Re: [PyMOL] accurate way to change/process b-factor in PDB
Hi João Thanks! it worked fine! >>Just make sure not to have 0.0 bfactors in there! true :) I normalized them by adding 1 to all. Cheers Afonso On Thu, Jul 4, 2013 at 1:13 PM, João Rodrigues wrote: > Hi Afonso, > > PyMOL allows for Python scripting so in principle you could do something > like: > > import math > alter structure, b=math.log(b, 10) > > Just make sure not to have 0.0 bfactors in there! > > Cheers, > > João > > > 2013/7/4 Afonso Duarte > >> Dear All, >> >> >> I have a pdb file composed by several chains where the b-factor column >> was replaced by a physical property of the proteins. I am now trying to >> color according to b-factor and to obtain a better representation of the >> properties described. i.e. I am interested in calculating the log of the >> b-factor and place that value in the b-factor column. >> >> I tried to export this column form the pdb, process it and then import it >> back, but due to the presence of different chains the b-factors got messed >> up. >> >> Would it be possible to do this kind of math operation directly in >> Pymol? >> >> >> Best >> >> >> Afonso >> >> >> -- >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> ___ >> 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 >> > > -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ 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] accurate way to change/process b-factor in PDB
Dear All, I have a pdb file composed by several chains where the b-factor column was replaced by a physical property of the proteins. I am now trying to color according to b-factor and to obtain a better representation of the properties described. i.e. I am interested in calculating the log of the b-factor and place that value in the b-factor column. I tried to export this column form the pdb, process it and then import it back, but due to the presence of different chains the b-factors got messed up. Would it be possible to do this kind of math operation directly in Pymol? Best Afonso -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ 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] how to obtain the values from ramp_new
Deal All, I am using the ramp_new command to obtain a hotspot interaction pattern between 2 proteins (like Surface Colored by Distance from a Point from http://www.pymolwiki.org/index.php/Ramp_New). It works fine but now I want to check the values that originate this coloring in the surface of the protein. I am assuming that they stay in memory (as no file is created in the process). I tried to convert them to b-factors and them remove them from the pdb but without success. Does anybody have a hint/idea that I can try to obtain these values? Best Afonso -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d___ 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] how to create a custom rainbow according to residue number
Hi Thomas, Thanks! indeed it does the job! Cheers Afonso On Tue, Sep 4, 2012 at 3:00 PM, Thomas Holder wrote: > Hi Afonso, > > this should do the job: > http://pymolwiki.org/index.php/Spectrumany > > Example: > PyMOL> run spectrumany.py > PyMOL> spectrumany resi, lime green forest, chain A+C+E > PyMOL> spectrumany resi, lightblue blue density, chain B+D+F > > Hope that helps. > > Cheers, > Thomas > > Afonso Duarte wrote, On 09/04/12 15:15: >> >> Dear All, >> >> I'm using Pymol1.4 in windows and I have a protein build-up by 6 >> domains organized in pairs in an anti-parallel fashion ( i.e. if A and >> V are the domains: AV AV AV) (the domains are structurally homologous >> but the sequence is different). >> >> I want to color the two domains in different colors (i.e. A green and >> V blue) but then I want this colors to be in a gradient according to >> the sequence (i.e. A should be colored from light green to dark green >> and V colored from light blue to dark blue). >> >> As I understood one cannot create new color schemes in the spectrum >> command (if yes I would just color them individually) am i right? >> For that reason I'm thinking of creating a ramp that I would color >> with that color scheme, for this i need to create a selection >> containing the residue number of the residues involved. Is there a way >> to directly create a list of residue number in Pymol ? >> >> Best >> >> Afonso >> >> ### >> Afonso Duarte >> ITQB-UNL >> Portugal > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] how to create a custom rainbow according to residue number
Dear All, I'm using Pymol1.4 in windows and I have a protein build-up by 6 domains organized in pairs in an anti-parallel fashion ( i.e. if A and V are the domains: AV AV AV) (the domains are structurally homologous but the sequence is different). I want to color the two domains in different colors (i.e. A green and V blue) but then I want this colors to be in a gradient according to the sequence (i.e. A should be colored from light green to dark green and V colored from light blue to dark blue). As I understood one cannot create new color schemes in the spectrum command (if yes I would just color them individually) am i right? For that reason I'm thinking of creating a ramp that I would color with that color scheme, for this i need to create a selection containing the residue number of the residues involved. Is there a way to directly create a list of residue number in Pymol ? Best Afonso ####### Afonso Duarte ITQB-UNL Portugal -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] how to change the color of ramps?
Hi Jason, Thanks for the info and lines of script. It did the job :) . Best Afonso On Sun, Sep 18, 2011 at 5:55 AM, Jason Vertrees wrote: > Hi Alfonso, > > PyMOL knows about more spectrum types but cannot take advantage of > them (at this point). You will need to do something different if you > want to use a different palette. It's not hard and here's how. > > I'll adapt that same script using PDB 1HUG. Since you want to color > the distance from all atoms to any given point (here chosen at the > origin=(0,0,0)) we need to get all the atom distances from 1HUG to the > origin. We then put those distances into the b-factor column and > color. I posted the details of the spectrum command and this script on > the PyMOLWiki (http://www.pymolwiki.org/index.php/Spectrum). > > # returns the length of the distance between atom A and atom B > > diff_len = lambda x,y : math.sqrt((x[0]-y[0])*(x[0]-y[0]) + > (x[1]-y[1])*(x[1]-y[1]) + (x[2]-y[2])*(x[2]-y[2])) > > # fetch 1hug from the PDB > > fetch 1hug, async=0 > > # show it as surface > > as surface > > # create the pseudoatom at the origin > > pseudoatom pOrig, pos=(0,0,0), label=origin > > # these are special PyMOL variables that will hold # the coordinates of > # the atoms and the pseudoatom > > stored.origCoord = [] > stored.distCoord = [] > > # copy the coordinates into those special variables > > iterate_state 1, pOrig, stored.origCoord.append((x,y,z)) > iterate_state 1, 1hug, stored.distCoord.append((x,y,z)) > > # extend origCoord to be the same length as the other > > stored.origCoord *= len(stored.distCoord) > > # calculate the distances > > newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord) > > # put them into the b-factor of the protein > > alter 1hug, b=newB.pop(0) > > # color by rainbow_rev or any other > # palette listed in "help spectrum" > > spectrum b, rainbow_rev, 1hug > > Cheers, > > -- Jason > > > On Sat, Sep 17, 2011 at 1:44 PM, Afonso Duarte > wrote: >> Dear All, >> >> I am using the ramp_new command to color the surface of protein A >> according to the distance of protein B (i.e. like in the wiki example >> ramp_new proximityRamp, pOrig, 1hug, range=[5,65], color=rainbow). >> However I would like to color the surface of protein A in the inverse >> rainbow color... from what understood we only can use (afmhot >> grayscale object rainbow traditional grayable hot >> ocean and sludge), >> >> Does anybody have a suggestion on how to change the colors of the ramp >> or just to obtain a reverse rainbow ? >> >> >> Best >> >> Afonso >> >> -- >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> http://p.sf.net/sfu/rim-devcon-copy2 >> ___ >> 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 > -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ 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] how to change the color of ramps?
Dear All, I am using the ramp_new command to color the surface of protein A according to the distance of protein B (i.e. like in the wiki example ramp_new proximityRamp, pOrig, 1hug, range=[5,65], color=rainbow). However I would like to color the surface of protein A in the inverse rainbow color... from what understood we only can use (afmhot grayscaleobject rainbow traditional grayable hot ocean and sludge), Does anybody have a suggestion on how to change the colors of the ramp or just to obtain a reverse rainbow ? Best Afonso -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA http://p.sf.net/sfu/rim-devcon-copy2 ___ 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 when running APBS 1.1.0 in Pymol 1.3 - protein is misplaced
> Dear All, > > I am running APBS 1.1.0. via the "APBS Tools2" plugin on Pymol 1.3 (either on > Linux or Vista). > As usual i fetch a pdb structure and then do a "set grid" and then "run APBS". > This works fine for most of the proteins I am working on, however I found out > that in some of the pdbs (downloaded directly from the PDB databank) I get > half of the protein outside of the box (pymol_generated). This leads to the > calculation of only half of the electrostatics of the molecule... > I am sending in attach a pic of what I get in my screen... > does any body know how to solve this problem ? > Best > > Afonso > > -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ 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] Strange pattern on the cartoon representation
That's exactly what I just found out! Thanks! but I don't understand why sometimes it happens and other times it does not happen. Cheers Afonso On Tue, May 18, 2010 at 4:17 PM, Matthew Franklin < matthew.frank...@imclone.com> wrote: > I suspect Afonso's talking about a moire / halftone dot pattern like the > one at this link: > > http://www.uvm.edu/~hag/presentations/maze2004/moire.html<http://www.uvm.edu/%7Ehag/presentations/maze2004/moire.html> > > I have no idea what would cause this, but if you have two identical copies > of a molecule, in the same representation, strange things can happen. For > example: > > load myprotein.pdb > hide everything > show cartoon > show spheres, residue 100 > create myproteincopy, myprotein > ray > > Sure enough, this creates a very odd speckled pattern on the raytraced > cartoon surface, but not on the spheres. It's not really a regular moire > pattern, but it could be considered a "newspaper pattern". > > So, Afonso, I think this is the culprit. Somewhere before you did your > raytracing, you set up two identical objects, which are both visible at > once. Try turning off the visibility of one of these (by clicking on its > name in the list in the PyMOL viewer) and the effect should go away. > > Hope that helps, > > Matt > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems, > a wholly owned subsidiary of Eli Lilly & Company > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > > -Original Message- > > From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] > > Sent: Tuesday, May 18, 2010 6:54 AM > > To: Afonso Duarte > > Cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Strange pattern on the cartoon representation > > > > Hi Afonso, > > > > Can you tell which newspaper? And does it show the date? :) > > Seriously, it's difficult to make out more, unless you give more > > information, like a link to the image, or the series of commands you > > used to get to the point you're at. What you describe might be caused > > by two interfering surfaces,e.g., trying to show two times the same > > thing as cartoon. > > > > Cheers, > > > > Tsjerk > > > > On Tue, May 18, 2010 at 12:42 PM, Afonso Duarte > > wrote: > > > Dear All, > > > > > > I am making some figures using ray. When the processing is finished I > > get a > > > strange pattern (like newspaper paper pattern) in my cartoon > > > representations, Spheres and sticks representations are OK only the > > cartoon. > > > I have tried to change the options on the cartoon representation but > > without > > > any sucess. > > > > > > Did any body had such problem before? > > > > > > Best > > > > > > Afonso > > > > > > - > > - > > > > > > > > > ___ > > > 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- > > us...@lists.sourceforge.net > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > > post-doctoral researcher > > Molecular Dynamics Group > > Groningen Institute for Biomolecular Research and Biotechnology > > University of Groningen > > The Netherlands > > > > --- > > --- > > > > ___ > > 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 > Confidentiality Note: > This e-mail, and any attachment to it, contains privileged and confidential > information intended only for the use of the individual(s) or entity named > on the e-mail. If the reader of this e-mail is not the intended recipient, > or the employee or agent responsible for delivering it to the intended > recipient, you are hereby notified that reading it is strictly prohibited. > If you have received this e-mail in error, please immediately return it to > the sender and delete it from your system. > > Thank you. > > -- ___ 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] Strange pattern on the cartoon representation
Hi Tsjerk, I found the reason of the problem. It wasn't a texture error (I checked that before) but for some strange reason if I have the same molecule loaded twice in cartoon with 40% gray and if both are visible I will get that effect. PS : the reason why I have the same pdb open is make it easier to select things). Thanks for the feed back! Cheers Afonso On Tue, May 18, 2010 at 2:17 PM, Tsjerk Wassenaar wrote: > Hi Afonso, > > I haven't seen this before. It seems to be a different texture. Did > you touch any of the settings (like ray_texture)? Surely you didn't > just use 'ray' after you loaded the structure. It wouldn't have shown > up as cartoon to begin with. If you give the full set of commands you > used, it will probably allow us to pinpoint the cause of a newspaper > being printed on your protein :) > > (oh, and use reply-to-all to keep the discussion on the list :)) > > Cheers, > > Tsjerk > > On Tue, May 18, 2010 at 1:04 PM, Afonso Duarte > wrote: > > Hi Tsjerk, > > > > You are completely right ... I should have included an example. > > This picture was made with > > ray 1200,1200 > > then saved as a png > > I also tried only ray and other values but no luck, I thought it could be > > memory problems but restarting also did not fixed it. > > > > Cheers > > > > Afonso > > > > On Tue, May 18, 2010 at 12:53 PM, Tsjerk Wassenaar > > wrote: > >> > >> Hi Afonso, > >> > >> Can you tell which newspaper? And does it show the date? :) > >> Seriously, it's difficult to make out more, unless you give more > >> information, like a link to the image, or the series of commands you > >> used to get to the point you're at. What you describe might be caused > >> by two interfering surfaces,e.g., trying to show two times the same > >> thing as cartoon. > >> > >> Cheers, > >> > >> Tsjerk > >> > >> On Tue, May 18, 2010 at 12:42 PM, Afonso Duarte < > afonsomdua...@gmail.com> > >> wrote: > >> > Dear All, > >> > > >> > I am making some figures using ray. When the processing is finished I > >> > get a > >> > strange pattern (like newspaper paper pattern) in my cartoon > >> > representations, Spheres and sticks representations are OK only the > >> > cartoon. > >> > I have tried to change the options on the cartoon representation but > >> > without > >> > any sucess. > >> > > >> > Did any body had such problem before? > >> > > >> > Best > >> > > >> > Afonso > >> > > >> > > >> > > -- > >> > > >> > > >> > ___ > >> > 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 > >> > > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> post-doctoral researcher > >> Molecular Dynamics Group > >> Groningen Institute for Biomolecular Research and Biotechnology > >> University of Groningen > >> The Netherlands > > > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > -- ___ 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] Strange pattern on the cartoon representation
Dear All, I am making some figures using ray. When the processing is finished I get a strange pattern (like newspaper paper pattern) in my cartoon representations, Spheres and sticks representations are OK only the cartoon. I have tried to change the options on the cartoon representation but without any sucess. Did any body had such problem before? Best Afonso -- ___ 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] how to create a new .pdb from 3 pdb's?
Hi Tsjerk, It did work! Thanks! Afonso On Sun, Mar 28, 2010 at 7:05 PM, Tsjerk Wassenaar wrote: > Hi Afonso, > > If you want to connect one object to another, you want to check out > the fuse command (help fuse) > > fuse atom_to_be_connected_from_object1, atom_to_be_connected_from_object2 > > Hope it helps, > > Tsjerk > > On Sun, Mar 28, 2010 at 4:33 PM, Afonso Duarte > wrote: >> Dear All, >> >> I want to create molecule in Pymol by combining 3 different pdbs. >> Two of them are form the pdb data bank and one was created via pymol. >> I have the 3 of them open in pymol but now I am trying to figure out >> how to connect the termini of the polypeptides in pymol. >> >> I searched the wiki/manuals and the web but could not find a way how >> to do it. Is it possible to do it using pymol? if yes what are the >> commands to do so ? >> >> Thanks! >> >> Best >> >> Afonso >> >> -- >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> ___ >> 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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] how to create a new .pdb from 3 pdb's?
Dear All, I want to create molecule in Pymol by combining 3 different pdbs. Two of them are form the pdb data bank and one was created via pymol. I have the 3 of them open in pymol but now I am trying to figure out how to connect the termini of the polypeptides in pymol. I searched the wiki/manuals and the web but could not find a way how to do it. Is it possible to do it using pymol? if yes what are the commands to do so ? Thanks! Best Afonso -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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
