pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] 12th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

This is a reminder that the upcoming registration deadline (Apr 15th, 2019), please submit your application before the deadline if you are interested in attending this year's school.

Thanks.

Charles, Garib and Qingping


On 1/3/19 8:09 AM, Qingping Xu wrote:

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping

[PyMOL] Greetings

[Dr S. A. P. <drs...@uo...>]

Dear all,
I am a PyMol user from past two years now. I need to know 'how can we bring
two amino acid residues closer in the PyMol window' to avoid huge spacing
in between.
Attached is a PyMol session file for reference.

Thanks and regards.
Shahzad

-- 
*With best wishes*
*Shahzad A. Pandith, PhD*
*INSPIRE Faculty*
*Department of Botany*
*University of Kashmir*
*Voice: +91 959 660 6625, +91 941 935 4745*
*Email: **pan...@ya... <pan...@ya...>*

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04/10/19,
5:25:20 PM

Re: [PyMOL] Seeing more H-bonds than expected

[Neena S. E. <nee...@gm...>]

Thank you Jared for the detailed explanation!

Neena

On Tue, 9 Apr 2019 at 12:35, Jared Sampson <jar...@co...>
wrote:

> Hi Neena -
>
> PyMOL shows all the potential H-bonds, but not all of them will be formed
> at all times. Any single proton can only participate in one H-bond at a
> time, but remember a crystal structure is an average structure based on the
> ensemble of states present in the protein crystal (or on the EM grid for
> cryo-EM structures).  It's ok to have "too many" polar contacts...it just
> means the atoms have options for where to interact.
>
> Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds.  See
> perhaps McDonald & Thornton, JMB (1994)
> https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (
> nee...@gm...) wrote:
>
> Hello PyMOL users,
>
> Hydrogen bond finder on Pymol sometimes gave me unexpected observations
> like:
> more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on.
> This is even after setting H-bond center cutoff to 3.0 A. Any insight would
> be appreciated.
>
> Thank you for sharing your knowledge,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Seeing more H-bonds than expected

[Jared S. <jar...@co...>]

Hi Neena - 

PyMOL shows all the potential H-bonds, but not all of them will be formed at all times. Any single proton can only participate in one H-bond at a time, but remember a crystal structure is an average structure based on the ensemble of states present in the protein crystal (or on the EM grid for cryo-EM structures).  It's ok to have "too many" polar contacts...it just means the atoms have options for where to interact.

Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds.  See perhaps McDonald & Thornton, JMB (1994) https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion.

Hope that helps.

Cheers,
Jared 


On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (nee...@gm...) wrote:

Hello PyMOL users,

Hydrogen bond finder on Pymol sometimes gave me unexpected observations like:
more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on. This is even after setting H-bond center cutoff to 3.0 A. Any insight would be appreciated.

Thank you for sharing your knowledge,
Neena
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Re: [PyMOL] Pymol Activation

[Thomas H. <tho...@sc...>]

Hi Julia,

As a student, you can register for a free educational license:

https://pymol.org/edu/

Cheers,
  Thomas


> On Apr 4, 2019, at 8:54 PM, Julia Garcia <jmi...@uc...> wrote:
> 
> Hello, 
> 
> I am currently a student and I am using pymol in one of my classes. I was able to download the software, but I am confused on whether I need to activate it or skip the activation (image attached below). I was told that this software was free to use as a student, but in order to activate it I have to pay for a subscription. If you could help clarify how to properly set up pymol on my computer that would be greatly appreciated.
> 
> Thank you,
> 
> Julia Garcia

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Seeing more H-bonds than expected

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

Hydrogen bond finder on Pymol sometimes gave me unexpected observations
like:
more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on.
This is even after setting H-bond center cutoff to 3.0 A. Any insight would
be appreciated.

Thank you for sharing your knowledge,
Neena

[PyMOL] Pymol Activation

[Julia G. <jmi...@uc...>]

Hello,

I am currently a student and I am using pymol in one of my classes. I was
able to download the software, but I am confused on whether I need to
activate it or skip the activation (image attached below). I was told that
this software was free to use as a student, but in order to activate it I
have to pay for a subscription. If you could help clarify how to properly
set up pymol on my computer that would be greatly appreciated.

Thank you,

Julia Garcia

[PyMOL] PDBe-KB ligand centric pages survey

[Lukas P. <lp...@eb...>]

Dear PyMOL community,

 

We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is available at https://bit.ly/2FFmHFG

 

Recently, we have introduced protein-specific aggregated views on the structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in Europe Knowledge Base (PDBe-KB). We highlight the available information related to structures of specific proteins, including structural and functional annotations, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. 

 

Thank you for your time,

Lukas

 

 

--

Lukas Pravda, Ph.D.

Bioinformatician/Scientific Programmer

 

Protein Data Bank in Europe (PDBe)

European Bioinformatics Institute (EMBL-EBI)

Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD

United Kingdom

 

 

 

 

[PyMOL] Can’t access Dropbox on iPad

[John A. <joh...@gm...>]

Any suggestions on how to get PyMOL to see Dropbox? Nothing happens when I
press the tab; once, I got an error message about authentication being an
issue and to email Schrodinger. TIA

Re: [PyMOL] auto focus after creating

[Jared S. <jar...@co...>]

Hi again, Michael - 

This can be adjusted either globally via the `auto_zoom` setting:

	set auto_zoom, off

or when loading a PDB with the `load` or `fetch` commands:

	load my_structure.pdb, zoom=0
	fetch 1xyz, async=0, zoom=0

Here I also include `async=0` as you would in a script to make PyMOL wait until the file is loaded to continue.

Hope that helps.

Cheers,
Jared

https://pymolwiki.org/index.php/Auto_zoom
https://pymolwiki.org/index.php/Load
https://pymolwiki.org/index.php/Fetch



On March 28, 2019 at 1:18:08 AM, Michael Morgan (mic...@gm...) wrote:

Hello,

 

When I create an object, it will be zoomed and focused. Where can I change setting for this?

 

Thanks.

 

Michael

 

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Re: [PyMOL] rename/assign residue names

[Jared S. <jar...@co...>]

Hi Michael -

Assuming you already have your atoms selected in a selection called e.g. `sele` and you want the new residue name to be e.g. `XYZ`, you can achieve this on the PyMOL command line:

alter sele, resn='XYZ'
save XYZ.pdb, sele

Hope that helps.

Cheers,
Jared
On March 27, 2019 at 8:36:13 PM, Michael Morgan (mic...@gm...) wrote:

Dear all,

 

I need assign some residue names in a PDB file. Basically, I need the following: select a group of atoms, assign a residue name to the group and save into the PDB file. Can this be done by pymol or vmd? Editing the original PDB Text is not a good idea because it is very difficult to pick the group of atoms.

 

Thank you very much.

 

Michael

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[PyMOL] auto focus after creating

[Michael M. <mic...@gm...>]

Hello,

 

When I create an object, it will be zoomed and focused. Where can I change
setting for this? 

 

Thanks.

 

Michael

 

[PyMOL] rename/assign residue names

[Michael M. <mic...@gm...>]

Dear all,

 

I need assign some residue names in a PDB file. Basically, I need the
following: select a group of atoms, assign a residue name to the group and
save into the PDB file. Can this be done by pymol or vmd? Editing the
original PDB Text is not a good idea because it is very difficult to pick
the group of atoms. 

 

Thank you very much.

 

Michael

Re: [PyMOL] How to best create a sliding window (a selection of specific residues) and compare specific residue names+numbers in pymol/python?

[Thomas H. <tho...@sc...>]

Hi Anne,

This is not at all an obvious question, it's quite advanced! Impressive code snippet for a newbie :-)

For the sliding window question, I suggest to have a look at the implementation of "local_rms" from the psico package:

https://github.com/speleo3/pymol-psico/blob/master/psico/fitting.py

Example usage:

import psico.fitting
fetch 1akeA, async=0
fetch 4akeA, async=0
local_rms 1akeA, 4akeA, window=5

It calculates the RMSD of the entire sliding window, not only one residue. And it only considers the C-alpha atoms (remove the "and guide" selector which is passed to Matchmaker to include all atoms).

My question would be: What does the RMSD of a single residue really tell you? The number will reflect something in between the fit of the sliding window and the sidechain conformation of the center residue. Are you interested in both? Or only one of them?

Cheers,
  Thomas


> On Feb 22, 2019, at 6:28 PM, Anne Nierobisch <ann...@ke...> wrote:
> 
> Hi,
> 
> I need to calculate the RMSD for the same residue, e.g. 131Thr, from 2 pdb files for the same target. As I need a local alignment, I use a sliding window of 5 residues (the residue of interest is in the middle.)
> I have adapted the script from https://pymolwiki.org/index.php/RmsdByResidue (also see below my code below) by adding a sliding window, but I need advice on the following:
> 
> - I would need to check whether I am actually comparing the intended residues, e.g. 131Thr, 131Thr, or whether the same residues (e.g. His, Asp, His), with specific residue names and numbers   are in the selection I have chosen from both pdb files for my sliding window. 
> The reason:
> I have coded up the script below, but often it skips and doesn't compare two residues,  because the atom count is different between the residue from protein A and protein B. 
> (It is exactly double the number, I have already checked and excluded problems like occupancy and different conformations as potential causes.)
> 
> - I constructed a sliding window by selecting two residues before the residue of interest and two residues which follow said residue. (I know that residues can be missing, I am working on this.)
> Is there a better way for constructing a sliding window? I have not found such a method in pymol.
> 
> For anyone interested, I have attached a code snipplet below.
> I am sorry, if these seem like obvious questions, but I tried various approaches and I feel that I need a push in the right direction. I have the feeling that I am missing something fundamental. 
> 
> Many thanks for any suggestion!
> Anne (Newbie in Pymol)
> 
> ######################################
> 
> Code snipplet (Python/Pymol interface):
>   referenceProteinChain = cmd.fetch(pbdstructure1)
>   targetProteinChain = cmd.fetch(pdbstructure2)
>   sel = referenceProteinChain
>   list_atoms = [[133, 133]] # example list, I want to calculate the rmsd between residue 133 and residue 133 of two pdb structures
> 
> for j in list_atoms:
>    # I formulate my sliding window of 5 residues, my residue of interest is in the middle
>     ref_begin = int(j[0])-2
>     ref_end = int(j[0])+2
>     target_begin = int(j[1])-2
>     target_end = int(j[1])+2
> 
>     # I create a selection for the reference protein and the target protein 
>     cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B and not Alt C and not alt D  and resi %s-%s" 
>     cmd.alter("ref_gzt", "chain='A'")
>     cmd.alter("ref_gzt", "segi=''")
>     cmd.create("target_gzt", targetProteinChain+" and polymer and  not alt B and not Alt C and not alt D  and resi %s-%s" %(target_begin,target_end) )
>     cmd.alter("target_gzt", "chain='A'")
>     cmd.alter("target_gzt", "segi=''")
> 
>     # I align my selected 5 residues for a local alignment window
>     cmd.align("target_gzt","ref_gzt",object="align", cycles =5) 
> 
> 
>    # select alpha carbon of in reference structure to loop over
>     calpha=cmd.get_model(sel+" and name CA and not alt B and not Alt C and not alt D  and resi %s-%s" %(ref_begin,ref_end) )
> 
>    ## here I loop over all residues in the sliding window and calculte the rmsd for my residues of interest.
>     for g in calpha.atom : I loop over the slinding window
>         if g.resi == str(j[0]): ## we select only our residue of interest within the sliding window
>             if cmd.count_atoms("ref_gzt and polymer and resi "+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi):
> 
>                 ## calculte the pairwise RMSD between the residues I specified in list_atoms 
>                 rmsdRes=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi,"target_gzt and polymer and resi "+g.resi)

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] cmd.get_model

[Thomas H. <tho...@sc...>]

Hi Jeong,

cmd.get_model() has not been replaced or removed. What error do you get?

This code should work:

from pymol import cmd
print(cmd.get_model())

Cheers,
  Thomas

> On Mar 22, 2019, at 3:16 AM, 정보성 <qh...@ka...> wrote:
> 
> Hi All,
>  
> My Pymol version is 2.1.1 and I can not find the cmd.get_model in my version.
> but there is document of 'get_model' in pymol wiki (https://pymolwiki.org/index.php/Get_Model)
> is it replaced some other cmd?
> I want to use 'cmd.get_model', if anyone can give the python code of 'get_model'?
>  
> Thanks
>  
> Jeong.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] 12th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

Just a friendly reminder that the registration for the upcoming CCP4/APS School will close on Apr 15th, 2019. Please apply if you plan to attend.

Thanks.

Charles, Garib and Qingping


On 1/3/19 8:09 AM, Qingping Xu wrote:

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping

Re: [PyMOL] fix cartoon backbone

[h. a. s. <h.a...@gm...>]

Thank you.

Interestingly…
These alter commands do work on the DNA in my original working .pse file, the file that contains all of the structures.
They do work on the “save molecule” as a cif file that I shared with you, if I open it into PyMOL by itself.
They also work if I open the chain F.cif into my original working .pse file. This will fix the new chain F but not the old chain F.

Something about saving the chain out as a cif file and bringing it back in alters something besides just the atom naming. 

> On Mar 22, 2019, at 1:43 PM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Adam,
> 
> The atom naming is nonstandard. If you fix that, the cartoon will be complete.
> 
> alter name P01, name="P"
> alter name O01, name="O5'"
> alter name O02, name="OP1"
> alter name O03, name="OP2"
> unbond name OP1, name O3'+O5'
> unbond name OP2, name O3'+O5'
> 
> PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately the mmCIF spec doesn't make this straight forward). You could save to MMTF instead, it stores all bonds.
> 
> Cheers,
>  Thomas
> 
> 
>> On Mar 22, 2019, at 5:42 PM, h. adam steinberg <h.a...@gm...> wrote:
>> 
>> Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.
>> 
>> Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?
>> 
>> I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.
>> 
>> I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!
>> 
>> <chain F.cif>
>> 
>>> On Mar 22, 2019, at 11:31 AM, Jared Sampson <jar...@co...> wrote:
>>> 
>>> Hi Adam -
>>> 
>>> The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:
>>> 
>>> alter all, segi=""
>>> 
>>> Hope that helps.
>>> 
>>> Cheers,
>>> Jared
>>> 
>>> 
>>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.a...@gm...) wrote:
>>> 
>>>> 
>>>> 
>>>>> On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st...> wrote:
>>>>> 
>>>>> The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.
>>>>> 
>>>>> --
>>>>> Kevin Jude, PhD
>>>>> Structural Biology Research Specialist, Garcia Lab
>>>>> Howard Hughes Medical Institute
>>>>> Stanford University School of Medicine
>>>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>>> Phone: (650) 723-6431
>>>>> 
>>>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm...> wrote:
>>>>> Hi All,
>>>>> 
>>>>> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.
>>>>> 
>>>>> Thanks!
>>>>> 
>>>>> Adam
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

Re: [PyMOL] fix cartoon backbone

[Thomas H. <tho...@sc...>]

Hi Adam,

The atom naming is nonstandard. If you fix that, the cartoon will be complete.

alter name P01, name="P"
alter name O01, name="O5'"
alter name O02, name="OP1"
alter name O03, name="OP2"
unbond name OP1, name O3'+O5'
unbond name OP2, name O3'+O5'

PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately the mmCIF spec doesn't make this straight forward). You could save to MMTF instead, it stores all bonds.

Cheers,
  Thomas


> On Mar 22, 2019, at 5:42 PM, h. adam steinberg <h.a...@gm...> wrote:
> 
> Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.
> 
> Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?
> 
> I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.
> 
> I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!
> 
> <chain F.cif>
> 
>> On Mar 22, 2019, at 11:31 AM, Jared Sampson <jar...@co...> wrote:
>> 
>> Hi Adam -
>> 
>> The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:
>> 
>> alter all, segi=""
>> 
>> Hope that helps.
>> 
>> Cheers,
>> Jared
>> 
>> 
>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.a...@gm...) wrote:
>> 
>>> 
>>> 
>>>> On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st...> wrote:
>>>> 
>>>> The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.
>>>> 
>>>> --
>>>> Kevin Jude, PhD
>>>> Structural Biology Research Specialist, Garcia Lab
>>>> Howard Hughes Medical Institute
>>>> Stanford University School of Medicine
>>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>> Phone: (650) 723-6431
>>>> 
>>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm...> wrote:
>>>> Hi All,
>>>> 
>>>> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.
>>>> 
>>>> Thanks!
>>>> 
>>>> Adam

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] fix cartoon backbone

[h. a. s. <h.a...@gm...>]

Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.

Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?

I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.

I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!



> On Mar 22, 2019, at 11:31 AM, Jared Sampson <jar...@co...> wrote:
> 
> Hi Adam -
> 
> The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:
> 
> alter all, segi=""
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.a...@gm... <mailto:h.a...@gm...>) wrote:
> 
>> 
>> 
>>> On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st... <mailto:kj...@st...>> wrote:
>>> 
>>> The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.
>>> 
>>> --
>>> Kevin Jude, PhD
>>> Structural Biology Research Specialist, Garcia Lab
>>> Howard Hughes Medical Institute
>>> Stanford University School of Medicine
>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>> Phone: (650) 723-6431 <tel:%28650%29%20723-6431>
>>> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>>> Hi All,
>>> 
>>> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.
>>> 
>>> Thanks!
>>> 
>>> Adam
>>> 
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>> 
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Re: [PyMOL] fix cartoon backbone

[Jared S. <jar...@co...>]

Hi Adam -

The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:

alter all, segi=""

Hope that helps.

Cheers,
Jared


On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.a...@gm...) wrote:



On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st...> wrote:

The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm...> wrote:
Hi All,

I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.

Thanks!

Adam

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Re: [PyMOL] fix cartoon backbone

[h. a. s. <h.a...@gm...>]

I’ve altered the chain names and I’ve altered the residue numbers, sorted, and rebuilt but I’m still not getting a complete cartoon.

I see in obj02 there is an “A” in front of my “D” chain 16-33, and a “B” in front of my “D” chain 34-46, similar for obj03. I’m assuming that is now the issue. Is there some type of alter command for that part? 



> On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st...> wrote:
> 
> The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431 <tel:%28650%29%20723-6431>
> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
> Hi All,
> 
> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.
> 
> Thanks!
> 
> Adam
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>

Re: [PyMOL] Pymol recolour B factors

[Robert C. <rob...@qu...>]

Hi Mark,

In that data2bfactor.py script (which I wrote) you need to provide the molecular object name, not a file name.  In other words in your example you should load the 1d3z.pdb file as an object (defaults to 1d3z as object name).  Then after using the run command to load the script into your pymol session then you can type:

data2b_res 1d3z, shift_to_b.txt

The other script you mention works the same way.  The pdb file needs to be loaded into PyMOL as a molecular object first.

Cheers,
Rob

On Fri, 2019-03-22 11:36  +0000,  Dr Mark Bostock <mj...@ca...> wrote:

> Hello,
> 
> I'm trying to recolour the B factors in a pymol file with chemical
> shift differences (from NMR data). There's a nice script here for
> this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> (data2bfactor.py) and also a simpler one here 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffigshare.com%2Farticles%2FPymol_script_loadBfacts_py%2F1176991&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&amp;sdata=jDmJ4NSc%2F%2BXy5IG%2BRCCsQOmqh1Xj9l4j6gTMEmJB6Zc%3D&amp;reserved=0.
> 
> In both cases after loading the script with the run command, when I
> execute the script I get the following error
> 
> data2b_res 1d3z.pdb, shift_to_b.txt
> Selector-Error: Invalid selection name "1d3z.pdb".
> ( 1d3z.pdb )<--
> 
> The pdb file and list of new b-factor values are in the same
> directory and can be filled in with tab-completion. I've also tried
> using the full file path but get a similar error. I've tried with a
> couple of different pdb files as well so it's not just a problem with
> that particular pdb file.
> 
> I'd be grateful if anyone has any experience with this or suggestions
> as to what is going wrong.
> 
> Thanks in advance,
> 
> Mark
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
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-- 
Robert L. Campbell, Ph.D.
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

[PyMOL] Pymol recolour B factors

[Dr M. B. <mj...@ca...>]

Hello,

I'm trying to recolour the B factors in a pymol file with chemical shift 
differences (from NMR data). There's a nice script here for this 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ (data2bfactor.py) and 
also a simpler one here 
https://figshare.com/articles/Pymol_script_loadBfacts_py/1176991.

In both cases after loading the script with the run command, when I execute 
the script I get the following error

data2b_res 1d3z.pdb, shift_to_b.txt
Selector-Error: Invalid selection name "1d3z.pdb".
( 1d3z.pdb )<--

The pdb file and list of new b-factor values are in the same directory and 
can be filled in with tab-completion. I've also tried using the full file 
path but get a similar error. I've tried with a couple of different pdb 
files as well so it's not just a problem with that particular pdb file.

I'd be grateful if anyone has any experience with this or suggestions as to 
what is going wrong.

Thanks in advance,

Mark

[PyMOL] cmd.get_model

[<qh...@ka...>]

Hi All,My Pymol version is 2.1.1 and I can not find the cmd.get_model in my version.but there is document of 'get_model' in pymol wiki (https://pymolwiki.org/index.php/Get_Model)is it replaced some other cmd?I want to use 'cmd.get_model', if anyone can give the python code of 'get_model'?ThanksJeong.

[PyMOL] fix cartoon backbone

[h. a. s. <h.a...@gm...>]

Hi All,

I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.

Thanks!

Adam