pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all,

I have several concatinated PDB files and am trying to calculate RMSDs of
each state(or frame) within the PDB files with respect to reference file.
How can I loop over the states within the concatenated PDB files?

I tried to do this:

#load PDBs
load reference.pdb, ref
load 100samples-1.pdb, md1, multiplex=0
load 100samples-2.pdb, md2, multiplex=0

python
group = ["md1", "md2"]
for i in group:
 for j in i:
  rmsd = cmd.pair_fit(j, "ref")
  print rmsd
python end

but it assigned j to "m" then "d" etc. instead of the states within md1,
md2...? Should I load the concatenated PDBs differently or what is the
issue?

Thanks!

-- 
Ara

Hi!

Recently, i have been trying to assemble a PyMol video of the
phosphorylation of the MAP kinase ERK from deactivated to activated to
deactivated stages. While I have had success showing the conformational
change from inactivated to activated (using *morph mout, 1ERK, 2ERK*), not
only am I not sure how to important a phosphate image to show what causes
the change, but I also do not know how to fuse the two morph mout scenes
between the deactivated to the activated and the activated to the
deactivated.

Would any of you happen to have any general ideas or some past email
suggestions as to how to solve this? I know I've tried ImageJ (but the
quality is always so poor and i have to make multiple images form my videos
and then fuse them together) as well as a variety of other steps using just
the PyMol program but I haven't found anything.

-Mel

Hello pymol-users, fyi ...

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A paper titled "DSSR, an integrated software tool for dissecting the
spatial structure of RNA" recently appeared in *Nucleic Acids Research* (
http://nar.oxfordjournals.org/cgi/content/full/gkv716). Starting from a
three-dimensional atomic coordinate file in either PDB or PDBx/mmCIF
format, DSSR, the new software product described in the paper, analyzes and
annotates RNA tertiary structures and uncovers a broad range of structural
features in a consistent and easily accessible framework. The software is
implemented in ANSI C as a stand-alone, command-line program and is
self-contained. The binaries for common operating systems (Mac OS X, Linux,
and Windows) are tiny (<1MB), without runtime dependencies on third-party
libraries. DSSR is efficient and robust due to comprehensive tests against
all nucleic-acid-containing structures in the PDB and continued refinements
based on user feedback.

DSSR identifies canonical and noncanonical base pairs, including those with
modified nucleotides, in any tautomeric or protonation state. The software
detects higher-order (three or more) coplanar base associations, termed
multiplets. It finds arrays of stacked pairs, classifies them by base-pair
identity and backbone connectivity, and distinguishes a stem of covalently
connected canonical pairs from a helix of stacked pairs of arbitrary
type/linkage. DSSR also pinpoints the coaxial stacking of multiple stems
within a single helix and lists the isolated canonical pairs that lie
outside of a stem. The program characterizes "closed" loops of various
types (hairpin, bulge, internal, and junction loops) and pseudoknots of
high complexity. Notably, DSSR employs isolated pairs and the ends of
stems, whether pseudoknotted or not, to define junction loops. This new,
inclusive definition provides a novel perspective on the spatial
organization of RNA, even for small molecules such as the viral tRNA mimic
from turnip yellow mosaic virus and the *env22* twister ribozyme.

In short, DSSR is to RNA what DSSP is to proteins for defining secondary
structures, but with more functionality: DSSR includes quantitative
descriptions of local base-pair geometry; assignments of common names and
classifications of base pairs; listings of commonly used sugar-phosphate
backbone parameters, continuous base stacks, and non-pairing interactions
(including those involving phosphate groups); and detections of ribose
zipper motifs, A-minor motifs, G-tetrads, U-turns, kissing loops, and
kink-turns.

The publication includes significant new scientific findings that are
enabled by the innovative analysis algorithms implemented in the software.
Moreover, the paper introduces an appealing and highly informative
"cartoon-block" representation of RNA structure that combines PyMOL cartoon
schematics with color-coded rectangular base (or base-pair) blocks. As a
follow-up to the publication, the 3DNA Forum includes all of the scripts
and data files associated with the article in a new section titled
"DSSR-NAR paper" (http://forum.x3dna.org/dssr-nar-paper/). The Forum also
contains links to an updated version of the DSSR User Manual (
http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). Any interested party
should be able to reproduce the tabulated data and figures (including the
supplementary data) reported in the article. Moreover, with the details
provided in "RNA cartoon-block representations with PyMOL and DSSR" (
http://forum.x3dna.org/dssr-nar-paper/rna-cartoon-block-representations-with-pymol-and-dssr/),
schematic images identical to those in the paper and the post can be easily
generated. Any questions related to the paper are welcomed on the 3DNA
Forum. Dr. Xiang-Jun Lu, the lead author of the paper and the person
spearheading the Forum, aims to respond promptly to any reported issues.

[This message is cross-posted on ccp4bb, pdb-l, and pymol-users. I
apologize for any duplicate copies you may receive.]

Xiang-Jun

--
Xiang-Jun Lu (PhD)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

Hi Osvaldo,

Thank you for your suggestion! Today I tried the APBS again and it works
this time. Just right after reading your email, I think I've figured out
what the problem is. I think the molecule must be in the same location for
both calculation and rendering. I guess last time, I used different files.
Even they are the exactly same molecules, somehow in pymol the locations of
molecules are not aligned. For example I have two files A and B which are
the identical molecules but not aligned. If I used A to do APBS
calculation, but opened the output with B, it will be completely white. If
I aligned B with A first, and save B as a new pdb file B'. I am able to
render the colors in B' with the original APBS output I calculated from A.


Best,
Xiao


2015-07-26 15:30 GMT-07:00 Osvaldo Martin <alo...@gm...>:

> Hi Victor,
>
> You should never use the build-in "generate vacuum electrostatic
> potential" function for any real analysis. The theoretically correct
> approach is to use the Poisson-Boltzman equation (as implemented for
> example in the APBS plugin). Other approaches like generalized Born models
> or SASA methods can be justified for things like Molecular Dynamics, i.e.
> when you need to compute the electrostatic energy contributions very often
> (at expense of reducing the accuracy of your computations).
> Could you provide an example of your "white" molecules? I would like to
> see if I can reproduce your observation.
>
>
> Cheers,
> Osvaldo.
>
>
>
> On Sun, Jul 26, 2015 at 3:48 AM, Victor Xiao <vic...@gm...>
> wrote:
>
>> Dear All,
>>
>> First, I am trying to compare surface electrostatic potential among
>> several members from a protein family. I was able to use build-in function
>> in pymol (generate vacuum electrostatic potential). However, the range of
>> potential for each molecule is automatically set up and they are different.
>> (e.g, one could be -5 to 5 and another one could be -10 to 10, so the color
>> scales between these two molecule are not comparable. A -5 potential will
>> be compeletely red in the first molecule, but is only light red in the
>> second molecule). Can I set the potential to the same range in order to
>> compare?
>>
>> Second, a off-topic question, I also tried to use APBS calculation. By
>> this way I was able to render most of molecules in red-white-blue scale,
>> but a few of molecules are completely white. I couldn't find where the
>> problem is.
>>
>>
>> Any comment or suggestion will be appreciated. Thank you very much!
>>
>> Best,
>> Xiao
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Hi Victor,

You should never use the build-in "generate vacuum electrostatic potential"
function for any real analysis. The theoretically correct approach is to
use the Poisson-Boltzman equation (as implemented for example in the APBS
plugin). Other approaches like generalized Born models or SASA methods can
be justified for things like Molecular Dynamics, i.e. when you need to
compute the electrostatic energy contributions very often (at expense of
reducing the accuracy of your computations).
Could you provide an example of your "white" molecules? I would like to see
if I can reproduce your observation.


Cheers,
Osvaldo.



On Sun, Jul 26, 2015 at 3:48 AM, Victor Xiao <vic...@gm...> wrote:

> Dear All,
>
> First, I am trying to compare surface electrostatic potential among
> several members from a protein family. I was able to use build-in function
> in pymol (generate vacuum electrostatic potential). However, the range of
> potential for each molecule is automatically set up and they are different.
> (e.g, one could be -5 to 5 and another one could be -10 to 10, so the color
> scales between these two molecule are not comparable. A -5 potential will
> be compeletely red in the first molecule, but is only light red in the
> second molecule). Can I set the potential to the same range in order to
> compare?
>
> Second, a off-topic question, I also tried to use APBS calculation. By
> this way I was able to render most of molecules in red-white-blue scale,
> but a few of molecules are completely white. I couldn't find where the
> problem is.
>
>
> Any comment or suggestion will be appreciated. Thank you very much!
>
> Best,
> Xiao
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear All,

First, I am trying to compare surface electrostatic potential among several
members from a protein family. I was able to use build-in function in pymol
(generate vacuum electrostatic potential). However, the range of potential
for each molecule is automatically set up and they are different. (e.g, one
could be -5 to 5 and another one could be -10 to 10, so the color scales
between these two molecule are not comparable. A -5 potential will be
compeletely red in the first molecule, but is only light red in the second
molecule). Can I set the potential to the same range in order to compare?

Second, a off-topic question, I also tried to use APBS calculation. By this
way I was able to render most of molecules in red-white-blue scale, but a
few of molecules are completely white. I couldn't find where the problem is.


Any comment or suggestion will be appreciated. Thank you very much!

Best,
Xiao

Big thank you to all of you!

I really need to find some time to better learn code. :/


> On Jul 23, 2015, at 4:36 PM, Sampson, Jared <Jar...@ny...> wrote:
> 
> I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.net <" rel="nofollow">http://sourceforge.net/> email address is currently down due to SF server issues), to ensure it is added to this thread in the archive:
> 
>> This is due to chain identifier conflict. He's merging 6 models with identical identifiers. A simple fix would be:
>> 
>> fetch 3ow9, type=pdb1, async=0
>> split_states 3ow9
>> alter 3ow9_000*, segi=model[-1]
>> create combined, 3ow9_000*
> 
> Changing the chain IDs as Rob suggested would also work.
> 
> Cheers,
> 
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/ <" rel="nofollow">http://kong.med.nyu.edu/>
> 
> 
> 
> 
> 
> 
> On Jul 23, 2015, at 2:42 PM, Robert Campbell <rob...@QU... <mailto:rob...@QU...>> wrote:
> 
>> Hi Adam,
>> 
>> I think you also want to make sure that each strand as a distinct chain
>> ID if you want the cartoon representation to work correctly.
>> 
>> Unfortunately that means you have to use "alter" but to change the
>> chain IDs on the objects created by the split_states command before
>> merging them all into one object.
>> 
>> It worked for me when I tried that with 3ow9.
>> 
>> Cheers,
>> Rob
>> 
>> On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg"
>> <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>> 
>>> Hi All,
>>> 
>>> If you fetch 3ow9 in PyMOL,
>>> split_states to get all six of the strands,
>>> select all, then copy to object,
>>> You only get the two strands, not all six, I need all six to be
>>> duplicated into one object so I can make a long amyloid fibril.
>>> 
>>> If I open the pdb file for 3ow9 in text edit and remove all the text
>>> for the individual models (and the waters), then open that file in
>>> PyMOL I get all six strands, but all the cartoon secondary structure
>>> is missing except for the two original strands. I tired running the
>>> alter command in PyMOL, it changes the secondary structure in the
>>> other objects I have open but not in this pdb.
>>> 
>>> I see the Sheet entry in the pdb file but I don’t know how to
>>> duplicate and change the sheet entry so it applies to the other four
>>> strands in the file.
>>> 
>>> Could someone point me to a place on the web that explains how to
>>> change the sheet entry (I’d like to learn how to do it)? or tell me
>>> how to fix this pdb file?
>>> 
>>> Thanks!
>>> 
>>> 
>>> 
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>> 
>> 
>> 
>> 
>> 
>> -- 
>> Robert L. Campbell, Ph.D.
>> Senior Research Associate/Adjunct Assistant Professor
>> Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
>> Queen's University, 
>> Kingston, ON K7L 3N6  Canada
>> Tel: 613-533-6821
>> <rob...@qu... <mailto:rob...@qu...>>  http://pldserver1.biochem.queensu.ca/~rlc <" rel="nofollow">http://pldserver1.biochem.queensu.ca/~rlc>
>> 
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users>
>> Archives: http://www.mail-archive.com/pym...@li... <" rel="nofollow">http://www.mail-archive.com/pym...@li...>
> 
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================
> 

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

I'm posting the following solution on behalf of Thomas Holder (whose sourceforge.net<http://sourceforge.net> email address is currently down due to SF server issues), to ensure it is added to this thread in the archive:

This is due to chain identifier conflict. He's merging 6 models with identical identifiers. A simple fix would be:

fetch 3ow9, type=pdb1, async=0
split_states 3ow9
alter 3ow9_000*, segi=model[-1]
create combined, 3ow9_000*

Changing the chain IDs as Rob suggested would also work.

Cheers,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jul 23, 2015, at 2:42 PM, Robert Campbell <rob...@QU...<mailto:rob...@QU...>> wrote:

Hi Adam,

I think you also want to make sure that each strand as a distinct chain
ID if you want the cartoon representation to work correctly.

Unfortunately that means you have to use "alter" but to change the
chain IDs on the objects created by the split_states command before
merging them all into one object.

It worked for me when I tried that with 3ow9.

Cheers,
Rob

On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg"
<h.a...@gm...<mailto:h.a...@gm...>> wrote:

Hi All,

If you fetch 3ow9 in PyMOL,
split_states to get all six of the strands,
select all, then copy to object,
You only get the two strands, not all six, I need all six to be
duplicated into one object so I can make a long amyloid fibril.

If I open the pdb file for 3ow9 in text edit and remove all the text
for the individual models (and the waters), then open that file in
PyMOL I get all six strands, but all the cartoon secondary structure
is missing except for the two original strands. I tired running the
alter command in PyMOL, it changes the secondary structure in the
other objects I have open but not in this pdb.

I see the Sheet entry in the pdb file but I don’t know how to
duplicate and change the sheet entry so it applies to the other four
strands in the file.

Could someone point me to a place on the web that explains how to
change the sheet entry (I’d like to learn how to do it)? or tell me
how to fix this pdb file?

Thanks!



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





--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...<mailto:rob...@qu...>>  http://pldserver1.biochem.queensu.ca/~rlc

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=================================

Hi Adam,

I think you also want to make sure that each strand as a distinct chain
ID if you want the cartoon representation to work correctly.

Unfortunately that means you have to use "alter" but to change the
chain IDs on the objects created by the split_states command before
merging them all into one object.

It worked for me when I tried that with 3ow9.

Cheers,
Rob

On Thu, 2015-07-23 09:23 EDT, "H. Adam Steinberg"
<h.a...@gm...> wrote:

> Hi All,
> 
> If you fetch 3ow9 in PyMOL,
> split_states to get all six of the strands,
> select all, then copy to object,
> You only get the two strands, not all six, I need all six to be
> duplicated into one object so I can make a long amyloid fibril.
> 
> If I open the pdb file for 3ow9 in text edit and remove all the text
> for the individual models (and the waters), then open that file in
> PyMOL I get all six strands, but all the cartoon secondary structure
> is missing except for the two original strands. I tired running the
> alter command in PyMOL, it changes the secondary structure in the
> other objects I have open but not in this pdb.
> 
> I see the Sheet entry in the pdb file but I don’t know how to
> duplicate and change the sheet entry so it applies to the other four
> strands in the file.
> 
> Could someone point me to a place on the web that explains how to
> change the sheet entry (I’d like to learn how to do it)? or tell me
> how to fix this pdb file?
> 
> Thanks!
> 
> 
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 




-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

Hi Adam,

You can use iterate to get the secondary structure designation, and then
use alter to apply it to the other chains.

secstruc=[]
iterate model1 and n. ca, secstruc.append(ss)

s1=list(secstruc)
alter model2 and n. ca, ss=s1.pop(0)

The last two lines need to be repeated, including the copying of the
secondary structure list, because the pop will consume the list.

Hope it helps,

Tsjerk

On Thu, Jul 23, 2015 at 5:53 PM, H. Adam Steinberg <
h.a...@gm...> wrote:

> The secondary structure is only there for the first set of strands, and
> then that is used for the other strands when you split_states, but how do I
> change that entry so it applies to the other strands?
>
> Here is that entry from the file that I attached:
>
> SHEET    1   A 2 LEU A   2  PHE A   5  0
>
> SHEET    2   A 2 LEU B   2  PHE B   5 -1  O  VAL B   3   N  PHE A   4
>
> On Jul 23, 2015, at 10:48 AM, Smith Liu <smi...@16...> wrote:
>
> I think the secondary structure record (SS) has been lost during your
> splitting. So just add and edit the SS record in the PDB file to the lost
> ones.
>
> Smith
>
>
>
>
>
> At 2015-07-23 22:23:24, "H. Adam Steinberg" <h.a...@gm...>
> wrote:
>
> Hi All,
>
> If you fetch 3ow9 in PyMOL,
> split_states to get all six of the strands,
> select all, then copy to object,
> You only get the two strands, not all six, I need all six to be duplicated
> into one object so I can make a long amyloid fibril.
>
> If I open the pdb file for 3ow9 in text edit and remove all the text for
> the individual models (and the waters), then open that file in PyMOL I get
> all six strands, but all the cartoon secondary structure is missing except
> for the two original strands. I tired running the alter command in PyMOL,
> it changes the secondary structure in the other objects I have open but not
> in this pdb.
>
> I see the Sheet entry in the pdb file but I don’t know how to duplicate
> and change the sheet entry so it applies to the other four strands in the
> file.
>
> Could someone point me to a place on the web that explains how to change
> the sheet entry (I’d like to learn how to do it)? or tell me how to fix
> this pdb file?
>
> Thanks!
>
>
>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> 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.

I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones.


Smith







At 2015-07-23 22:23:24, "H. Adam Steinberg" <h.a...@gm...> wrote:
Hi All,


If you fetch 3ow9 in PyMOL,
split_states to get all six of the strands,
select all, then copy to object,
You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.


If I open the pdb file for 3ow9 in text edit and remove all the text for the individual models (and the waters), then open that file in PyMOL I get all six strands, but all the cartoon secondary structure is missing except for the two original strands. I tired running the alter command in PyMOL, it changes the secondary structure in the other objects I have open but not in this pdb.


I see the Sheet entry in the pdb file but I don’t know how to duplicate and change the sheet entry so it applies to the other four strands in the file.


Could someone point me to a place on the web that explains how to change the sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb file?


Thanks!

The secondary structure is only there for the first set of strands, and then that is used for the other strands when you split_states, but how do I change that entry so it applies to the other strands?

Here is that entry from the file that I attached:

SHEET    1   A 2 LEU A   2  PHE A   5  0                                        
SHEET    2   A 2 LEU B   2  PHE B   5 -1  O  VAL B   3   N  PHE A   4  

> On Jul 23, 2015, at 10:48 AM, Smith Liu <smi...@16...> wrote:
> 
> I think the secondary structure record (SS) has been lost during your splitting. So just add and edit the SS record in the PDB file to the lost ones.
> 
> Smith
> 
> 
> 
> 
> 
> At 2015-07-23 22:23:24, "H. Adam Steinberg" <h.a...@gm...> wrote:
> Hi All,
> 
> If you fetch 3ow9 in PyMOL,
> split_states to get all six of the strands,
> select all, then copy to object,
> You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.
> 
> If I open the pdb file for 3ow9 in text edit and remove all the text for the individual models (and the waters), then open that file in PyMOL I get all six strands, but all the cartoon secondary structure is missing except for the two original strands. I tired running the alter command in PyMOL, it changes the secondary structure in the other objects I have open but not in this pdb.
> 
> I see the Sheet entry in the pdb file but I don’t know how to duplicate and change the sheet entry so it applies to the other four strands in the file.
> 
> Could someone point me to a place on the web that explains how to change the sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb file?
> 
> Thanks!
> 
> 
> 

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

Hi All,

If you fetch 3ow9 in PyMOL,
split_states to get all six of the strands,
select all, then copy to object,
You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.

If I open the pdb file for 3ow9 in text edit and remove all the text for the individual models (and the waters), then open that file in PyMOL I get all six strands, but all the cartoon secondary structure is missing except for the two original strands. I tired running the alter command in PyMOL, it changes the secondary structure in the other objects I have open but not in this pdb.

I see the Sheet entry in the pdb file but I don’t know how to duplicate and change the sheet entry so it applies to the other four strands in the file.

Could someone point me to a place on the web that explains how to change the sheet entry (I’d like to learn how to do it)? or tell me how to fix this pdb file?

Thanks!



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

Hi Leila,

Both methods works for me. You are using a really old PyMOL version. I
don't know if that is the problem but I think you should upgrade PyMOL.

Osvaldo
PS: Please use the reply button, to keep the whole conversation on the same
thread.


On Tue, Jul 14, 2015 at 10:49 AM, leila karami <kar...@gm...>
wrote:
I am sure that I am in working directory. To prevent this mistake, I
selected desktop as working directory. (I put out.pdbqt and pr.pdb files in
desktop and then load them).

I am using pymol-0_99rc6-bin-win32 on windows 7.

My input files are as follows:

https://www.dropbox.com/s/hx94orra4pumx82/out.pdbqt?dl=0
https://www.dropbox.com/s/2d09zkoqguwjujc/pr.pdb?dl=0

Please guide me to solve this problem.

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On Tue, Jul 14, 2015 at 10:38 AM, Osvaldo Martin <alo...@gm...>
wrote:

> Both methods work for me. Are you sure you are opening the correct
> obj3.pdb file? Maybe you are saving the obj3.pdb file to a different
> directory and opening an old obj3 file.
>
> Wich PyMOL version are you using and on which operating system?
>
>
> On Tue, Jul 14, 2015 at 10:25 AM, leila karami <kar...@gm...>
> wrote:
>
>> Dear Osvaldo,
>>
>> I used 2 following ways:
>>
>> 1)
>> load out.pdbqt,obj1
>> load pr.pdb, obj2
>> split_states obj1
>> create obj3, (obj1_0001, obj2)
>> save obj3.pdb, obj3
>>
>> 2)
>> load out.pdbqt,obj1
>> load pr.pdb, obj2
>> split_states obj1
>> save obj3.pdb, (obj1_0001, obj2)
>>
>> Unfortunately, in both cases, when I open obj3.pdb file using the text
>> editor, there as only END word.
>>
>>
>> ------------------------------------------------------------------------------
>> Don't Limit Your Business. Reach for the Cloud.
>> GigeNET's Cloud Solutions provide you with the tools and support that
>> you need to offload your IT needs and focus on growing your business.
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>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

I am sure that I am in working directory. To prevent this mistake, I
selected desktop as working directory. (I put out.pdbqt and pr.pdb files in
desktop and then load them).

I am using pymol-0_99rc6-bin-win32 on windows 7.

My input files are as follows:

https://www.dropbox.com/s/hx94orra4pumx82/out.pdbqt?dl=0
https://www.dropbox.com/s/2d09zkoqguwjujc/pr.pdb?dl=0

Please guide me to solve this problem.

Both methods work for me. Are you sure you are opening the correct obj3.pdb
file? Maybe you are saving the obj3.pdb file to a different directory and
opening an old obj3 file.

Wich PyMOL version are you using and on which operating system?


On Tue, Jul 14, 2015 at 10:25 AM, leila karami <kar...@gm...>
wrote:

> Dear Osvaldo,
>
> I used 2 following ways:
>
> 1)
> load out.pdbqt,obj1
> load pr.pdb, obj2
> split_states obj1
> create obj3, (obj1_0001, obj2)
> save obj3.pdb, obj3
>
> 2)
> load out.pdbqt,obj1
> load pr.pdb, obj2
> split_states obj1
> save obj3.pdb, (obj1_0001, obj2)
>
> Unfortunately, in both cases, when I open obj3.pdb file using the text
> editor, there as only END word.
>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
> https://www.gigenetcloud.com/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Thanks. Heres how I did it:

import __main__
__main__.pymol_argv = ['pymol', '-qc']
import pymol
import os
from pymol import *

pymol.finish_launching()


two = '/protein_files/1GZX.pdb'
name1 = os.path.basename(one)
name2 = os.path.basename(two)

# To get filename without extension: one.split(".",1)[0]

cmd.load(one, name1)
cmd.load(two, name2)
rms = cmd.align(name1, name2)

print(rms)

cmd.quit()

On Tue, Jul 14, 2015 at 2:02 AM, Gazal <gaz...@gm...> wrote:

> Thanks, I tried using python like you suggested but received these errors:
>
> Symmetry-Error: Urecognized space group symbol 'P 21 21 2 A'.
> Symmetry-Error: Unable to get matrices.
>
> I used the method given by Osvaldo.
> And to test if it works I removed the lines from pdb files where it
> mentioned the space groups.
>
> And I think it works now...
>
> I get following RMSD value:
> (1.246872901916504, 581, 5, 2.418435573577881, 669, 94.0, 113)
>
> these values are:
> RMSD
> No. of atoms for which we get RMSD
> No. of cycles
> ??
> No. of atoms aligned
> ??
> ??
>
> :)
>
> But still there is this space group problem.. Any suggestions to beat that?
>
>
>
> Many thanks.
>
> --
> Gazal
>
> On Sat, Jul 11, 2015 at 10:17 PM, David Hall <li...@co...>
> wrote:
>
>> I assume you are referring to
>> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py
>>
>> That is a script that creates a function. To turn it into a program, you
>> need to set up what you read in and what you output.
>>
>> In python, this is often done by command line arguments that can read
>> from sys.argv
>>
>> import sys
>>
>> arg1 = sys.argv[1]
>> arg2 = sys.argv[2]
>>
>> cmd.load(arg1, “protein1”)
>> cmd.load(arg2, “protein2”)
>>
>> You can have the definition of fitting in your script, then call
>>
>> fitting(“protein1”, ????, “protein2”, ????)
>>
>> I left in questions for the select1 and select2 arguments of the function
>> since it is not at all clear what you would like to put in as arguments
>> there.
>>
>> Beyond that, I would recommend reading up on python assuming you are not
>> familiar with the language.
>>
>> -David
>>
>>
>> On Jul 11, 2015, at 10:00 AM, Gazal <gaz...@gm...> wrote:
>>
>> Thank you for your help, Osvaldo and David.
>>
>> I tried using the command but did not get the RMS as expected.. Following
>> are the results:
>>
>> 1.
>> pymol -cqr fitting.py 1A6M.pdb 4OE9.txt
>> PyMOL>run fitting.py,main
>> HEADER    OXYGEN TRANSPORT                        26-FEB-98   1A6M
>> TITLE     OXY-MYOGLOBIN, ATOMIC RESOLUTION
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: MYOGLOBIN;
>> COMPND   3 CHAIN: A
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  Symmetry: Found 2 symmetry operators.
>>  CmdLoad: "1A6M.pdb" loaded as "1A6M".
>> HEADER    PROTEIN BINDING                         12-JAN-14   4OE9
>> TITLE     THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: COMM DOMAIN-CONTAINING PROTEIN 9;
>> COMPND   3 CHAIN: A, B;
>> COMPND   4 FRAGMENT: COMMD9, UNP RESIDUES  1-117;
>> COMPND   5 ENGINEERED: YES;
>> COMPND   6 MUTATION: YES
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  Symmetry: Found 1 symmetry operators.
>>  CmdLoad: "4OE9.txt" loaded as "4OE9.txt".
>>
>> 2.
>> pymol -cqr fitting.py --1A6M.pdb 4OE9.txt
>> PyMOL>run fitting.py,main
>>
>> Do I need to import Pymol module in the shell script to use the pymol
>> scripts like you did in python?
>> Am I missing something?
>>
>> ​Thanks​
>>
>> --
>> ​Gazal​
>>
>> On Fri, Jul 10, 2015 at 11:36 PM, David Hall <li...@co...>
>> wrote:
>>
>>> http://www.pymolwiki.org/index.php/Command_Line_Options
>>>
>>> see the -c and -r options. I also use -q
>>>
>>> pymol -qcr script.py — arg1 arg2 arg3
>>>
>>>
>>> On Jul 10, 2015, at 8:44 AM, Gazal <gaz...@gm...> wrote:
>>>
>>> Hi,
>>>
>>> I'm trying to find the RMSD values for batch purposes. The command which
>>> I found works for the Pymol-command line.
>>> I was hoping if I could get an idea about using the python script
>>> fitting.py in my shell script without triggering the Pymol GUI.
>>>
>>> Thanks in advance.
>>>
>>> Gazal
>>>
>>> ------------------------------------------------------------------------------
>>> Don't Limit Your Business. Reach for the Cloud.
>>> GigeNET's Cloud Solutions provide you with the tools and support that
>>> you need to offload your IT needs and focus on growing your business.
>>> Configured For All Businesses. Start Your Cloud Today.
>>>
>>> https://www.gigenetcloud.com/_______________________________________________
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>>>
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> Don't Limit Your Business. Reach for the Cloud.
>> GigeNET's Cloud Solutions provide you with the tools and support that
>> you need to offload your IT needs and focus on growing your business.
>> Configured For All Businesses. Start Your Cloud Today.
>>
>> https://www.gigenetcloud.com/_______________________________________________
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>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>

Dear Osvaldo,

I used 2 following ways:

1)
load out.pdbqt,obj1
load pr.pdb, obj2
split_states obj1
create obj3, (obj1_0001, obj2)
save obj3.pdb, obj3

2)
load out.pdbqt,obj1
load pr.pdb, obj2
split_states obj1
save obj3.pdb, (obj1_0001, obj2)

Unfortunately, in both cases, when I open obj3.pdb file using the text
editor, there as only END word.

Hi Leila,

I can't reproduce your error. Your code works for me.

Did you try the following

save obj3.pdb, obj1_0001, obj2


Cheers,
Osvaldo



On Tue, Jul 14, 2015 at 5:02 AM, leila karami <kar...@gm...>
wrote:

> Dear pymol users,
>
> I am visualizing autodock vina results using PyMOL:
>
> I open out.pdbqt (containing 9 docked conformations of ligand)
> I open pr.pdb (containing protein structure)
>
> I want to have 1 pdb file containing one of conformations of ligand
> (for example number 1 which is the best pose) + protein structure.
> To this, I used following:
>
> load out.pdbqt,obj1
> load pr.pdb, obj2
>
> split_states obj1
>
> create obj3, (obj1_0001, obj2)
>
> save obj3.pdb, obj3
>
> In pymol, I see the following:
>
> all
> obj1
> obj2
> obj1_0001
> obj1_0002
> obj1_0003
> obj1_0004
> obj1_0005
> obj1_0006
> obj1_0007
> obj1_0008
> obj1_0009
> obj3
>
> After deactivating all except obj3, in obj3, I see protein + first state
> of my ligand in pymol, but when I open obj3.pdb file using the text editor,
> there as only END word. I want to use this obj3.pdb file as an input for
> ligplot program.
>
> What is the reason of this state?
>
> Best,
> Leila
>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
> https://www.gigenetcloud.com/
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear pymol users,

I am visualizing autodock vina results using PyMOL:

I open out.pdbqt (containing 9 docked conformations of ligand)
I open pr.pdb (containing protein structure)

I want to have 1 pdb file containing one of conformations of ligand
(for example number 1 which is the best pose) + protein structure.
To this, I used following:

load out.pdbqt,obj1
load pr.pdb, obj2

split_states obj1

create obj3, (obj1_0001, obj2)

save obj3.pdb, obj3

In pymol, I see the following:

all
obj1
obj2
obj1_0001
obj1_0002
obj1_0003
obj1_0004
obj1_0005
obj1_0006
obj1_0007
obj1_0008
obj1_0009
obj3

After deactivating all except obj3, in obj3, I see protein + first state of
my ligand in pymol, but when I open obj3.pdb file using the text editor,
there as only END word. I want to use this obj3.pdb file as an input for
ligplot program.

What is the reason of this state?

Best,
Leila

Thanks, I tried using python like you suggested but received these errors:

Symmetry-Error: Urecognized space group symbol 'P 21 21 2 A'.
Symmetry-Error: Unable to get matrices.

I used the method given by Osvaldo.
And to test if it works I removed the lines from pdb files where it
mentioned the space groups.

And I think it works now...

I get following RMSD value:
(1.246872901916504, 581, 5, 2.418435573577881, 669, 94.0, 113)

these values are:
RMSD
No. of atoms for which we get RMSD
No. of cycles
??
No. of atoms aligned
??
??

:)

But still there is this space group problem.. Any suggestions to beat that?



Many thanks.

--
Gazal

On Sat, Jul 11, 2015 at 10:17 PM, David Hall <li...@co...> wrote:

> I assume you are referring to
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py
>
> That is a script that creates a function. To turn it into a program, you
> need to set up what you read in and what you output.
>
> In python, this is often done by command line arguments that can read from
> sys.argv
>
> import sys
>
> arg1 = sys.argv[1]
> arg2 = sys.argv[2]
>
> cmd.load(arg1, “protein1”)
> cmd.load(arg2, “protein2”)
>
> You can have the definition of fitting in your script, then call
>
> fitting(“protein1”, ????, “protein2”, ????)
>
> I left in questions for the select1 and select2 arguments of the function
> since it is not at all clear what you would like to put in as arguments
> there.
>
> Beyond that, I would recommend reading up on python assuming you are not
> familiar with the language.
>
> -David
>
>
> On Jul 11, 2015, at 10:00 AM, Gazal <gaz...@gm...> wrote:
>
> Thank you for your help, Osvaldo and David.
>
> I tried using the command but did not get the RMS as expected.. Following
> are the results:
>
> 1.
> pymol -cqr fitting.py 1A6M.pdb 4OE9.txt
> PyMOL>run fitting.py,main
> HEADER    OXYGEN TRANSPORT                        26-FEB-98   1A6M
> TITLE     OXY-MYOGLOBIN, ATOMIC RESOLUTION
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: MYOGLOBIN;
> COMPND   3 CHAIN: A
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  Symmetry: Found 2 symmetry operators.
>  CmdLoad: "1A6M.pdb" loaded as "1A6M".
> HEADER    PROTEIN BINDING                         12-JAN-14   4OE9
> TITLE     THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: COMM DOMAIN-CONTAINING PROTEIN 9;
> COMPND   3 CHAIN: A, B;
> COMPND   4 FRAGMENT: COMMD9, UNP RESIDUES  1-117;
> COMPND   5 ENGINEERED: YES;
> COMPND   6 MUTATION: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  Symmetry: Found 1 symmetry operators.
>  CmdLoad: "4OE9.txt" loaded as "4OE9.txt".
>
> 2.
> pymol -cqr fitting.py --1A6M.pdb 4OE9.txt
> PyMOL>run fitting.py,main
>
> Do I need to import Pymol module in the shell script to use the pymol
> scripts like you did in python?
> Am I missing something?
>
> ​Thanks​
>
> --
> ​Gazal​
>
> On Fri, Jul 10, 2015 at 11:36 PM, David Hall <li...@co...>
> wrote:
>
>> http://www.pymolwiki.org/index.php/Command_Line_Options
>>
>> see the -c and -r options. I also use -q
>>
>> pymol -qcr script.py — arg1 arg2 arg3
>>
>>
>> On Jul 10, 2015, at 8:44 AM, Gazal <gaz...@gm...> wrote:
>>
>> Hi,
>>
>> I'm trying to find the RMSD values for batch purposes. The command which
>> I found works for the Pymol-command line.
>> I was hoping if I could get an idea about using the python script
>> fitting.py in my shell script without triggering the Pymol GUI.
>>
>> Thanks in advance.
>>
>> Gazal
>>
>> ------------------------------------------------------------------------------
>> Don't Limit Your Business. Reach for the Cloud.
>> GigeNET's Cloud Solutions provide you with the tools and support that
>> you need to offload your IT needs and focus on growing your business.
>> Configured For All Businesses. Start Your Cloud Today.
>>
>> https://www.gigenetcloud.com/_______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
>
> https://www.gigenetcloud.com/_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>

Dear Leila,

What you want is the create <" rel="nofollow">http://www.pymolwiki.org/index.php/Create>
command, you should write something like:

create new_object, (pose1, protein)


Cheers,

Osvaldo.


On Mon, Jul 13, 2015 at 3:58 AM, leila karami <kar...@gm...>
wrote:

Dear PyMOL users,
>
> I am visualizing autodock vina results using PyMOL:
>
> I open out.pdbqt (containing 9 docked conformations of ligand)
> I open pr.pdb (containing protein structure)
>
> I want to have 1 pdb file containing one of conformations of ligand (for
> example number 1 which is the best pose) + protein structure. To this, I
> used File, Save molecule,
>
> a new window was opened: Which object or selection would you like to save?
>
> out.pdbqt
> pr.pdb
>
> How to select both of them?
>
> Any help will highly appreciated?
>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
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Dear Leila,

What OS are jou using ? If it is windows you may try the for windows 
modified PyMol plugin de Daniel Seeliger from  our web site 
(http://eipl.cnrs-mrs.fr/bioinformatic.php), which allows to create a 
poses.pdb file usable in PyMol and its measurements wizard.

best regards
Goetz

Le 13/07/2015 08:58, leila karami a écrit :
> Dear PyMOL users,
>
> I am visualizing autodock vina results using PyMOL:
>
> I open out.pdbqt (containing 9 docked conformations of ligand)
> I open pr.pdb (containing protein structure)
>
> I want to have 1 pdb file containing one of conformations of ligand 
> (for example number 1 which is the best pose) + protein structure. To 
> this, I used File, Save molecule,
>
> a new window was opened: Which object or selection would you like to save?
>
> out.pdbqt
> pr.pdb
>
> How to select both of them?
>
> Any help will highly appreciated?
>
>
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-- 
-------------------------------------------------------------------
Goetz Parsiegla, PhD, Maître de Conférences Aix-Marseille Université (AMU)

Research :
Laboratory of Enzymology at Interfaces and Physiology of Lipolysis (EIPL)
UMR 7282 CNRS et Aix-Marseille Université - Director : Frédéric Carrière
31 Chemin Joseph-Aiguier
F-13402 MARSEILLE cedex 20, France
tel: 33 (0)4 91 16 41 92 - fax: 33 (0)4 91 71 58 57

Teaching :
Polytech Marseille Departement of Biological Engineering
Case 925 -Campus de Luminy
163, Avenue de Luminy
13288 Marseille CEDEX 09
FRANCE

Email: Goe...@im...
-------------------------------------------------------------------

Dear PyMOL users,

I am visualizing autodock vina results using PyMOL:

I open out.pdbqt (containing 9 docked conformations of ligand)
I open pr.pdb (containing protein structure)

I want to have 1 pdb file containing one of conformations of ligand (for
example number 1 which is the best pose) + protein structure. To this, I
used File, Save molecule,

a new window was opened: Which object or selection would you like to save?

out.pdbqt
pr.pdb

How to select both of them?

Any help will highly appreciated?