Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

[Thomas Holder]

This is fixed in SVN rev 4150.

Cheers,
  Thomas

On 22 Feb 2016, at 05:53, Thomas Holder  wrote:

> Hi all,
> 
> The bug seems to be that the "pdb_insure_orthogonal" setting is only applied 
> to the first model. Turning the setting off shows the correct assembly:
> 
> set pdb_insure_orthogonal, off
> load 1hho.pdb1
> 
> If "pdb_insure_orthogonal" is on, PyMOL will apply the SCALE transformation, 
> which might be necessary to correctly line up with the corresponding electron 
> density map.
> 
> Ioannis, you can file bug reports on https://sf.net/p/pymol/bugs/ but 
> reporting a bug here on the pymol-users list is equally effective :)
> 
> Cheers,
>  Thomas
> 
> On 22 Feb 2016, at 04:44, Ioannis Michalopoulos  
> wrote:
> 
>> Dear all,
>> 
>> Thank you for your informative answers.
>> 
>> For various reasons, I am not yet willing to move to cif.
>> 
>> Indeed remark 285 of the 1hho header:
>> 
>> http://www.rcsb.org/pdb/files/1HHO.pdb?headerOnly=YES
>> 
>> reads:
>> 
>> REMARK 285   
>>
>> REMARK 285 THE ENTRY COORDINATES
>> REMARK 285 ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.
>> 
>> Rasmol 2.7.5.2 displays both states of the biological structure, but, 
>> unfortunately, it does not recognise the secondary structure elements of the 
>> second state.
>> 
>> The fact that Rasmol and the three html embedded viewers in the PDB page:
>> 
>> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO=1
>> 
>> display the second state, means that Pymol is the one that has the issue, as 
>> Ezra mentioned.
>> 
>> As PyMOL's failure to recognise non-standard crystal frames is a major 
>> issue, 
>> I think I have to report it to PyMOL developers. How do I do a bug report on 
>> PyMOL 1.8.0.0? I just joined your emailing list and I am not sure how to do 
>> that.
>> 
>> Thank you in advance.
>> 
>> Best Regards,
>> 
>> Ioannis
>> 
>> On Monday 22 of February 2016 05:53:08 Ezra Peisach wrote:
>>> 1hho does have a non-standard crystal frame. (see remark 285)
>>> 
>>> If you load the assembly PDB file in rasmol - it displays properly. Pymol
>>> is having the issue.
>>> 
>>> However, if you fetch the cif file in pymol, and ask it to display the
>>> assembly - it does the right thing.
>>> 
>>> set assembly, 1
>>> fetch 1hho
>>> 
>>> 
>>> Ezra
>>> 
>>> On Mon, Feb 22, 2016 at 5:04 AM, Spencer Bliven 
>>> 
>>> wrote:
 This looks like a bug in the PDB's file, and you should definitely let
 them know about it. It's a particularly weird case since the second model
 doesn't correspond to any of the valid crystallographic operators.
 Probably
 it is a problem with the very non-standard crystal frame specified by the
 SCALE matrix in the PDB file. These are always problematic, to the point
 that some tools (e.g. EPPIC ) will ignore them
 completely.
 
 While waiting for the PDB to fix the file, you can generate the biological
 unit from the symmetry operators using:
 
 fetch 1hho, async=0
 symexp sym, 1hho, 1hho, 2
 
 -Spencer
 
 On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns 
 
 wrote:
> Dear Ioannis,
> 
>  I was wondering about that, too.  Given the prominence of hemoglobin
> 
> structure and oxygen binding in Biochemistry education, the 1 HHO
> structure
> seems to be a bad biological structure to calculate incorrectly.  I guess
> an email to the PDB might be in order (if it is intentional, they could
> at
> least explain it in that case).
> 
>   Best Regards,
> 
> Jim
> 
> 
> From: Ioannis Michalopoulos 
> Sent: Monday, February 22, 2016 4:05 PM
> To: Jame R.Ketudat-Cairns
> Subject: Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
> 
> Dear Jim,
> 
> Thank you for your prompt answer which worked perfectly. I was writing a
> tutorial for my students and I found many incorrectly calculated
> biological
> units. I wonder if we should complain to PDB about it, or wait and see
> what
> PyMOL can do about it, first.
> 
> Best Regards,
> 
> Ioannis
> 
> On Monday 22 of February 2016 02:09:05 you wrote:
>> Dear Ioannis,
>> 
>>  The 1HHO biological unit seems to be calculated incorrectly (just
> 
> spun
> 
>> around the y-axis 180 degrees).  I found that the symexp command works
> 
> for
> 
>> this: symexp sym, 1hho, (1hho), 1
>> Best Regards,
>> 
>>   Jim
>> 
>> 
>> From: Ioannis Michalopoulos 
>> Sent: Monday, February 22, 2016 3:39 AM
>> To: 

Re: [PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

[Thomas Holder]

Hi Max,

If you send me the loop.pdb file then I'll have a look at the issue.

Cheers,
  Thomas

On 23 Feb 2016, at 09:03, Ebert Maximilian  wrote:

> Hi there,
> 
> maybe the subject is a little bit misleading but i couldn’t find any better 
> description. Basically I am trying to align two PDB structures, one is from 
> the PDB directly and the other one is a file containing conformation 
> information about a specific loop of the protein from the PDB. So I try to 
> align this loop to the residues 211-220 of the PDB structures. My commands go 
> like this:
> 
> fetch 1g68
> load loop.pdb
> align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop
> 
> instead of aligning on the 40 atoms as expected I align solely on 8, which 
> are the N atoms. If I change the n. selection to O for instance I get 
> ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This 
> is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid 
> 1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works 
> as expected. To even make it more weird if I use Python:
> 
> import __main__
> __main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
> import pymol
> pymol.cmd.fetch('1g68’)
> pymol.cmd.load('loop.pdb’)
> pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220, 
> quiet=0)
> 
> it works as well. Does anybody understands what is happening here?
> 
> Thank you very much,
> 
> Max
> 
> PS: If you need the PDB files let me know. I don’t know if this list acceptes 
> files

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

[Ebert Maximilian]

Hi there,

maybe the subject is a little bit misleading but i couldn’t find any better 
description. Basically I am trying to align two PDB structures, one is from the 
PDB directly and the other one is a file containing conformation information 
about a specific loop of the protein from the PDB. So I try to align this loop 
to the residues 211-220 of the PDB structures. My commands go like this:

fetch 1g68
load loop.pdb
align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop

instead of aligning on the 40 atoms as expected I align solely on 8, which are 
the N atoms. If I change the n. selection to O for instance I get 
ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This 
is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid 
1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works 
as expected. To even make it more weird if I use Python:

import __main__
__main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
import pymol
pymol.cmd.fetch('1g68’)
pymol.cmd.load('loop.pdb’)
pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220, 
quiet=0)

it works as well. Does anybody understands what is happening here?

Thank you very much,

Max

PS: If you need the PDB files let me know. I don’t know if this list acceptes 
files
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[PyMOL] [ccp4bb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016

[Sanishvili, Ruslan]

Dear Colleagues,

We are pleased to announce the 9th annual CCP4 crystallographic summer school 
at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details 
can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php

Title: CCP4 crystallographic school: From data collection to structure 
refinement and beyond

Dates: June 21 through 29, 2016

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

The school comprises
Data collection workshop the first three days: beamline training and data 
collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only 
the participants' crystals will be used.
Crystallographic computation workshop: The rest of the time after data 
collection 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.
There will be model data sets available for tutorials but data, provided by 
participants, will have higher priority for the hands-on sessions.

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 21. The application form, the 
program, contact info and other details can be found at 
http://www.ccp4.ac.uk/schools/APS-2016/index.php

Registration fees: The registration fee for the selected participants is $400 
for the academic 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 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
rsanishv...@anl.gov

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