[ccp4bb] Structural Biology Postdoc at Princeton

[Philip D. Jeffrey]

An NIH-funded postdoctoral research position is available immediately in the 
Hughson lab at Princeton University. Our group’s research focuses on the 
remarkable protein machinery that generates the interior architecture of 
eukaryotic cells by orchestrating the formation and fusion of cargo-carrying 
transport vesicles. Our recent discoveries lay the foundation for exciting new 
projects studying how membrane tethering proteins work together with membrane 
fusion proteins to ensure accurate and efficient cargo delivery. This work will 
combine structural techniques (cryoEM, crystallography) with mechanism-directed 
functional studies. If this sounds interesting, please apply to join our team 
by sending your CV, a cover letter describing your research interests, and 
contact information for three references to  
hugh...@princeton.edu .



Princeton University is renowned for its scientific excellence and collegial, 
interactive environment. Located in Princeton, New Jersey, a vibrant community 
of about 30,000 people, it is just a quick train ride away from New York City 
and Philadelphia. Princeton University is an equal opportunity employer, and 
all qualified applicants will receive consideration for employment without 
regard to race, color, religion, sex, sexual orientation, gender identity, 
national origin, disability status, protected veteran status, or any other 
characteristic protected by law.



Fred Hughson

Professor of Molecular Biology

Princeton University

Princeton, NJ 08544




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Problem with peakmax

[Philip D. Jeffrey]

Paul was a little too terse, perhaps.
In script form

peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx
keywords in here
EOF-pmx

at least that's what works for me in Csh.  Bash proselytizers will correct me 
as necessary...

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Mohamed Ibrahim 

Sent: Tuesday, June 8, 2021 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Problem with peakmax

Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim 
mailto:mohamed.ibra...@hu-berlin.de>> wrote:
Thanks Paul,
Is it possible to add Ctrl-D to my bash script?

Best regards,

On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The peakmax from the GUI 
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file 
> works fine, when I use the GUI. Any ideas,
> how to solve this problem?
>
> command used
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>

Ctrl-D



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of 
www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are 
available at https://www.jiscmail.ac.uk/policyandsecurity/


--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931


--
​
​
--
Dr. Mohamed Ibrahim
Postdoctoral Researcher




Humboldt University


Berlin, Germany


Tel: +49 30 209347931



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Lowering R factor from small molecule structure

[Philip D. Jeffrey]

R1 of 17% is bad for small molecule.
0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs 
then these might be too aggressive for small molecule-type refinement stats - 
try a more conservative cutoff lie 0.9 and see how that changes R1.  However I 
suspect it's more to do with how your model is fitting the data.

Have you refined anisotropic Bfactors ?
Have you added hydrogens ?

I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for 
the refinements - I use the latter and it's somewhat Coot like with useful 
features that are particular to small molecule.  Also PLATON has some things 
(like expand-to-P1 and Squeeze) that, respectively, might be useful to explore 
space group issues and disordered solvent.  PLATON also has a means to check 
for some forms of twinning.

Phil Jeffrey
Princeton

From: CCP4 bulletin board  on behalf of Jacob Summers 
<60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, June 3, 2021 2:49 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lowering R factor from small molecule structure

Greetings!

I am currently trying to reduce the R factor of a cyclic small molecule peptoid 
in ShelXle. The max resolution of the molecule is 0.8 angstroms. The molecule 
itself fits the density very well, but there are a few unexplained densities 
around the molecule which do not seem to be anything in the crystallization 
conditions. The R1 factor of the refinement is 17.07% but I am unsure how to 
lower this value. Any ideas on how to better refine this molecule or fill 
densities to lower the R1 factor? I do not have much experience working with 
small molecule refinement or with ShelX.

Thanks so much,
Jacob Summers



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of 
www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are 
available at https://www.jiscmail.ac.uk/policyandsecurity/



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

[Philip D. Jeffrey]

You're casting yourself in the Emma Thompson role for the remake of "I Am 
Legend" ?

Phil


From: CCP4 bulletin board  on behalf of Jacob Keller 

Sent: Wednesday, February 17, 2021 2:09 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

But does it end better than the current best-seller "Smoldering Pandemic 
Paralyzes Human Race, Fuels Contention, Kills Millions, Drives the Rest Mad?"

JPK



On Wed, Feb 17, 2021 at 12:40 PM David Schuller 
mailto:schul...@cornell.edu>> wrote:
I read that book. It does not end well.


On 2/17/21 12:33 PM, Jacob Keller wrote:
It would seem to me that it should be possible to generate versions of the 
Covid virus that would:

A. be extremely contagious and yet
B. be clinically benign, and
C. confer immunity to the original covid virus.

If, then, this virus could be released, with appropriate "kill switch" 
safeguards built in, would this not solve the world's pandemic problems? Is 
there any reason, practically, why this approach would not be feasible?

Maybe we don't really know enough to manipulate A, B, C yet?

Or maybe it's too scary for primetime...nightmare bio-warfare apocalypse?

Has this sort of thing been done, or does it have a name?

Jacob
--

+

Jacob Pearson Keller

Assistant Professor

Department of Pharmacology and Molecular Therapeutics

Uniformed Services University

4301 Jones Bridge Road

Bethesda MD 20814

jacob.kel...@usuhs.edu; 
jacobpkel...@gmail.com

Cell: (301)592-7004

+



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


--

+

Jacob Pearson Keller

Assistant Professor

Department of Pharmacology and Molecular Therapeutics

Uniformed Services University

4301 Jones Bridge Road

Bethesda MD 20814

jacob.kel...@usuhs.edu; 
jacobpkel...@gmail.com

Cell: (301)592-7004

+



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Bug in mmCIF handling of UNK residues?

[Philip D. Jeffrey]

And if the actual residue ID is ambiguous ?  UNK is exactly what you should 
use.  There's also a distinction between getting it to work in the refinement 
program and having it properly annotated in PDB - e.g. I've encountered some 
monomer inconsistencies between Coot and Phenix.

The RCSB ligand page for UNK is strange and isn't going to reduce the confusion:
https://www.rcsb.org/ligand/UNK
but is consistent with them allowing Cgamma in UNK residues.

But from:
https://www.wwpdb.org/documentation/procedure

"Use of UNX/UNL/UNK There are times when an amino acid residue, nucleotide, 
atom, or ligand is unidentified. These ligand codes should be used in the 
following cases:

  *   UNX: unknown atom or ion
  *   UNL: unknown ligand
  *   UNK: unknown amino acid
  *   N: unknown nucleotide

UNX UNX is the code for one atom or ion, by itself, when author does not know 
the identity of that atom or ion. NOTE: The ligand name is UNX, but the atom 
name is UNK. The atom type is "X".

UNL UNL is the code for unknown ligand. This is for where author has added 
atoms to the coordinates to satisfy the electron density but the true ligand 
identity is not known. . For example, see PDB entry 3MHO.

UNK UNK is the code for unknown amino acid only. For example, a poly-ALA or 
poly-GLY chain would be processed as poly-UNK, if the author does not know how 
the coordinates align with the sequence and the residue numbering is arbitrary. 
The sequence would be poly UNK and the residues in coordinates would be listed 
as UNK. The sequence, if it is known, may be listed in the REMARK 999 and its 
mmCIF tokens. (If the authors do know the alignment of sequence and 
coordinates, the poly-ALA or poly-GLY residues should be changed to match the 
sequence). The atom names of UNK are N,CA,CB,CG,O,C, and the atom types are 
N,C,C,C,O,C. We are aware of issue regarding where atom passed CG but amino 
acid identity is not known, and the issues for the break in electron densi 
between UNK residues."


So in the case I indicated - Nyv1 - I was using it in the way described above - 
I can see backbone but there's a 1 residue ambiguity as to the residue 
assignment.  I "voted" by giving it a residue number but actual assignment was 
uncertain because the segment overlaps upon itself by symmetry, blurring the 
already unexceptional electron density.  This is the only time I've used it but 
IMHO the correct usage - using an actual residue like ALA assigns the wrong​ 
sequence to the residue in most cases.

I do not remember if UNK is successfully refined in phenix (I might have used 
ALA) but it would take you 10 seconds in a text editor to make the change if 
you were using PDB format.


Phil Jeffrey

Princeton


From: CCP4 bulletin board  on behalf of Nicholas Larsen 
<5741fb55e4af-dmarc-requ...@jiscmail.ac.uk>
Sent: Saturday, February 13, 2021 8:24 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Bug in mmCIF handling of UNK residues?

I hope this doesn't confuse the discussion, but my understanding was "UNK" 
stood for "unknown" residue and this will cause errors.  UNK naming convention 
is the default output of Schrodinger when generating ligand PDB files.  Coot 
will display the PDB containing "UNK" as a residue, but if you try to use the 
CIF file to real-space refine, the ligand will blow up.   I found that renaming 
the residue in the output PDB and regenerating the CIF file with the corrected 
RESID name solved the problem.  So in my experience, the problem is the name 
"UNK" and this just needs to be switched to something else.  Has anyone else 
seen this?
Nick

On Sat, Feb 13, 2021 at 4:29 PM Tristan Croll 
mailto:ti...@cam.ac.uk>> wrote:
Browsing backwards through a dozen or so of the most recent UNK-containing 
structures, I haven't found a counter-example yet - apart from those where the 
UNK residues are a single contiguous stretch and given their own chain ID. So a 
recent problem?

From: Philip D. Jeffrey mailto:pjeff...@princeton.edu>>
Sent: 12 February 2021 19:56
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>; Tristan Croll 
mailto:ti...@cam.ac.uk>>
Subject: Re: Bug in mmCIF handling of UNK residues?

Doesn't seem to be the case for all instances: that table isn't present in 5BV0 
despite the N-terminal residues of Nyv1 being modeled as UNK in the 
Vps16:Vps33:Nyv1 complex due to a symmetry overlap.  Nyv1, C165-179 are UNK 
with partial occupancy, which is the N-terminal part of the model for that 
chain, then there's a gap of 3 missing residues, and then there's polypeptide 
model which we've assigned to sequence, all in the same chain.

Not sure if the missing table is something that turned up after the deposition 
date (June 2015), or if it's related to the missing residues between the UNK 
segment

Re: [ccp4bb] Bug in mmCIF handling of UNK residues?

[Philip D. Jeffrey]

Doesn't seem to be the case for all instances: that table isn't present in 5BV0 
despite the N-terminal residues of Nyv1 being modeled as UNK in the 
Vps16:Vps33:Nyv1 complex due to a symmetry overlap.  Nyv1, C165-179 are UNK 
with partial occupancy, which is the N-terminal part of the model for that 
chain, then there's a gap of 3 missing residues, and then there's polypeptide 
model which we've assigned to sequence, all in the same chain.

Not sure if the missing table is something that turned up after the deposition 
date (June 2015), or if it's related to the missing residues between the UNK 
segment and the defined amino acids.

Phil Jeffrey
Princeton

From: CCP4 bulletin board  on behalf of Tristan Croll 

Sent: Friday, February 12, 2021 1:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Bug in mmCIF handling of UNK residues?

Hi all,

If I open (as far as I can tell) the mmCIF for any structure in the wwPDB that 
contains both defined amino acids and UNK in the same chain, then the UNK 
section is treated as covalently bonded to the flanking sequence. This appears 
to be a bug in the mmCIF generation itself, not in the viewing software 
(ChimeraX, in this case): if I look in 7kzn as a random example, I see:


loop_
_pdbx_validate_polymer_linkage.id
_pdbx_validate_polymer_linkage.PDB_model_num
_pdbx_validate_polymer_linkage.auth_atom_id_1
_pdbx_validate_polymer_linkage.auth_asym_id_1
_pdbx_validate_polymer_linkage.auth_comp_id_1
_pdbx_validate_polymer_linkage.auth_seq_id_1
_pdbx_validate_polymer_linkage.PDB_ins_code_1
_pdbx_validate_polymer_linkage.label_alt_id_1
_pdbx_validate_polymer_linkage.auth_atom_id_2
_pdbx_validate_polymer_linkage.auth_asym_id_2
_pdbx_validate_polymer_linkage.auth_comp_id_2
_pdbx_validate_polymer_linkage.auth_seq_id_2
_pdbx_validate_polymer_linkage.PDB_ins_code_2
_pdbx_validate_polymer_linkage.label_alt_id_2
_pdbx_validate_polymer_linkage.dist
1 1 C X UNK 345 ? ? N X UNK 348 ? ? 10.08
2 1 C X UNK 396 ? ? N X UNK 403 ? ? 28.65
3 1 C Y UNK 281 ? ? N Y UNK 284 ? ? 6.72
4 1 C Y UNK 387 ? ? N Y UNK 394 ? ? 22.26
5 1 C Y UNK 420 ? ? N Y UNK 424 ? ? 12.82


Considering that the coords themselves generally seem fine, I guess this is 
happening post deposition?

Best regards,

Tristan



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Tyr pushed out during refinement

[Philip D. Jeffrey]

As Paul observes, there's a bona fide email list for phenix, but in fact 
comparing REFMAC to phenix.refine might be useful to see if this really is a 
program bug or if it's a bug in the model.   Sometimes one is better than the 
other.

For phenix.refine:
Put the Tyr in the "right" place and scour the .geo file created at the start 
of refinement for bad angles or bonds or bumps etc.  This will tell you what 
the offending energy term is, if there is one.  If not, try turning off the 
rotamer fixing aspect of phenix.refine.  I've had aspects of the algorithm 
"anti-refine" a structure (geometry, Rwork, Rfree all got worse at once) so I 
tend to streamline the process and run it as:
  strategy=individual_sites+individual_adp+occupancies   (+tls if you're using 
it)
from the command line (since I'm a Luddite and mostly eschew the GUI).  For 
example if it's enforcing rotamers during NCS refinement it could pull your 
s/chain out of density.

But also try REFMAC if the problem persists.

Cheers
Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Paul Emsley 

Sent: Monday, October 19, 2020 2:58 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Tyr pushed out during refinement



On 19/10/2020 19:52, Boniecki, Michal wrote:

I have a problem during refining with one of the Tyr residues. It is constantly 
pushed out of the position during refinement in all 4 chains in ASU.
I have tried to exclude it from refinement in phenix but it is refined anyway 
out of the position with wrong geometry. Is there a possibility to fix it 
during refinement?


If this is a question about refinement in phenix, then this may not be the most 
useful mailing list. If this is a question about how to pin down atoms and 
tweak bonds and contacts in Coot or Refmac, then we can proceed.


Regards,

Paul.




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] on space group P 3 2 1

[Philip D. Jeffrey]

:: which indicates the 6 molecules are far away from each other.
Those are just the symmetry operators for space group P321.  It tells you 
nothing about how far apart the molecules are, although the cell dimensions do 
in fact impose some constraints.

However look at REMARK 350 in the PDB format file, which describes the 
orthogonal space operator to (probably) generate what you had in mind.

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Smith Lee 
<0459ef8548d5-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, September 25, 2020 9:35 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] on space group P 3 2 1

Dear All,

For pdb ID 1g4a, it is of space group P 3 2 1. In the paper for this pdb 
(Crystal Structures of the HslVU Peptidase–ATPase Complex Reveal an 
ATP-Dependent Proteolysis Mechanism), it has been configured to compact hexamer 
from the pdb 1g4a, with the pdb 1g4a can be regarded from a dimer.

For the sapce group P 3 2 1,
the listing of symmetry operators was as following,
  X, Y, Z
 -Y,  X -Y, Z
  -X +Y,-X, Z
  Y, X,-Z
   X -Y,-Y,-Z
 -X, -X +Y,-Z

which indicates the 6 molecules are far away from each other.

Then by which method, we can get the pdb for the compact hexamer as shown in 
the figure 3 in the paper, from the pdb 1g4a?

I am looking forward to getting your advice.

Smith



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Resolution cutoff in CCP4

[Philip D. Jeffrey]

Sanity check:
Please check that the number of the reflections in the .mtz file is the same as 
in the .sca file.
Please check that the cell dimensions in the MTZ file are the same as in the 
header of the .sca file

If that's true, and it probably is, then this is a general issue with SCALEPACK 
- it appears to apply the resolution cut on cell dimensions from the .x files 
(possibly the first one) that then can differ significantly from the 
post-refined cell dimensions.  Somewhat rarely it shows up as a large effect, 
as here,  but the major issue is that the resolution values in SCALEPACK are 
inaccurate.

Of course you still want scaling stats - perhaps try to integrate with the cell 
dimensions fixed to the post-refined values.  Or switch to XDS.

Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Vatsal Purohit 

Sent: Thursday, September 24, 2020 5:40 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Resolution cutoff in CCP4


Hi everyone,



I’ve been having an issue with the CCP4 program scatomtz to convert .sca 
generated from HKL2000 into .mtz. While my resolution cutoff in HKL2000 is 
higher (~ 2.0 A), this program cuts it off at 2.2 A even if I set a higher 
resolution limit in this program. Has anyone else experienced this? Any ideas 
on how to deal with this issue would be appreciated!



Regards,

Vatsal



Sent from Mail for Windows 10





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] How to save two superposed protein structures in PDB format

[Philip D. Jeffrey]

Hello Abhik

In coot use: Calculate>Merge Molecules to append one structure to another.  
Coot will change the chain labels for you, which might work out OK in this case.

Alternatively, I've done a lot of this in my time:
Make a copy of the reference PDB file
Open it in a simple text edit (emacs, vi etc)
Go to the end, remove the PDB 'END' statement
(Many programs stop reading a PDB file when they see an END)
Append the second, superimposed file.
For most chain labels you can also change them in a text editor but 'C' 'O' and 
'N' will cause you trouble.  You can do it easily in Coot.
This would take no more than 15 seconds in emacs.

>From the command line:
grep -v 'END' reference.pdb > reference2.pdb
egrep '^ATOM|^HETATM' superimposed.pdb >> reference2.pdb
(text editor to change chain labels, if you care, but there are ways to do that 
from the command line too)

Cheers
Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Abhik 
Mukhopadhyay 
Sent: Monday, September 14, 2020 4:55 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] How to save two superposed protein structures in PDB format

Hi,
How can I save two superposed protein structures in  PDB format? Is there any 
way I can do this in coot or pymol? There is only one chain in those two PDB 
structures.

Thanks in advance,
Abhik





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/