pymol-psico/blob/master/psico/electrostatics.py As Jason said in that earlier thread, the volume API is work in progress and will probably change soon. Cheers, Thomas Per Larsson wrote, On 11/21/12 19:01: Following up myself on this. I did some more digging on Google, and putting together bits and pieces this is what I have currently. It works, but does not (yet) allow me to scale the colors according to eg. the max and min values of my density (which I do not know how to access). I guess that means I have a new question about accessing details about the density-object. Thanks /Per load density.dx, d cmd.volume(density,d,1.0) bg_color white from pmg_tk.skins.normal.ColorRampModel import ColorRamp r = ColorRamp(nColors=256) r.addColor(0,(0,0,0,0),0) r.addColor(2,(0.39,0.67,1,0.01),0) r.addColor(130,(0,1,0.50,0.25),0) r.addColor(192,(1,0.0,0.0,0.25),0) r.addColor(255,(1,0,0,0.25),0) ramp_colors = r.getRamp() cmd.volume_color(density,ramp_colors) 21 nov 2012 kl. 17:30 skrev Per Larsson: Hi pymol-users I have previously been able to make quite nice visualizations of my volume object, containing the time-averaged density of atoms from a MD-simulation. For making even more improvement, I'd like to be able to use a script (either python or pml) to control which regions of density gets which color. I've found this thread http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10294.html that suggests it to be possible, but understanding how to use that for my case is unfortunately (yet) a bit beyond my current pymol-skills. Ideally I would want to have a solution that allows me to load in my volume-file (in .dx format), assign colors to different regions of density systematically (the Volume-GUI is great, but somewhat tricky to make quick changes with), and display the result on screen. Is such a thing possible? Thanks /Per -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] assigning secondary strux to artificial AAs
Hi Jonny, I think it should be sufficient to have the atom names along the backbone correct (CA, N, C) and to have increasing residue numbering. If you like you can send me your file and I'll have a look. Cheers, Thomas Johnny Pham wrote, On 11/15/12 09:41: Hi, I was wondering if I have unnatural amino acids in beta sheet mimicking peptides, is there a way to have them show up as a beta sheet in the cartoon representation? I understand the code: alter 1-11/, ss='S' as an example of assigning residues 1-11 as a beta sheet but how do I tackle artificial amino acids. Thanks! -Johnny -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] MacPyMOL 1.4 vs 1.5 problem with color
Thanks Thomas, that does work. On Nov 23, 2012, at 6:31 AM, Thomas Holder wrote: Hi Adam, this seems to be not yet fully implemented with the new shader rendering. So you may turn shaders off for now: PyMOL unset use_shaders Ray tracing is not affected, so you still can generate high quality figures with correct colors: PyMOL ray Hope that helps. Cheers, Thomas H. Adam Steinberg wrote, On 11/20/12 03:40: Hi all, If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? --- set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapA - Thanks in advance for the help! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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
