pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all, 

I have recently tried to install PyMod via the bundle and unfortunately when i select run and try to click on .py or .txt files it won't let me. I have, also, tried to paste the whole script directly but it ended in "incorrect privileges" even though I am the admin. 

If anyone could help me out that would be great.

All the best

Joe 

Hi João,

On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 
and "--use-msgpackc=no" I get a working pymol with revision 4170.

Have you tried creating a new user and test pymol from that account? 
That should help you identify if it is solely a problem with your own 
account.

HTH,
Folmer

On 2017-03-28 03:15, João M. Damas wrote:
> Nobody experiencing the same issues? Any tips on what I may be doing 
> wrong on the installation?
>
> João
>
> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jm...@it... 
> <mailto:jm...@it...>> wrote:
>
>     Dear all,
>
>     I started experiencing segmentation fault on a pymol that I had
>     installed through the omnia channel on conda.
>
>     Then, I decided to install from scratch using this recipe:
>     https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
>     <" rel="nofollow">https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN>
>
>     Still getting the segmentation fault, so maybe something changed
>     in my system and it's conflicting with?
>
>     The segmentation fault is not on launching PyMOL, but rather when
>     I do stuff: loading a PDB file, building a fragment. Like this:
>
>     ```
>     ./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
>     "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
>     "$@"
>     ```
>
>     Curiously, when I load a 1.740 session (.pse file I had saved), it
>     works (no segmentation fault), I can even perform commands like
>     select and stuff, and they work. If I load a more recent 1.803
>     session, it also seg faults:
>
>     ```
>      Executive: Loading version 1.803 session...
>     ./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
>     "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
>     "$@"
>     ```
>
>     Any clues? Am I doing something wrong?
>
>     Thanks,
>     João
>
>     -- 
>     João M. Damas
>     PhD Student
>     Protein Modelling Group
>     ITQB-UNL, Oeiras, Portugal
>     Tel:+351-214469613 <tel:21%20446%209613>
>
>
>
>
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>
>
> ------------------------------------------------------------------------------
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>
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Nobody experiencing the same issues? Any tips on what I may be doing wrong
on the installation?

João

On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jm...@it...> wrote:

> Dear all,
>
> I started experiencing segmentation fault on a pymol that I had installed
> through the omnia channel on conda.
>
> Then, I decided to install from scratch using this recipe:
> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
>
> Still getting the segmentation fault, so maybe something changed in my
> system and it's conflicting with?
>
> The segmentation fault is not on launching PyMOL, but rather when I do
> stuff: loading a PDB file, building a fragment. Like this:
>
> ```
> ./pymol: line 3: 28505 Segmentation fault      "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> ```
>
> Curiously, when I load a 1.740 session (.pse file I had saved), it works
> (no segmentation fault), I can even perform commands like select and stuff,
> and they work. If I load a more recent 1.803 session, it also seg faults:
>
> ```
>  Executive: Loading version 1.803 session...
> ./pymol: line 3: 29221 Segmentation fault      "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> ```
>
> Any clues? Am I doing something wrong?
>
> Thanks,
> João
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613 <21%20446%209613>
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

Dear Colleagues,

This is a friendly reminder for the 10th annual CCP4 crystallographic school “From data collection to structure refinement and beyond”, held from June 16 to 26 at Advanced Photon Source (APS), Argonne National Laboratory (ANL). If you are interested attending, please take a look at the original announcement below for more details. For all details, please visit the school web site http://www.ccp4.ac.uk/schools/APS-2017/index.php


With best wishes,
Garib, Ronan and Nukri

Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

________________________________
From: Sanishvili, Ruslan
Sent: Wednesday, February 01, 2017 2:57 PM
To: pym...@li...
Subject: 10th CCP4/APS Crystallographic School in the USA

Dear Colleagues,

We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php

Dates: June 19 through 26, 2017

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

The school comprises
Data collection workshop: 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 http://www.ccp4.ac.uk/schools/APS-school/publications.php

Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, 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 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php

Registration 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, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses.

We hope to see you at the school.
Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

Perfect.
Thanks again Thomas.

Abhinav


-----Original Message-----
From: Thomas Holder [mailto:tho...@sc...]
Sent: Wednesday, March 22, 2017 2:05 PM
To: Kumar, Abhinav
Cc: pym...@li...
Subject: Re: [PyMOL] selection of residues

Hi Abhinav,

- Object name is the "model" variable. Check this page:
  https://pymolwiki.org/index.php/Iterate#Exposed_Variables
- Limit selection to enabled objects: "enabled" selection keyword
- Limit selection to one atom per residue: "byca" will do the trick for proteins

iterate byca (rep sticks & enabled), print(model,chain,resi,resn)

Cheers,
  Thomas

> iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn)


On 22 Mar 2017, at 16:43, Kumar, Abhinav <AK...@in...> wrote:

> Hi Thomas,
> Thanks very much. It works well.
> However, can you please help me refine the print out?
> I want to include the object name and print only once the residue info for each residue. Currently it prints for all atoms of residues.
> I tried the following:
> iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn)
>
> Thanks,
> Abhinav
>
> -----Original Message-----
> From: Thomas Holder [mailto:tho...@sc...]
> Sent: Wednesday, March 22, 2017 1:15 PM
> To: Kumar, Abhinav
> Cc: pym...@li...
> Subject: Re: [PyMOL] selection of residues
>
> Hi Abhinav,
>
> You can select by representation, e.g.:
>
> iterate rep sticks, print(chain, resi)
>
> or directly add labels on CA atoms:
>
> label byca rep sticks, resi
>
> Hope that helps.
>
> Cheers,
>  Thomas
>
> On 22 Mar 2017, at 15:43, Kumar, Abhinav <AK...@in...> wrote:
>
>> Hi,
>> Is there a way of extracting residue information from a session file in which a few residues are shown in sticks representation?
>> I am interested in changing representation/adding labels to only those residues with stick representation.
>>
>> Thanks,
>> Abhinav
>>
>> Abhinav Kumar, PhD
>> Senior Scientist, Data Science & Computational Biology Intrexon, Inc.
>> 329 Oyster Point Blvd., South San Francisco, CA 94080
>> (650) 597-4072 | ak...@in...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


________________________________

CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error.

Hi Abhinav,

- Object name is the "model" variable. Check this page:
  https://pymolwiki.org/index.php/Iterate#Exposed_Variables
- Limit selection to enabled objects: "enabled" selection keyword
- Limit selection to one atom per residue: "byca" will do the trick for proteins

iterate byca (rep sticks & enabled), print(model,chain,resi,resn)

Cheers,
  Thomas

> iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn)


On 22 Mar 2017, at 16:43, Kumar, Abhinav <AK...@in...> wrote:

> Hi Thomas,
> Thanks very much. It works well.
> However, can you please help me refine the print out?
> I want to include the object name and print only once the residue info for each residue. Currently it prints for all atoms of residues.
> I tried the following:
> iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn)
> 
> Thanks,
> Abhinav
> 
> -----Original Message-----
> From: Thomas Holder [mailto:tho...@sc...]
> Sent: Wednesday, March 22, 2017 1:15 PM
> To: Kumar, Abhinav
> Cc: pym...@li...
> Subject: Re: [PyMOL] selection of residues
> 
> Hi Abhinav,
> 
> You can select by representation, e.g.:
> 
> iterate rep sticks, print(chain, resi)
> 
> or directly add labels on CA atoms:
> 
> label byca rep sticks, resi
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> On 22 Mar 2017, at 15:43, Kumar, Abhinav <AK...@in...> wrote:
> 
>> Hi,
>> Is there a way of extracting residue information from a session file in which a few residues are shown in sticks representation?
>> I am interested in changing representation/adding labels to only those residues with stick representation.
>> 
>> Thanks,
>> Abhinav
>> 
>> Abhinav Kumar, PhD
>> Senior Scientist, Data Science & Computational Biology Intrexon, Inc.
>> 329 Oyster Point Blvd., South San Francisco, CA 94080
>> (650) 597-4072 | ak...@in...

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,
Thanks very much. It works well.
However, can you please help me refine the print out?
I want to include the object name and print only once the residue info for each residue. Currently it prints for all atoms of residues.
I tried the following:
iterate rep sticks, print(cmd.get_names(enabled_only=1),chain,resi,resn)

Thanks,
Abhinav

-----Original Message-----
From: Thomas Holder [mailto:tho...@sc...]
Sent: Wednesday, March 22, 2017 1:15 PM
To: Kumar, Abhinav
Cc: pym...@li...
Subject: Re: [PyMOL] selection of residues

Hi Abhinav,

You can select by representation, e.g.:

iterate rep sticks, print(chain, resi)

or directly add labels on CA atoms:

label byca rep sticks, resi

Hope that helps.

Cheers,
  Thomas

On 22 Mar 2017, at 15:43, Kumar, Abhinav <AK...@in...> wrote:

> Hi,
> Is there a way of extracting residue information from a session file in which a few residues are shown in sticks representation?
> I am interested in changing representation/adding labels to only those residues with stick representation.
>
> Thanks,
> Abhinav
>
> Abhinav Kumar, PhD
> Senior Scientist, Data Science & Computational Biology Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | ak...@in...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


________________________________

CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error.

Hi Abhinav,

You can select by representation, e.g.:

iterate rep sticks, print(chain, resi)

or directly add labels on CA atoms:

label byca rep sticks, resi

Hope that helps.

Cheers,
  Thomas

On 22 Mar 2017, at 15:43, Kumar, Abhinav <AK...@in...> wrote:

> Hi,
> Is there a way of extracting residue information from a session file in which a few residues are shown in sticks representation?
> I am interested in changing representation/adding labels to only those residues with stick representation.
>  
> Thanks,
> Abhinav
>  
> Abhinav Kumar, PhD
> Senior Scientist, Data Science & Computational Biology
> Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | ak...@in...

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,
Is there a way of extracting residue information from a session file in which a few residues are shown in sticks representation?
I am interested in changing representation/adding labels to only those residues with stick representation.

Thanks,
Abhinav

Abhinav Kumar, PhD
Senior Scientist, Data Science & Computational Biology
Intrexon, Inc.
329 Oyster Point Blvd., South San Francisco, CA 94080
(650) 597-4072 | ak...@in...<mailto:ak...@in...>



________________________________

CONFIDENTIAL TRANSMISSION - This message, including any attachments, is confidential and may be privileged. If you are not the intended recipient, please delete it without further distribution and reply to the sender that you have received the message in error.

Dear all,

I started experiencing segmentation fault on a pymol that I had installed
through the omnia channel on conda.

Then, I decided to install from scratch using this recipe:
https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN

Still getting the segmentation fault, so maybe something changed in my
system and it's conflicting with?

The segmentation fault is not on launching PyMOL, but rather when I do
stuff: loading a PDB file, building a fragment. Like this:

```
./pymol: line 3: 28505 Segmentation fault      "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
```

Curiously, when I load a 1.740 session (.pse file I had saved), it works
(no segmentation fault), I can even perform commands like select and stuff,
and they work. If I load a more recent 1.803 session, it also seg faults:

```
 Executive: Loading version 1.803 session...
./pymol: line 3: 29221 Segmentation fault      "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
```

Any clues? Am I doing something wrong?

Thanks,
João

-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

Dear all,
Is there a function or script which in simple way can find a complementary
base-pairs in my (deoxy)ribonucleic acid?

Suppose I have some double stranded RNA/DNA structure loaded into PyMOL.
Now I've chosen some nocleotyde or set of many nucleotydes and just want to
find residues of its complementary base-pairs (A-T, A-U, C-G).

Thanks a lot,
Paweł

The error is due to you not surrounding AlnAB in quotes, so python treats it as a variable which has not been defined.

That said, align modifies the coordinates of the existing object, the object created just shows the correspondence of residues used for alignment. To save the superimposed coordinates, you use the existing objects.

-David

> On Mar 13, 2017, at 1:31 AM, Sanaa Syed <san...@gm...> wrote:
> 
> Hello,
> Can somebody please help me with creating aligned object using pymol API? i want   to split chains from my protein and superimpose first chain on the rest. the chains get loaded. and superimposed as well but i am unable to save superimposed coordinates in a new file because no object is created.  this is my script:
> list1=["chain_A","chain_B","chain_C","chain_D"]
> for every in list1:
>         cmd.load("/home/sanaa/pymol/"+every+".pdb")
> object_list=cmd.get_object_list()
> aligned=[ ]
> list2=[ ]
> #object=string(alignedA_B)
> for j in range(len(object_list)):
>        try:
>                         aligned=cmd.align(object_list[0],object_list[j+1],object=AlnAB)
>                         list2.append(aligned)
>         except IndexError:
>                 pass
> 
> this is giving me name error like:
> NameError: name 'AlnAB' is not defined
> 
> the object is not being created after calling the align command. it creates an object if i give the command directly on  pymol command line but not through the script. i have tried everything. please help!
> ------------------------------------------------------------------------------
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Hello,
Can somebody please help me with creating aligned object using pymol API? i
want   to split chains from my protein and superimpose first chain on the
rest. the chains get loaded. and superimposed as well but i am unable to
save superimposed coordinates in a new file because no object is created.
 this is my script:
list1=["chain_A","chain_B","chain_C","chain_D"]
for every in list1:
        cmd.load("/home/sanaa/pymol/"+every+".pdb")
object_list=cmd.get_object_list()
aligned=[ ]
list2=[ ]
#object=string(alignedA_B)
for j in range(len(object_list)):
       try:
                        aligned=cmd.align(object_list[
0],object_list[j+1],object=AlnAB)
                        list2.append(aligned)
        except IndexError:
                pass

this is giving me name error like:
NameError: name 'AlnAB' is not defined

the object is not being created after calling the align command. it creates
an object if i give the command directly on  pymol command line but not
through the script. i have tried everything. please help!

Dear All,
I am relative new with PyMol and I am having trouble finding my way around. I wish to perform a rmsd for each atom  from 

1) a boundle of 20 conformers 
2) two different align structures, in PyMol such that the results of each atom pair can be displayed or plotted as a function of the amino acid sequence  in a pairwise manner. 

Can someone give me some tips on this?

Thanks as lot 
Celestine 

Hi All,

I have a python program that i am running in PyMOL. This program utilizes
Matplotlib to plot some results, and i would like to have a Matplotlib
interactive window appear once the code has finished running.

For example, the part of my code to produce the plot:

from pymol import cmd
import sys
import subprocess
import numpy as np
import matplotlib.pyplot as plt

fig1, ax1 = plt.subplots()
ax1.plot([1,2,3], [1,2,3], 'bs')
ax2 = ax1.twinx()
ax2.plot([1,2,3], [1,2,3], 'r^')

fig1.tight_layout()
plt.show()

If i run this section of my code in a shell, the plot properly appears in
an interactive matplotlib window. However, when i have been running it in
the PyMOL Tcl-Tk GUI, nothing is appearing at all. If i run savefig(), the
plot saves, so i know that it is being created properly. Is there any way
to make the interactive matplotlib window appear when running the script
from PyMOL?

I recognize that this is a similar question to the question posted here:
https://sourceforge.net/p/pymol/mailman/message/26788523/
however, this was using pylab and i believe they were running it from a
shell, not directly in PyMOL to begin with, and the solution proposed
(using show()) is not working for me.

Thanks for your thoughts!
Rene

-- 
*Rene Francolini*
Carnegie Mellon University
M.S. Computational Biology 2016
B.S. Biological Sciences 2015
------
LinkedIn: www.linkedin.com/in/rfrancolini
Email: ren...@gm...

Greetings,

We are happy to announce the release of PyMOL v1.8.6. PyMOL sponsors can download ready-to-use installers from http://pymol.org/download . The open-source code has been pushed to sourceforge svn (revision 4170).

Exciting new features include:

- Fast MMTF load support. MMTF is a new binary format for PDB structures which allows for very small file sizes while being self contained with explicit bond orders and formal charges. MMTF files now load into PyMOL about 5x as fast as mmCIF files. Learn more about MMTF at http://mmtf.rcsb.org/

- Ray tracing support for chromadepth (Incentive feature)

- Edge smoothing for partial surfaces (Incentive feature)

- A convenient CTRL-L shortcut to zoom on organic molecules

Find the complete release notes at:
http://pymol.org/d/media:new186

We've also added several new pages to the PyMOLWiki documenting old and new stuff:
https://pymolwiki.org/index.php?title=Special:RecentChanges&from=20170220000000&days=30

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi All,

I have been working on a python code that i am running in pymol. This code
takes in two files, one of which is a multi-model ligand pdb file that has
already been run through autodock vina. Therefore, each model within the
pdb file has a remark saying: "REMARK VINA RESULT:" followed by the binding
energy and RMSD values.

The goal of my code is to iterate through the atoms within different states
of the ligand and run some calculations--which is currently working very
well. However, i would like to add some other capabilities to the code,
including being able to take the autodock vina binding energy result into
account.

Due to the ability of iterating through the states of the pdb file as well
as running other pymol commands on these files, i am using the pymol
command 'cmd.load()' to import the files instead of the python command of
'open()'.

Looking through pymol archives i saw a brief mention that when opening a
pdb file with cmd.load(), it ignores and thus does not store any line that
starts with "REMARK"... is this always the case? or is there an option that
allows the user to store the information that is in the remarks?

The few solutions i have found online regarding being able to access the
information in a REMARK statement all take in the file with open(), and
proceed to look if the line has a certain string. This seems very
cumbersome, as the files i am working with will have anywhere from 20 to
100 models and i would have to go about a very convoluted process to get
each state's binding energy. Also, as far as my understanding goes, if you
use open() to read the file, you will not be able to run other pymol
commands on the file (such as cmd.iterate_state, cmd.pseudoatom, etc) which
are vital for my code.

So i am currently at a standstill when it comes to reading and storing the
binding affinities for each state of the multi-model pdb file. It would be
great if i could just create a list that contained all of the binding
affinities. Are there any ideas out there to help remedy this problem?

Thanks very much,
Rene


-- 
*Rene Francolini*
Carnegie Mellon University
M.S. Computational Biology 2016
B.S. Biological Sciences 2015
------
LinkedIn: www.linkedin.com/in/rfrancolini
Email: ren...@gm...
Phone: (973) 303-5203

I have used the script in example 4 here
https://pymolwiki.org/index.php/Get_Area to get the areas for a certain
pdb. I want to be able to distinguish though which residue has which area.

I can get the sequence using get_fastastr, but I want to modify the above
script to iterate over the sequence and output ( name and sequence ID,
area) pairs.

Regards.

Hi Tom,

As you have analyzed very correctly, volume is only available with on-screen rendering. I've added a section to the PyMOLWiki which describes the options and limitations:

https://pymolwiki.org/index.php/Volume#Ray_Tracing

Hope that helps.

Cheers,
  Thomas

On 23 Feb 2017, at 13:19, Thomas Grant <tom...@gm...> wrote:

> Dear all,
> 
> I've written a .pml script to render volumes and save png files. The script works fine when running it from the GUI, but for some reason when I run in command line mode with pymol -cqr myscript.pml the image saved is blank.  
> 
> It appears that when running from the command line it automatically ray traces the image, even when I set ray = 0 in the png command, and since volumes don't work well with ray tracing, the images end up blank.
> 
> I tried setting ray_volume=1, but that still doesn't fix the problem.
> 
> My script is below, as is the output from the command line and from the GUI.  Notice that when running from the command line there is a "Ray: render time:" line that doesn't appear when running from the GUI.
> 
> Thanks for any insight.
> 
> Tom
> 
> myscript.pml:
> $>cat myscript.pml:
> bg white
> fetch 1oky, type=2fofc, async=0
> volume 1okyVol, 1oky_2fofc
> set ray_volume, 1
> png volume.png, ray=0
> 
> command line output (doesn't work):
> $>pymol -cqr myscript.pml:
> PyMOL>bg white
> PyMOL>fetch 1oky, type=2fofc, async=0
>  ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.
>  BRIXStrToMap: Map Size 102 x 99 x 92
>  BRIXStrToMap: Range = -0.906629 to 2.095844
>  BRIXStrToMap: Calculated Mean =   -0.006, Sigma =    0.251
>  BRIXStrToMap: Normalizing...
>  Crystal: Unit Cell          124.162  124.162   47.300
>  Crystal: Alpha Beta Gamma    90.000   90.000  120.000
>  Crystal: RealToFrac Matrix
>  Crystal:    0.0081    0.0046   -0.0000
>  Crystal:    0.0000    0.0093   -0.0000
>  Crystal:    0.0000    0.0000    0.0211
>  Crystal: FracToReal Matrix
>  Crystal:  124.1625  -62.0812    0.0000
>  Crystal:    0.0000  107.5279    0.0000
>  Crystal:    0.0000    0.0000   47.3000
>  Crystal: Unit Cell Volume   631499.
>  CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".
> PyMOL>volume 1okyVol, 1oky_2fofc
>  Executive: object "1okyVol" created.
>  Volume: created "1okyVol"
> PyMOL>set ray_volume, 1
>  Setting: ray_volume set to on.
> PyMOL>png volume.png, ray=0
>  Ray: render time: 0.01 sec. = 242165.4 frames/hour (0.01 sec. accum.).
>  ScenePNG: wrote 640x480 pixel image to file "volume.png".
> 
> GUI output (works):
> $>pymol -qr myscript.pml:
>  Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 1.20.
> PyMOL>bg white
> PyMOL>fetch 1oky, type=2fofc, async=0
>  ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.
>  BRIXStrToMap: Map Size 102 x 99 x 92
>  BRIXStrToMap: Range = -0.906629 to 2.095844
>  BRIXStrToMap: Calculated Mean =   -0.006, Sigma =    0.251
>  BRIXStrToMap: Normalizing...
>  Crystal: Unit Cell          124.162  124.162   47.300
>  Crystal: Alpha Beta Gamma    90.000   90.000  120.000
>  Crystal: RealToFrac Matrix
>  Crystal:    0.0081    0.0046   -0.0000
>  Crystal:    0.0000    0.0093   -0.0000
>  Crystal:    0.0000    0.0000    0.0211
>  Crystal: FracToReal Matrix
>  Crystal:  124.1625  -62.0812    0.0000
>  Crystal:    0.0000  107.5279    0.0000
>  Crystal:    0.0000    0.0000   47.3000
>  Crystal: Unit Cell Volume   631499.
>  CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".
> PyMOL>volume 1okyVol, 1oky_2fofc
>  Executive: object "1okyVol" created.
>  Volume: created "1okyVol"
> PyMOL>set ray_volume, 1
>  Setting: ray_volume set to on.
> PyMOL>png volume.png, ray=0
>  ScenePNG: wrote 640x480 pixel image to file "volume.png".
> 
> 
> 
> 
> --
> Thomas D. Grant, Ph.D.
> Staff Scientist
> BioXFEL Science and Technology Center
> Hauptman-Woodward Medical Research Institute
> 700 Ellicott St.
> Buffalo, NY 14203

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

clearing the "rank" property also works for me, then the script should not depend on retain_order anymore:

    currentName = "%s_%s" % (solutionPymolString, currentChain)
    cmd.alter(currentName, "chain='%s';rank=-1" % currentChain)

However, I think there is also a problem with your script, you're creating copies of copies, every iteration will pick up the previously created chains and create another copy of the whole thing. Creating the copies in a new object will fix this:

newPymolString = 'newobj'
cmd.create(newPymolString, "none")

angle = 360.0/monomers
chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
for i in range(1, monomers):
        currentChain = chains[i]
        currentName = "%s_%s" % (solutionPymolString, currentChain)
        cmd.create(currentName, solutionPymolString, 1, 1)
        cmd.rotate([1, 0, 0], i * angle, currentName, 1, 0, None, [0, 0, 0])
        cmd.alter(currentName, "chain='%s';rank=-1" % currentChain)
        cmd.create(newPymolString, newPymolString + ' or ' + currentName, 1, 1)
        cmd.delete(currentName)


Cheers,
  Thomas

On 01 Mar 2017, at 14:10, Thomas Holder <tho...@sc...> wrote:

> Hi Gregor,
> 
> Looks like retain_order is on for her. This should fix it:
> 
> PyMOL> set retain_order, off
> 
> https://pymolwiki.org/index.php/Retain_order
> 
> Cheers,
>  Thomas
> 
> On 01 Mar 2017, at 10:28, Gregor Hagelüken <hag...@pc...> wrote:
> 
>> Hi,
>> 
>> I use a python script to copy an object, rotate it, alter its chain ID and then merge it with the original object.
>> Here is the relevant part of my script:
>> 
>> 			angle = 360.0/monomers
>> 			chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
>> 			for i in range(1, monomers):
>> 				currentChain = chains[i]
>> 				cmd.create("%s_%s" %(solutionPymolString, currentChain), solutionPymolString, 1, 1)
>> 				cmd.rotate([1, 0, 0], i * angle, "%s_%s" %(solutionPymolString, currentChain), 1, 0, None, [0, 0, 0])
>> 				cmd.alter("%s_%s" %(solutionPymolString, currentChain), "chain='%s'" %currentChain)
>> 				cmd.create("%s" %(solutionPymolString), "%s or %s_%s" %(solutionPymolString, solutionPymolString, currentChain), 1, 1)
>> 				cmd.delete("%s_%s" %(solutionPymolString, currentChain))
>> 
>> This works fine with PyMOL 1.8.3 and 1.8.5 on my computer (macOS Sierra).
>> 
>> I have given the script to another person and for her it produces a very strange result.
>> The resulting structure is only visible in lines or sticks mode. And it looks like this in the sequence viewer:
>> <PastedGraphic-2.tiff>
>> 
>> She used the same input structure as I did but she has PyMOL 1.8.4 and uses Windows. Could this be a PyMOL bug?
>> 
>> Cheers,
>> Gregor
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Gregor,

Looks like retain_order is on for her. This should fix it:

PyMOL> set retain_order, off

https://pymolwiki.org/index.php/Retain_order

Cheers,
  Thomas

On 01 Mar 2017, at 10:28, Gregor Hagelüken <hag...@pc...> wrote:

> Hi,
> 
> I use a python script to copy an object, rotate it, alter its chain ID and then merge it with the original object.
> Here is the relevant part of my script:
> 
> 			angle = 360.0/monomers
> 			chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
> 			for i in range(1, monomers):
> 				currentChain = chains[i]
> 				cmd.create("%s_%s" %(solutionPymolString, currentChain), solutionPymolString, 1, 1)
> 				cmd.rotate([1, 0, 0], i * angle, "%s_%s" %(solutionPymolString, currentChain), 1, 0, None, [0, 0, 0])
> 				cmd.alter("%s_%s" %(solutionPymolString, currentChain), "chain='%s'" %currentChain)
> 				cmd.create("%s" %(solutionPymolString), "%s or %s_%s" %(solutionPymolString, solutionPymolString, currentChain), 1, 1)
> 				cmd.delete("%s_%s" %(solutionPymolString, currentChain))
> 
> This works fine with PyMOL 1.8.3 and 1.8.5 on my computer (macOS Sierra).
> 
> I have given the script to another person and for her it produces a very strange result.
> The resulting structure is only visible in lines or sticks mode. And it looks like this in the sequence viewer:
> <PastedGraphic-2.tiff>
> 
> She used the same input structure as I did but she has PyMOL 1.8.4 and uses Windows. Could this be a PyMOL bug?
> 
> Cheers,
> Gregor

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

I use a python script to copy an object, rotate it, alter its chain ID and then merge it with the original object.
Here is the relevant part of my script:

			angle = 360.0/monomers
			chains = ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
			for i in range(1, monomers):
				currentChain = chains[i]
				cmd.create("%s_%s" %(solutionPymolString, currentChain), solutionPymolString, 1, 1)
				cmd.rotate([1, 0, 0], i * angle, "%s_%s" %(solutionPymolString, currentChain), 1, 0, None, [0, 0, 0])
				cmd.alter("%s_%s" %(solutionPymolString, currentChain), "chain='%s'" %currentChain)
				cmd.create("%s" %(solutionPymolString), "%s or %s_%s" %(solutionPymolString, solutionPymolString, currentChain), 1, 1)
				cmd.delete("%s_%s" %(solutionPymolString, currentChain))

This works fine with PyMOL 1.8.3 and 1.8.5 on my computer (macOS Sierra).

I have given the script to another person and for her it produces a very strange result.
The resulting structure is only visible in lines or sticks mode. And it looks like this in the sequence viewer:


She used the same input structure as I did but she has PyMOL 1.8.4 and uses Windows. Could this be a PyMOL bug?

Cheers,
Gregor

Hi Thomas,

Thank you for your answer! Your solution works great!

It's very handy to directly set RGB colors using alter!


Thanks for your help!

Best,

Leonhard


On 28.02.2017 16:41, Thomas Holder wrote:
> Hi Leonhard,
>
> Very interesting analysis. I'm wondering if this slowdown actually scales with number of objects or rather total number of atoms.
>
> If your color scheme lookup by (object, resi) key is fast in Python (let's say you have it all in a dictionary), then you can use cmd.alter() with a single pass, which probably will be faster than cmd.color() in multiple passes. Example:
>
> colors = {
>   'obj1': {
>     1: 0xFF0000,
>     2: 0x333300,
>     3: 0x000066,
>   },
>   'obj2': {
>     1: 0x001234,
>     2: 0x121212,
>     3: 0x009900,
>   },
> }
>
> cmd.alter('all', 'color = 0x40000000 | colors[model][resv]', space={'colors': colors})
> cmd.recolor()
>
> The magic number 040000000 is the cColor_TRGB_Bits mask which tells PyMOL that this is not a color index, but an RGB color.
>
> Instead of a dictionary lookup, you may also use a callback function.
>
> Check out these examples for alter with space argument:
> https://pymolwiki.org/index.php/Iterate#.22space.22_argument
>
> Cheers,
>   Thomas
>
> On 28 Feb 2017, at 09:34, Leonhard Heizinger <Leo...@ur...> wrote:
>
>> Hi,
>> coloring a certain residue in an object takes about 4 ms when only one
>> object is loaded in PyMol:
>>
>>  %time cmd.color("blue", "obj1of1 and resi 1")
>>  CPU times: user 3.33 ms, sys: 0 ns, total: 3.33 ms
>>  Wall time: 4.13 ms
>>
>> Performing the same operation when a lot of other objects (~300) are
>> loaded results in a highly increased execution time:
>>
>>  %time cmd.color("blue", "obj1of300 and resi 1")
>>  CPU times: user 243 ms, sys: 0 ns, total: 243 ms
>>  Wall time: 234 ms
>>
>> This is 60-fold increment compared to a PyMol Session with only one
>> object loaded. All structures in this example have ~240 residues.
>>
>> Consequently, coloring each residue of 300 objects in an individual
>> color would take more then 4.5 hours on my machine. Of course this use
>> case is pretty unlikely.
>>
>> In my case I only have limited number of colors (255 colors gradient)
>> which each residue could obtain. So I'm thinking about executing
>> cmd.color for each color (255 times), which should be faster. However
>> I'd still prefer to apply cmd.color per residue, so I don't have to
>> define bulky selections per color.
>>
>> Is there some way to accomplish this in a reasonable amount of time?
>> Thanks!
>>
>> Best,
>>
>> Leonhard

I'm looking for a python script to sample from the entire pdb. I want to
select pdb's with a certain attribute, or rule out a certain attribute, for
example membrane proteins. I also want to rule out pdb's that have metal
atoms in them.

I would appreciate all of your help.

Sincerest regards.