[phenixbb] Re: phenixbb Digest, Vol 235, Issue 4 (out of office)

29 Jul 2025

      Thank you for your e-mail. I am out of office until August 26th, 2025.
I will respond to your e-mail as soon as possible upon my return. 
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With kind regards,
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 29.7.25 20:38 >>>
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Today's Topics:

   1. Re: Structure with high clashscore ([email protected])
   2. Re: Structure with high clashscore (Pavel Afonine)
   3. Deadline Extended: Macromolecular Crystallography - CSHL Course
October 2025
      (Paul Adams)
   4. Phenix LigandFit RSCC calculation questions (Theo Teng)
   5. Re: Phenix LigandFit RSCC calculation questions (Bernhard Rupp)

----------------------------------------------------------------------

Message: 1
Date: Tue, 22 Jul 2025 15:09:07 -0000
From: [email protected]
Subject: [phenixbb] Re: Structure with high clashscore
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"

Hi, one more possibility - we find that if the structure is refined
without hydrogens, but one or more ligands do have hydrogens (not
intentionally), then Molprobity adds hydrogens to all residues and
clashscore calculated by it (now including hydrogens) jumps a lot. The
remedy would be to delete all hydrogens from the structure before the
refinement (or refine with hydrogens added everywhere).
Best
Leonid

JEROME JOHNSON wrote:
...
Hello all,
I'm happy to join the forum! I have a problem with clashscores and
would be
grateful for support.
I have diffraction data for a 3HP-CoA Synthetase from N. maritimus
resolved
to 2.7 Angstroms. For MD, I used an alphafold structure (as I
understand
commonly results in high clashscore values) and after numerous rounds
of
refinement, the clashscore remains high at 11. I recently tried using
gromacs to energy minimize and got values of 5 and 3 (according to
molprobity), but after refinement these values immediately jumped back
up
to ~30.
I wondered if you could describe the best way to reduce these?
Attached is my latest round of refinement should you wish to take a
look!
Best,
Jerome
------------------------------

Message: 2
Date: Tue, 22 Jul 2025 10:29:20 -0500
From: Pavel Afonine 
Subject: [phenixbb] Re: Structure with high clashscore
To: [email protected], [email protected]
Message-ID: 
Content-Type: text/plain; charset=UTF-8; format=flowed

Hi All,
...
Hi, one more possibility - we find that if the structure is refined
without hydrogens, but one or more ligands do have hydrogens (not
intentionally), then Molprobity adds hydrogens to all residues and
clashscore calculated by it (now including hydrogens) jumps a lot. The
remedy would be to delete all hydrogens from the structure before the
refinement (or refine with hydrogens added everywhere).
this is an interesting observation. MolProbity always adds all H to 
compute clashscore -- one can't compute clashscore without H present. I 
suspect having H on ligands only triggers it to 'think' that H are 
already present, and it computes clashscore without adding H to 
everything else. Could you please send me the file off list (the one 
that has H only on the ligand)? I think we better investigate this..
...
...
I'm happy to join the forum! I have a problem with clashscores and
would be
grateful for support.
I have diffraction data for a 3HP-CoA Synthetase from N. maritimus
resolved
to 2.7 Angstroms. For MD, >> commonly results in high clashscore values) and after numerous rounds
of
refinement, the clashscore remains high at 11.
...
Dear Phenix developers,
I hope this message finds you well.
We had two specific questions about how the real-space correlation
coefficient (RSCC) is computed when using Phenix.LigandFit:
1. What radius is used around the ligand or search center when
calculating
the RSCC during ligand fitting? Is this radius fixed or adaptive?
2. Which CCTBX function(s) underlie the RSCC calculation used in
LigandFit?
We aim to compare the placements from LigandFit to other ligand
11 looks just fine. Note, clashscore=0 is not the goal because 
clashscore does not account for non-standard links and for example, can 
count as a severe clash atoms involved into nonstandard links, and 
similar. In Phenix Comprehensive Validation, go over the table of 
clashes, they are sorted, worst first, and check and try to address top 
few worst offenders.

Pavel

------------------------------

Message: 3
Date: Tue, 22 Jul 2025 10:52:38 -0700
From: Paul Adams 
Subject: [phenixbb] Deadline Extended: Macromolecular Crystallography
	- CSHL Course October 2025
To: [email protected], [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain;       charset=utf-8

Dear Colleagues,

For those of you that may have missed the deadline, the application
deadline has been extended to August 1st. 

A reminder that the Cold Spring Harbor Macromolecular Crystallography
course will take place October 12-28th this year (pleased see below for
more details). This comprehensive course is an outstanding place to
learn both the theoretical and practical aspects of macromolecular
crystallography. There are extensive lectures and practical sessions
from world recognized experts in crystallization, data collection, data
processing, structure solution, refinement, and validation. The goal of
the course is for researchers who have had some exposure to structural
biology to become experts in crystallography. This is an experience in
macromolecular crystallography learning that cannot be found anywhere
else, and the student/teacher ratio is often 1:1.

Please follow this link to the course web site:
https://meetings.cshl.edu/courses.aspx?course=C-CRYS

In particular, please note the information about the various
fellowships, scholarships, and stipends that are available. Most
applicants ultimately receive some form of financial support. 

If anyone has any questions please send me an e-mail, and we will be
happy to answer all queries.

  Paul Adams

--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL
(https://biosciences.lbl.gov) 
Principal Investigator, Computational Crystallography Initiative, LBL
(http://cci.lbl.gov) 
Vice President for Technology, the Joint BioEnergy Institute
(http://www.jbei.org) 
Principal Investigator, ALS-ENABLE, Advanced Light Source
(http://als-enable.lbl.gov) 
Laboratory Research Manager, ENIGMA Science Focus Area
(http://enigma.lbl.gov) 
Adjunct Professor, Department of Bioengineering, UC Berkeley
(http://bioeng.berkeley.edu) 
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley
(http://compbiochem.berkeley.edu) 

Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul 
ORCID: 0000-0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ [email protected] ][
1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ]
--

------------------------------

Message: 4
Date: Tue, 29 Jul 2025 14:34:52 -0400
From: Theo Teng 
Subject: [phenixbb] Phenix LigandFit RSCC calculation questions
To: [email protected]
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Dear Phenix developers,

I hope this message finds you well.

We had two specific questions about how the real-space correlation
coefficient (RSCC) is computed when using Phenix.LigandFit:

1. What radius is used around the ligand or search center when
calculating
the RSCC during ligand fitting? Is this radius fixed or adaptive?

2. Which CCTBX function(s) underlie the RSCC calculation used in
LigandFit?

We aim to compare the placements from Lig-- 

*Theodore W. Teng*
Harvard College | Class of 2027
A.B. student in Chemical and Physical Biology
Secondary in Global Health and Health Policy

------------------------------

Message: 5
Date: Tue, 29 Jul 2025 11:38:27 -0700
From: Bernhard Rupp 
Subject: [phenixbb] Re: Phenix LigandFit RSCC calculation questions
To: Theo Teng 
Cc: [email protected]
Message-ID:

Content-Type: text/plain; charset="UTF-8"

There is a modified quote from a famous statistician, which one might
keep
in mind on such ventures:

All ligands are wrong, but some are useful.
Cheers, BR

------------------------------------------------------
Bernhard Rupp
https://www.hofkristallamt.org/
[email protected]
[email protected]
+1 925 209 7429
+43 676 571 0536
------------------------------------------------------
People can be divided into three classes:
The few who make things happen;
The many who watch what is happening;
and the overwhelming majority who have
no clue what is happening.
------------------------------------------------------

On Tue, Jul 29, 2025 at 11:35 AM Theo Teng

wrote:

placement
...
methods, and your response would be appreciated.
Best regards,
--
*Theodore W. Teng*
Harvard College | Class of 2027
A.B. student in Chemical and Physical Biology
Secondary in Global Health and Health Policy
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