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From: Honegger A. <hon...@bi...> - 2016-04-26 09:31:39
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Hi Adam This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work. best regards Annemarie _______________________________ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: hon...@bi... websites http://www.bioc.uzh.ch/plueckthun http://www.bioc.uzh.ch/plueckthun/antibody http://www.bioc.uzh.ch/plueckthun/nanowelt > > > Message: 6 > Date: Mon, 25 Apr 2016 20:54:01 -0500 > From: harold steinberg <h.a...@gm...> > Subject: [PyMOL] morph issues > To: pymol-users <pym...@li...> > Message-ID: <0E8...@gm...> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine. > > In the structures that do not morph correctly a sample selection is: > /3j5r/A/B/ILE`573/CD1 > /3j5q/C/E/ILE`573/CD1 > > Notice that these files have an extra letter (?A? and ?C? before the chain identifier). > > In files that the morph does work this letter is missing (it?s a blank space): > /3lut//D/GLY`338/CA > > Is that what is messing up the morph? > > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 119, Issue 16 > ******************************************** |
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From: harold s. <h.a...@gm...> - 2016-04-26 11:16:25
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Hi Annemarie, Thank you for the answer. Do you know the command to remove the alternative conformation? > On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote: > > Hi Adam > > This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the > atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work. > > best regards > > Annemarie > _______________________________ > > Dr. Annemarie Honegger PhD > Department > of Biochemistry > Zürich University > Winterthurerstrasse 190 > CH-8057 Zürich > Switzerland > > e-Mail: hon...@bi... > > websites > http://www.bioc.uzh.ch/plueckthun > http://www.bioc.uzh.ch/plueckthun/antibody > http://www.bioc.uzh.ch/plueckthun/nanowelt > > > > > >> >> >> Message: 6 >> Date: Mon, 25 Apr 2016 20:54:01 -0500 >> From: harold steinberg <h.a...@gm...> >> Subject: [PyMOL] morph issues >> To: pymol-users <pym...@li...> >> Message-ID: <0E8...@gm...> >> Content-Type: text/plain; charset="utf-8" >> >> Hi all, >> >> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine. >> >> In the structures that do not morph correctly a sample selection is: >> /3j5r/A/B/ILE`573/CD1 >> /3j5q/C/E/ILE`573/CD1 >> >> Notice that these files have an extra letter (?A? and ?C? before the chain identifier). >> >> In files that the morph does work this letter is missing (it?s a blank space): >> /3lut//D/GLY`338/CA >> >> Is that what is messing up the morph? >> >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> Find and fix application performance issues faster with Applications Manager >> Applications Manager provides deep performance insights into multiple tiers of >> your business applications. It resolves application problems quickly and >> reduces your MTTR. Get your free trial! >> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >> >> ------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest, Vol 119, Issue 16 >> ******************************************** > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
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From: harold s. <h.a...@gm...> - 2016-04-26 11:21:42
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I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session. > On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote: > > Hi Annemarie, > > Thank you for the answer. Do you know the command to remove the alternative conformation? > > >> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote: >> >> Hi Adam >> >> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the >> atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work. >> >> best regards >> >> Annemarie >> _______________________________ >> >> Dr. Annemarie Honegger PhD >> Department >> of Biochemistry >> Zürich University >> Winterthurerstrasse 190 >> CH-8057 Zürich >> Switzerland >> >> e-Mail: hon...@bi... >> >> websites >> http://www.bioc.uzh.ch/plueckthun >> http://www.bioc.uzh.ch/plueckthun/antibody >> http://www.bioc.uzh.ch/plueckthun/nanowelt >> >> >> >> >> >>> >>> >>> Message: 6 >>> Date: Mon, 25 Apr 2016 20:54:01 -0500 >>> From: harold steinberg <h.a...@gm...> >>> Subject: [PyMOL] morph issues >>> To: pymol-users <pym...@li...> >>> Message-ID: <0E8...@gm...> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi all, >>> >>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine. >>> >>> In the structures that do not morph correctly a sample selection is: >>> /3j5r/A/B/ILE`573/CD1 >>> /3j5q/C/E/ILE`573/CD1 >>> >>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier). >>> >>> In files that the morph does work this letter is missing (it?s a blank space): >>> /3lut//D/GLY`338/CA >>> >>> Is that what is messing up the morph? >>> >>> >>> H. Adam Steinberg >>> 7904 Bowman Rd >>> Lodi, WI 53555 >>> 608/592-2366 >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> >>> ------------------------------ >>> >>> ------------------------------------------------------------------------------ >>> Find and fix application performance issues faster with Applications Manager >>> Applications Manager provides deep performance insights into multiple tiers of >>> your business applications. It resolves application problems quickly and >>> reduces your MTTR. Get your free trial! >>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>> >>> End of PyMOL-users Digest, Vol 119, Issue 16 >>> ******************************************** >> >> >> ------------------------------------------------------------------------------ >> Find and fix application performance issues faster with Applications Manager >> Applications Manager provides deep performance insights into multiple tiers of >> your business applications. It resolves application problems quickly and >> reduces your MTTR. Get your free trial! >> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
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From: harold s. <h.a...@gm...> - 2016-04-26 12:24:55
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When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command. Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other. I have tried it all the ways I can think of, I tried all possible combinations. These are .cif files not .pdb files. No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay. > On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote: > > Yes, you want to keep atoms that have no alternative conformation (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation, > therefore you specify: > > remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors <http://www.pymolwiki.org/index.php/Property_Selectors> , bottom of page > > best regards > > Annemarie > > _______________________________ > > Dr. Annemarie Honegger PhD > Department > of Biochemistry > Zürich University > Winterthurerstrasse 190 > CH-8057 Zürich > Switzerland > > e-Mail: hon...@bi... <mailto:hon...@bi...> > > websites > http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun> > http://www.bioc.uzh.ch/plueckthun/antibody <http://www.bioc.uzh.ch/plueckthun/antibody> > http://www.bioc.uzh.ch/plueckthun/nanowelt <http://www.bioc.uzh.ch/plueckthun/nanowelt> > > > > > > >> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote: >> >> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session. >> >> >>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote: >>> >>> Hi Annemarie, >>> >>> Thank you for the answer. Do you know the command to remove the alternative conformation? >>> >>> >>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote: >>>> >>>> Hi Adam >>>> >>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the >>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work. >>>> >>>> best regards >>>> >>>> Annemarie >>>> _______________________________ >>>> >>>> Dr. Annemarie Honegger PhD >>>> Department >>>> of Biochemistry >>>> Zürich University >>>> Winterthurerstrasse 190 >>>> CH-8057 Zürich >>>> Switzerland >>>> >>>> e-Mail: hon...@bi... <mailto:hon...@bi...> >>>> >>>> websites >>>> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun> >>>> http://www.bioc.uzh.ch/plueckthun/antibody >>>> http://www.bioc.uzh.ch/plueckthun/nanowelt >>>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> Message: 6 >>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500 >>>>> From: harold steinberg <h.a...@gm...> >>>>> Subject: [PyMOL] morph issues >>>>> To: pymol-users <pym...@li...> >>>>> Message-ID: <0E8...@gm...> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> Hi all, >>>>> >>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine. >>>>> >>>>> In the structures that do not morph correctly a sample selection is: >>>>> /3j5r/A/B/ILE`573/CD1 >>>>> /3j5q/C/E/ILE`573/CD1 >>>>> >>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier). >>>>> >>>>> In files that the morph does work this letter is missing (it?s a blank space): >>>>> /3lut//D/GLY`338/CA >>>>> >>>>> Is that what is messing up the morph? >>>>> >>>>> >>>>> H. Adam Steinberg >>>>> 7904 Bowman Rd >>>>> Lodi, WI 53555 >>>>> 608/592-2366 >>>>> >>>>> -------------- next part -------------- >>>>> An HTML attachment was scrubbed... >>>>> >>>>> ------------------------------ >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Find and fix application performance issues faster with Applications Manager >>>>> Applications Manager provides deep performance insights into multiple tiers of >>>>> your business applications. It resolves application problems quickly and >>>>> reduces your MTTR. Get your free trial! >>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >>>>> >>>>> ------------------------------ >>>>> >>>>> _______________________________________________ >>>>> PyMOL-users mailing list >>>>> PyM...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> >>>>> >>>>> End of PyMOL-users Digest, Vol 119, Issue 16 >>>>> ******************************************** >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Find and fix application performance issues faster with Applications Manager >>>> Applications Manager provides deep performance insights into multiple tiers of >>>> your business applications. It resolves application problems quickly and >>>> reduces your MTTR. Get your free trial! >>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >>>> _______________________________________________ >>>> PyMOL-users mailing list (PyM...@li...) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pym...@li... >>> >>> H. Adam Steinberg >>> 7904 Bowman Rd >>> Lodi, WI 53555 >>> 608/592-2366 >>> >> >> H. Adam Steinberg >> 7904 Bowman Rd >> Lodi, WI 53555 >> 608/592-2366 >> > H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
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From: Honegger A. <hon...@bi...> - 2016-04-26 13:17:01
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OK, after some trial and error I have found out a way that works. The two structures have the corresponding chains in different orders and with different chain labels: You can copy-paste the following commands into Pymol to follow that I did: #-------------------------------------------------------------------------------------------------------------------------------- # get the structures from the pdb: load http://www.rcsb.org/pdb/files/3j5r.pdb load http://www.rcsb.org/pdb/files/3j5q.pdb hide all show ribbon util.cbc # chain labels are not the same in both molecules, # chain A in 3j5r corresponds to chain B in 3j5q, B to E, C to D, D to G # chains A,C,F and A in 3j5q are additional small domains of unknown sequence # the order in the pdb file is B-A-C-D for 3j5r and D-B-E-G in 3j5q # additional "UNK" residues in 3j5q confuse the issue remove resn UNK # morphing a single chain, /3j5r//A to /3j5q//B create objA, /3j5r//A create objB, /3j5q//B morph objC, objA, objB # this works!!! delete objA objB objC #----------------------------------- # now all 4 chains: if I do morph objD, 3j5r, 3j5q # the wrong chains morph into each other delete objD #----------------------------------- # give corresponding chains the same chain label alter /3j5q//B, chain="A" alter /3j5q//E, chain="B" alter /3j5q//D, chain="C" alter /3j5q//G, chain="D" util.cbc morph objE, 3j5r, 3j5q # to change the chain identifiers is not enough!!! delete objE #----------------------------------- # is it possible to take objects apart and put them back to extract 3j5rA, /3j5r//A extract 3j5rB, /3j5r//B extract 3j5rC, /3j5r//C extract 3j5rD, /3j5r//D delete 3j5r extract 3j5qA, /3j5q//A extract 3j5qB, /3j5q//B extract 3j5qC, /3j5q//C extract 3j5qD, /3j5q//D delete 3j5q create 3j5r, 3j5rA or 3j5rB or 3j5rC or 3j5rD create 3j5q, 3j5qA or 3j5qB or 3j5qC or 3j5qD morph objF, 3j5r, 3j5q # still something strange happening, I am loosing atoms in chain B and D delete objF #----------------------------------- morph objG, 3j5rA, 3j5qA morph objH, 3j5rB, 3j5qB morph objI, 3j5rC, 3j5qC morph objJ, 3j5rD, 3j5qD # OK, this works #-------------------------------------------------------------------------------------------------------------------------------- although I do not understand haow you managed to get segment identifiers into your selections best regards Annemarie _______________________________ Dr. Annemarie Honegger PhD Department of Biochemistry Zürich University Winterthurerstrasse 190 CH-8057 Zürich Switzerland e-Mail: hon...@bi... websites http://www.bioc.uzh.ch/plueckthun http://www.bioc.uzh.ch/plueckthun/antibody http://www.bioc.uzh.ch/plueckthun/nanowelt > On 26 Apr 2016, at 14:24, harold steinberg <h.a...@gm...> wrote: > > When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command. > > Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other. I have tried it all the ways I can think of, I tried all possible combinations. > > These are .cif files not .pdb files. > > No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay. > >> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote: >> >> Yes, you want to keep atoms that have no alternative conformation (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation, >> therefore you specify: >> >> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors <http://www.pymolwiki.org/index.php/Property_Selectors> , bottom of page >> >> best regards >> >> Annemarie >> >> _______________________________ >> >> Dr. Annemarie Honegger PhD >> Department >> of Biochemistry >> Zürich University >> Winterthurerstrasse 190 >> CH-8057 Zürich >> Switzerland >> >> e-Mail: hon...@bi... <mailto:hon...@bi...> >> >> websites >> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun> >> http://www.bioc.uzh.ch/plueckthun/antibody <http://www.bioc.uzh.ch/plueckthun/antibody> >> http://www.bioc.uzh.ch/plueckthun/nanowelt <http://www.bioc.uzh.ch/plueckthun/nanowelt> >> >> >> >> >> >> >>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote: >>> >>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session. >>> >>> >>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote: >>>> >>>> Hi Annemarie, >>>> >>>> Thank you for the answer. Do you know the command to remove the alternative conformation? >>>> >>>> >>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote: >>>>> >>>>> Hi Adam >>>>> >>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the >>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work. >>>>> >>>>> best regards >>>>> >>>>> Annemarie >>>>> _______________________________ >>>>> >>>>> Dr. Annemarie Honegger PhD >>>>> Department >>>>> of Biochemistry >>>>> Zürich University >>>>> Winterthurerstrasse 190 >>>>> CH-8057 Zürich >>>>> Switzerland >>>>> >>>>> e-Mail: hon...@bi... <mailto:hon...@bi...> >>>>> >>>>> websites >>>>> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun> >>>>> http://www.bioc.uzh.ch/plueckthun/antibody <http://www.bioc.uzh.ch/plueckthun/antibody> >>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> Message: 6 >>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500 >>>>>> From: harold steinberg <h.a...@gm...> >>>>>> Subject: [PyMOL] morph issues >>>>>> To: pymol-users <pym...@li...> >>>>>> Message-ID: <0E8...@gm...> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine. >>>>>> >>>>>> In the structures that do not morph correctly a sample selection is: >>>>>> /3j5r/A/B/ILE`573/CD1 >>>>>> /3j5q/C/E/ILE`573/CD1 >>>>>> >>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier). >>>>>> >>>>>> In files that the morph does work this letter is missing (it?s a blank space): >>>>>> /3lut//D/GLY`338/CA >>>>>> >>>>>> Is that what is messing up the morph? >>>>>> >>>>>> >>>>>> H. Adam Steinberg >>>>>> 7904 Bowman Rd >>>>>> Lodi, WI 53555 >>>>>> 608/592-2366 >>>>>> >>>>>> -------------- next part -------------- >>>>>> An HTML attachment was scrubbed... >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Find and fix application performance issues faster with Applications Manager >>>>>> Applications Manager provides deep performance insights into multiple tiers of >>>>>> your business applications. It resolves application problems quickly and >>>>>> reduces your MTTR. Get your free trial! >>>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> PyMOL-users mailing list >>>>>> PyM...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>>> >>>>>> >>>>>> End of PyMOL-users Digest, Vol 119, Issue 16 >>>>>> ******************************************** >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Find and fix application performance issues faster with Applications Manager >>>>> Applications Manager provides deep performance insights into multiple tiers of >>>>> your business applications. It resolves application problems quickly and >>>>> reduces your MTTR. Get your free trial! >>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >>>>> _______________________________________________ >>>>> PyMOL-users mailing list (PyM...@li...) >>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>>> Archives: http://www.mail-archive.com/pym...@li... >>>> >>>> H. Adam Steinberg >>>> 7904 Bowman Rd >>>> Lodi, WI 53555 >>>> 608/592-2366 >>>> >>> >>> H. Adam Steinberg >>> 7904 Bowman Rd >>> Lodi, WI 53555 >>> 608/592-2366 >>> >> > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > |
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From: Thomas H. <tho...@sc...> - 2016-04-26 13:14:25
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Hi Adam and Annemarie,
There are no alt location in these files. In the slash notation, the second item is the segment identifier, which for mmCIF files in the label_asym_id field (the third item, chain, is the auth_asym_id field). For this example, the label_asym_id (segi) should be easier to match up between the two structures than the auth_asym_id (chain).
# To illustrate the arrangement of label_asym_ids:
fetch 3j5r 3j5q, async=0
as ribbon
set grid_mode
spectrum segi
label guide and resn ALA, segi
set_view (\
-0.985940218, -0.146149188, -0.081017971,\
0.152838722, -0.984706044, -0.083635844,\
-0.067555539, -0.094843410, 0.993197739,\
0.000000000, 0.000000000, -619.393493652,\
0.042427063, -0.005607605, 6.552642822,\
516.705444336, 722.081604004, -20.000000000 )
# So I would swap segi A and C for one of the structures to bring
# the chains into the same order. The chain identifier (third item in
# slash notation) doesn't affect sorting in this case, since the segi
# has higher priority.
stored.remap = {'A': 'C', 'C': 'A'}
alter 3j5q, segi = stored.remap.get(segi, segi)
sort
# illustrate that the order is the same now:
spectrum segi
label guide and resn ALA, segi
# Now the morphing should work as expected:
morph mout, 3j5r, 3j5q, refinement=0
Hope that helps.
See also:
http://pymolwiki.org/index.php/Selection_Macros
Cheers,
Thomas
On 26 Apr 2016, at 08:24, harold steinberg <h.a...@gm...> wrote:
> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
>
> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other. I have tried it all the ways I can think of, I tried all possible combinations.
>
> These are .cif files not .pdb files.
>
> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
>
>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
>>
>> Yes, you want to keep atoms that have no alternative conformation (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>> therefore you specify:
>>
>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors , bottom of page
>>
>> best regards
>>
>> Annemarie
>>
>> _______________________________
>>
>> Dr. Annemarie Honegger PhD
>> Department
>> of Biochemistry
>> Zürich University
>> Winterthurerstrasse 190
>> CH-8057 Zürich
>> Switzerland
>>
>> e-Mail: hon...@bi...
>>
>> websites
>> http://www.bioc.uzh.ch/plueckthun
>> http://www.bioc.uzh.ch/plueckthun/antibody
>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>
>>
>>
>>
>>
>>
>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm...> wrote:
>>>
>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>>
>>>
>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
>>>>
>>>> Hi Annemarie,
>>>>
>>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>>>
>>>>
>>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
>>>>>
>>>>> Hi Adam
>>>>>
>>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the
>>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>>>
>>>>> best regards
>>>>>
>>>>> Annemarie
>>>>> _______________________________
>>>>>
>>>>> Dr. Annemarie Honegger PhD
>>>>> Department
>>>>> of Biochemistry
>>>>> Zürich University
>>>>> Winterthurerstrasse 190
>>>>> CH-8057 Zürich
>>>>> Switzerland
>>>>>
>>>>> e-Mail: hon...@bi...
>>>>>
>>>>> websites
>>>>> http://www.bioc.uzh.ch/plueckthun
>>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> Message: 6
>>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>>> From: harold steinberg <h.a...@gm...>
>>>>>> Subject: [PyMOL] morph issues
>>>>>> To: pymol-users <pym...@li...>
>>>>>> Message-ID: <0E8...@gm...>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>>>
>>>>>> In the structures that do not morph correctly a sample selection is:
>>>>>> /3j5r/A/B/ILE`573/CD1
>>>>>> /3j5q/C/E/ILE`573/CD1
>>>>>>
>>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>>>
>>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>>> /3lut//D/GLY`338/CA
>>>>>>
>>>>>> Is that what is messing up the morph?
>>>>
>>>> H. Adam Steinberg
>>>> 7904 Bowman Rd
>>>> Lodi, WI 53555
>>>> 608/592-2366
>>>>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|
|
From: harold s. <h.a...@gm...> - 2016-04-26 15:20:40
|
Thank you both for taking the time to work this out, and explain how and why it works!
> On Apr 26, 2016, at 8:14 AM, Thomas Holder <tho...@sc...> wrote:
>
> Hi Adam and Annemarie,
>
> There are no alt location in these files. In the slash notation, the second item is the segment identifier, which for mmCIF files in the label_asym_id field (the third item, chain, is the auth_asym_id field). For this example, the label_asym_id (segi) should be easier to match up between the two structures than the auth_asym_id (chain).
>
> # To illustrate the arrangement of label_asym_ids:
>
> fetch 3j5r 3j5q, async=0
> as ribbon
> set grid_mode
> spectrum segi
> label guide and resn ALA, segi
> set_view (\
> -0.985940218, -0.146149188, -0.081017971,\
> 0.152838722, -0.984706044, -0.083635844,\
> -0.067555539, -0.094843410, 0.993197739,\
> 0.000000000, 0.000000000, -619.393493652,\
> 0.042427063, -0.005607605, 6.552642822,\
> 516.705444336, 722.081604004, -20.000000000 )
>
> # So I would swap segi A and C for one of the structures to bring
> # the chains into the same order. The chain identifier (third item in
> # slash notation) doesn't affect sorting in this case, since the segi
> # has higher priority.
>
> stored.remap = {'A': 'C', 'C': 'A'}
> alter 3j5q, segi = stored.remap.get(segi, segi)
> sort
>
> # illustrate that the order is the same now:
>
> spectrum segi
> label guide and resn ALA, segi
>
> # Now the morphing should work as expected:
>
> morph mout, 3j5r, 3j5q, refinement=0
>
> Hope that helps.
>
> See also:
> http://pymolwiki.org/index.php/Selection_Macros
>
> Cheers,
> Thomas
>
> On 26 Apr 2016, at 08:24, harold steinberg <h.a...@gm...> wrote:
>
>> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
>>
>> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other. I have tried it all the ways I can think of, I tried all possible combinations.
>>
>> These are .cif files not .pdb files.
>>
>> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
>>
>>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
>>>
>>> Yes, you want to keep atoms that have no alternative conformation (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>>> therefore you specify:
>>>
>>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors , bottom of page
>>>
>>> best regards
>>>
>>> Annemarie
>>>
>>> _______________________________
>>>
>>> Dr. Annemarie Honegger PhD
>>> Department
>>> of Biochemistry
>>> Zürich University
>>> Winterthurerstrasse 190
>>> CH-8057 Zürich
>>> Switzerland
>>>
>>> e-Mail: hon...@bi...
>>>
>>> websites
>>> http://www.bioc.uzh.ch/plueckthun
>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm...> wrote:
>>>>
>>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>>>
>>>>
>>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
>>>>>
>>>>> Hi Annemarie,
>>>>>
>>>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>>>>
>>>>>
>>>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
>>>>>>
>>>>>> Hi Adam
>>>>>>
>>>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the
>>>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>>>>
>>>>>> best regards
>>>>>>
>>>>>> Annemarie
>>>>>> _______________________________
>>>>>>
>>>>>> Dr. Annemarie Honegger PhD
>>>>>> Department
>>>>>> of Biochemistry
>>>>>> Zürich University
>>>>>> Winterthurerstrasse 190
>>>>>> CH-8057 Zürich
>>>>>> Switzerland
>>>>>>
>>>>>> e-Mail: hon...@bi...
>>>>>>
>>>>>> websites
>>>>>> http://www.bioc.uzh.ch/plueckthun
>>>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Message: 6
>>>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>>>> From: harold steinberg <h.a...@gm...>
>>>>>>> Subject: [PyMOL] morph issues
>>>>>>> To: pymol-users <pym...@li...>
>>>>>>> Message-ID: <0E8...@gm...>
>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>>>>
>>>>>>> In the structures that do not morph correctly a sample selection is:
>>>>>>> /3j5r/A/B/ILE`573/CD1
>>>>>>> /3j5q/C/E/ILE`573/CD1
>>>>>>>
>>>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>>>>
>>>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>>>> /3lut//D/GLY`338/CA
>>>>>>>
>>>>>>> Is that what is messing up the morph?
>>>>>
>>>>> H. Adam Steinberg
>>>>> 7904 Bowman Rd
>>>>> Lodi, WI 53555
>>>>> 608/592-2366
>>>>>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
|
|
From: Leonhard H. <Leo...@ur...> - 2016-12-01 12:40:58
|
I guess formatting didn't work out as i expected. So once again and
hopefully formatted:
Hi!
I stumbled upon some odd behavior when starting PyMol in an interactive
IPython Session.
PyMol can be launched from interactive IPython like this:
In [1]: import pymol
In [2]: from pymol import cmd
In [3]: pymol.finish_launching()
In [4]: cmd.fetch("1xyz")
So far, everything is normal.
However, when I want to get the coordinates of the structure the
following happens:
In [5]: cmd.get_coords("1xyz")
Out[5]:
array([[ 41., 25., 36.],
[ 40., 25., 35.],
[ 39., 24., 35.], ...,
[ 11., 26., 67.],
[ 4., 32., 95.],
[ 22., 45., 49.]], dtype=float32)
Even though the datatype is float32 apparently the decimals got lost
somehow.
The coordinates of the first atom should be: 41.511 25.152 36.876
Repeating the above in a normal interactive Python Session everything
works just fine:
>>> import pymol
>>> from pymol import cmd
>>> pymol.finish_launching()
>>> cmd.fetch("1xyz")
>>> cmd.get_coords("1xyz")
array([[ 41.51100159, 25.15200043, 36.87599945],
[ 40.9070015 , 25.55500031, 35.56299973],
[ 39.68399811, 24.70700073, 35.10599899], ...,
[ 11.88700008, 26.97699928, 67.03900146],
[ 4.45699978, 32.77299881, 95.16600037],
[ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
As I use IPython only for debugging of PyMol scripts/plugins this is not
a very big problem.
Still I'm interested in what causes this strange behavior. Is it a
problem/bug in IPython or in PyMol?
Maybe someone has more insights here and can give clarity!
Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
Thanks!
regards
Leonhard
|
|
From: Tsjerk W. <ts...@gm...> - 2016-12-01 15:35:59
|
Hi Leonhard,
I would guess it's the formatting setting of numpy in IPython. You can see
what one float really is:
print(cmd.get_coords("1xyz")[0,0])
Cheers,
Tsjerk
On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger <Leo...@ur...
> wrote:
> I guess formatting didn't work out as i expected. So once again and
> hopefully formatted:
>
>
> Hi!
>
> I stumbled upon some odd behavior when starting PyMol in an interactive
> IPython Session.
>
> PyMol can be launched from interactive IPython like this:
>
> In [1]: import pymol
> In [2]: from pymol import cmd
> In [3]: pymol.finish_launching()
> In [4]: cmd.fetch("1xyz")
>
> So far, everything is normal.
> However, when I want to get the coordinates of the structure the following
> happens:
>
> In [5]: cmd.get_coords("1xyz")
> Out[5]:
> array([[ 41., 25., 36.],
> [ 40., 25., 35.],
> [ 39., 24., 35.], ...,
> [ 11., 26., 67.],
> [ 4., 32., 95.],
> [ 22., 45., 49.]], dtype=float32)
>
> Even though the datatype is float32 apparently the decimals got lost
> somehow.
> The coordinates of the first atom should be: 41.511 25.152 36.876
>
> Repeating the above in a normal interactive Python Session everything
> works just fine:
>
> >>> import pymol
> >>> from pymol import cmd
> >>> pymol.finish_launching()
> >>> cmd.fetch("1xyz")
> >>> cmd.get_coords("1xyz")
> array([[ 41.51100159, 25.15200043, 36.87599945],
> [ 40.9070015 , 25.55500031, 35.56299973],
> [ 39.68399811, 24.70700073, 35.10599899], ...,
> [ 11.88700008, 26.97699928, 67.03900146],
> [ 4.45699978, 32.77299881, 95.16600037],
> [ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
>
> As I use IPython only for debugging of PyMol scripts/plugins this is not a
> very big problem.
> Still I'm interested in what causes this strange behavior. Is it a
> problem/bug in IPython or in PyMol?
> Maybe someone has more insights here and can give clarity!
>
> Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
>
> Thanks!
>
> regards
> Leonhard
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Tsjerk A. Wassenaar, Ph.D.
|
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