Re: [PyMOL] morph issues

[harold steinberg]

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  
> 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,\
>-0.06739,   -0.094843410,0.993197739,\
> 0.0,0.0, -619.393493652,\
> 0.042427063,   -0.005607605,6.552642822,\
>   516.705444336,  722.081604004,  -20.0 )
> 
> # 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  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  
>>> 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: honeg...@bioc.uzh.ch
>>> 
>>> 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  
 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 
>  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  
>> 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: honeg...@bioc.uzh.ch
>> 
>> websites
>> http://www.bioc.uzh.ch/plueckthun
>> http://www.bioc.uzh.ch/plueckthun/antibody
>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>> 

Re: [PyMOL] morph issues

[Honegger Annemarie]

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: honeg...@bioc.uzh.ch

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  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 > > 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: honeg...@bioc.uzh.ch 
>> 
>> 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 >> > wrote:
>>> 
>>> I ask because if I use the command "remove (not alt “”+A)” every atom 

Re: [PyMOL] morph issues

[Thomas Holder]

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,\
-0.06739,   -0.094843410,0.993197739,\
 0.0,0.0, -619.393493652,\
 0.042427063,   -0.005607605,6.552642822,\
   516.705444336,  722.081604004,  -20.0 )

# 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  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  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: honeg...@bioc.uzh.ch
>> 
>> 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  
>>> 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  
 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  
> 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: honeg...@bioc.uzh.ch
> 
> 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 
>> Subject: [PyMOL] morph issues
>> To: pymol-users 
>> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com>
>> Content-Type: text/plain; charset="utf-8"

Re: [PyMOL] morph issues

[harold steinberg]

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  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: honeg...@bioc.uzh.ch 
> 
> 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 > > 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 >> > 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 > 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: honeg...@bioc.uzh.ch 
 
 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 
> Subject: [PyMOL] morph issues
> To: pymol-users 
> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com>
> 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
> 

Re: [PyMOL] morph issues

[harold steinberg]

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  
> 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  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: honeg...@bioc.uzh.ch
>> 
>> 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 
>>> Subject: [PyMOL] morph issues
>>> To: pymol-users 
>>> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com>
>>> 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
>>> PyMOL-users@lists.sourceforge.net
>>> 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 (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
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


--
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
___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] morph issues

[Honegger Annemarie]

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: honeg...@bioc.uzh.ch

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 
> Subject: [PyMOL] morph issues
> To: pymol-users 
> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com>
> 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
> 
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