Re: [ccp4bb] wwPDB news: Prototype of PDB NextGen Archive now available

[Marcin Wojdyr]

Dear all,

I looked at the atom table (atom_site) in the NextGen archive. It has 5 new
columns: pdbx_label_index (another sequence ID) and four columns for SIFTS
mapping at atom level.
I used SIFTS in the past and having it in the coordinate file can simplify
things. But as was stated in the announcement, the mapping is provided at
many levels:

> Sequence mappings are provided in _pdbx_sifts_unp_segments and
_pdbx_sifts_xref_db_segments categories for each segment,
_pdbx_sifts_xref_db at residue level, and _atom_site at atom level.

I wonder, wouldn't it be sufficient to provide the mapping at the residue
level? Repeating it for every atom actually makes working with the files
harder.

For two reasons.

One is that additional identifiers will be confusing. IMO it's the main
problem with mmCIF from the beginning -- too many identifiers. Every atom
has two chain names, two sequence IDs, two residue names and two atom
names. My guess is the IUCr committee tried to make both depositors and PDB
happy. The depositor could name the chain or atom as they like, and if the
PDB doesn't like the names, they can use the second set of names. (please
correct me if you were there). Currently the PDB changes both sets of ids
during deposition, so the "author" IDs are not really author's, but we
still have these two sets. In some older entries author's chain B is PDB's
chain A, and author's chain A is PDB's chain B. I think it's not
controversial that having two alternative names for one thing is not
particularly helpful here and, in this respect, the PDB format was designed
better.
These are old problems and I don't have hope that the double naming will be
dropped. But the new file looks like this:

[image: new-cif.png]

It has four different sequence IDs.
2 – "author" ID, the same as in the PDB
1 – "label" ID
3 – new one, apparently the same as 2 for polymers and the same as 1 for
non-polymers 😳 Am I missing something?
4 – UniProt-compatible
Could we avoid it?

The second reason is bloat. I maintain code for working with CIF files
(it's even used in PDBe) and just yesterday a user commented that reading
5j7v-assembly1.cif (4.7GB) requires a lot of memory. If we store each word
from such a file in the simplest way in C++ (as a string), we use, say, 32
bytes per word. 5GB file with short words easily takes up 40GB of memory
just for storing the words. I could work on optimizing it, but it'd help if
the files were not bloated even more. The NextGen Archive has 24% more
words in the atom table. All redundant.

Thanks for reading,
Marcin



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Re: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem

[Jessica Rabuck-Gibbons]

Hi Michael,

I recently installed panDDAs on an older Linux system. It still runs Centos
7, which was nice since I've run into compatibility issues with
python3/python 2.7 on a newer Mac.

Here are the basic steps that I've had to follow:
--Install cpp4 7.0 and download the updates to get to the right version
(7.0.72)
--source the correct ccp4
--Installed panddas according to the instructions found on the panddas page
--*I installed an older version of Pymol that still used python 2.7, not
sure if this is 100% necessary, but I did it to try to make sure no more
python errors would happen
--In the classes.py script, change c=CommandManager('source of pymol') to
where my pymol was installed (my Linux box has a weird hard drive system)
Then panddas ran correctly! Hopefully the new version on Friday fix your
issues, but if they don't, feel free to let me know, and I can try to help
you troubleshoot more.


Thanks,
Jessica

On Tue, Feb 14, 2023 at 2:17 AM Michael Weyand <
michael.wey...@uni-bayreuth.de> wrote:

> Dear colleagues,
>
> First, I don't want to flood ccp4bb with all the concrete program error
> code(s). Therefore a more general description. I can give more details if
> needed. To the board or by direct mails to the real experts.
>
> I would like to use the Panndda/PanDEMIC
>  tools within our CCP4
> environment (version 8.0.008) but I ran in some Python issues, although
> CCP4 patch 8.0.005 claimed various py3 Python fixes for Pandda. Even more
> by using the 2to3  Python
> version converter I found a number of Python3 (syntax and more) issues in
> the *main* CCP4 Python3 folder/subfolders at
> /ccp4/ccp4-8.0/lib/python3.7/site-packages/
>
> Since my OS (openSuSE Leap 15.4) still comes with both Python version 2.7
> and 3.6 and CCP4 now comes (to my knowledge) with 3.7 I am confused what I
> have to correct/change to use the Pandda tools. By my error tracking I'm
> pretty sure that PATH and PYTHONPATH are directing to the CCP4 folders, but
> may be I'm wrong ...
>
> And/or what was changed to the Pandda tools in the 8.0.005 CCP4 patch?
> Obviously, they are not working at my site ... :-(
> For instance, all Pandda scripts are still coming with a Python3 obsolete
> program option "-Q" ?!?!
> Was my 8.0.005 patch not properly executed? CCP4i teils me nothing.
>
> It is a shame but my Python knowledge is more than limited. Therefore I
> ran 2to3 for all Pandda scripts but then main CCP4 Python tools/scripts
> showed up, again with some syntax errors (= missing version 2/3 conversion
> ??) in the code. After also correcting these first 2-3 issues there were -
> by executing "pandemic.adp" - still more and more Python issues
> appearing...
>
> Now I asked my self, what is wrong with my CCP4 installation? According to
> patch 8.0.005 these tools should run !!
>
> And why are there version 3 issues beyond the CCP4 python3.7 folder ??
> I'm confused. Any help is highly appreciated.
>
> Best,
> Michael
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Eleanor Dodson]

Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of
the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC .



It notes these atoms are too close but carries on refinement happily
enough..
But when I read the structure into COOT and try to refine the A copy say it
has a hissy fit and blows both copies out of the density...
This is  Coot version 0.9.8.7


  * From REFMAC log*

*Link info given in this sectoion is for information only*

*   If you want to use this links then either add them into the
pdb/mmcif file or use make link yes option*



* Status Link   Mon1  At1  alt1  ch1   res1  Mon2  At2  alt2  Ch2
 Res2   distM   distI*

*Unused  :.  LIG   C01   .  A 2001  LIG   C01   .  B
2001   0.599   1.524*

*Unused  :.  LIG   C01   .  A 2001  LIG   N02   .  B
2001   1.266   1.414*

*Unused  :.  LIG   C01   .  A 2001  LIG   C11   .  B
2001   1.863   1.507*

*Unused  :.  LIG   N02   .  A 2001  LIG   C01   .  B
2001   1.799   1.414*

*Unused  :.  LIG   N02   .  A 2001  LIG   N02   .  B
2001   0.398   1.304*

*Unused  :.  LIG   N02   .  A 2001  LIG   C11   .  B
2001   0.702   1.397*

*Unused  :.  LIG   C03   .  A 2001  LIG   N02   .  B
2001   1.287   1.397*

*Unused  :.  LIG   C03   .  A 2001  LIG   C03   .  B
2001   0.699   1.490*

*Unused  :.  LIG   C03   .  A 2001  LIG   C04   .  B
2001   1.313   1.490*



On Thu, 16 Feb 2023 at 17:25, Nigel Moriarty  wrote:

> Stuart
>
> The sum of occ in these three is 1.3 and it looks like you put the occ in
> the B-factor column.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Email : nwmoria...@lbl.gov
> Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> On Thu, Feb 16, 2023 at 9:10 AM Stuart McQuarrie <
> 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear everyone that replied, thanks so much for the help thus far.
>>
>> Just for info I’m using Coot for Windows version 0.9.6 EL and
>> phenix.refine version 1.20rc4-4416-000
>>
>> RE Eleanor:  It appears my version of coot/refmac do not support separate
>> ligands in the same space at <0.5 occupancy. As an experiment, I tried
>> adding ATP and ADP at 0.45 occupancy to a different structure of mine. I’m
>> able to real space refine in coot (so both .cifs loaded successfully) until
>> I edit->merge the 2nd ligand and then the bonds look wrong and when I try
>> RSR it wants to force the ligand out and explodes the molecule.
>>
>> Original message: I thought that REFMAC tolerated dual occupancies if the
>> sum of the two conformers was <= 1.0?
>> Eleanor
>> Will test..
>>
>> RE Pavel: I tried following that as a guide, however I’m running into an
>> issue with restraints:
>>
>> I have made some progress troubleshooting the big cyclic molecule (ca6)
>> and products (pA3). I re-editted the pdb; gave them the altlocs ABC; made
>> sure they were same chain ID and residue number. However, when I try to
>> real space refine with coot I get the error:
>>
>> “No restraints found! Non-existent or minimal description of restrained
>> residues. Are you sure that you read a non-minimal mmCIF dictionary for
>> this monomer? Are you sure the PDB residue name matches the dictionary
>> residue name? If not, try File -> Import CIF dictionary. Alternatively, did
>> you check that the atom names of the PDB file match those of the
>> restraints? The residues in the chain are out of order. This can cause
>> problems with residues selection. Suggest you re-order residues in
>> increasing order.
>>
>> I definitely loaded the cifs. But it only allows me to rsr the ligand
>> with altloc A. If cA6 is A then I can only rsr cA6. If pA3 is A then I can
>> only refine pA3. When I delete->residue/monomer the cA6 with altloc A I can
>> suddenly rsr the pA3, so both libraries must have been loaded successfully
>> prior. I have included the snippet with the ligands just incase anyone
>> wants to see. Funnily enough phenix.refmac allowed me to refine with no
>> errors but it looks like it just ignored the pA3 as it did not properly fit
>> itself into the density the way ca6 did.
>>
>> Original Message:
>> Hi Stuart,
>> the answer, I think, is here:
>>
>> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
>> Pavel
>>
>>
>> RE George: I added allow_duplicate_sequence_numbers() to my
>> coot-preferences but it didn’t seem to make a difference in my case. I
>> could already open 1EJG with no error. My issue now appears to be the
>> library file not recognising whichever ligand is not altloc A.
>>
>> Original Message:
>> Dear Stuart,
>> you have to add  allow_duplicate_sequence_numbers() to $HOME/.coot.py in
>> OSX or the appropriate place on Windows. For
>> Windows, as there is no $HOME, Coot uses .coot.py 

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Nigel Moriarty]

Stuart

The sum of occ in these three is 1.3 and it looks like you put the occ in
the B-factor column.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Feb 16, 2023 at 9:10 AM Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear everyone that replied, thanks so much for the help thus far.
>
> Just for info I’m using Coot for Windows version 0.9.6 EL and
> phenix.refine version 1.20rc4-4416-000
>
> RE Eleanor:  It appears my version of coot/refmac do not support separate
> ligands in the same space at <0.5 occupancy. As an experiment, I tried
> adding ATP and ADP at 0.45 occupancy to a different structure of mine. I’m
> able to real space refine in coot (so both .cifs loaded successfully) until
> I edit->merge the 2nd ligand and then the bonds look wrong and when I try
> RSR it wants to force the ligand out and explodes the molecule.
>
> Original message: I thought that REFMAC tolerated dual occupancies if the
> sum of the two conformers was <= 1.0?
> Eleanor
> Will test..
>
> RE Pavel: I tried following that as a guide, however I’m running into an
> issue with restraints:
>
> I have made some progress troubleshooting the big cyclic molecule (ca6)
> and products (pA3). I re-editted the pdb; gave them the altlocs ABC; made
> sure they were same chain ID and residue number. However, when I try to
> real space refine with coot I get the error:
>
> “No restraints found! Non-existent or minimal description of restrained
> residues. Are you sure that you read a non-minimal mmCIF dictionary for
> this monomer? Are you sure the PDB residue name matches the dictionary
> residue name? If not, try File -> Import CIF dictionary. Alternatively, did
> you check that the atom names of the PDB file match those of the
> restraints? The residues in the chain are out of order. This can cause
> problems with residues selection. Suggest you re-order residues in
> increasing order.
>
> I definitely loaded the cifs. But it only allows me to rsr the ligand with
> altloc A. If cA6 is A then I can only rsr cA6. If pA3 is A then I can only
> refine pA3. When I delete->residue/monomer the cA6 with altloc A I can
> suddenly rsr the pA3, so both libraries must have been loaded successfully
> prior. I have included the snippet with the ligands just incase anyone
> wants to see. Funnily enough phenix.refmac allowed me to refine with no
> errors but it looks like it just ignored the pA3 as it did not properly fit
> itself into the density the way ca6 did.
>
> Original Message:
> Hi Stuart,
> the answer, I think, is here:
>
> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
> Pavel
>
>
> RE George: I added allow_duplicate_sequence_numbers() to my
> coot-preferences but it didn’t seem to make a difference in my case. I
> could already open 1EJG with no error. My issue now appears to be the
> library file not recognising whichever ligand is not altloc A.
>
> Original Message:
> Dear Stuart,
> you have to add  allow_duplicate_sequence_numbers() to $HOME/.coot.py in
> OSX or the appropriate place on Windows. For
> Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
> directory for configuration - these can be found (added to) thedirectory in
> which Coot was installed (e.g. C:\WinCoot). Try with crambin (pdbcode
> 1EJG).This should give an error without allow_duplicate_sequence_numbers()
> but coot should start when added.
> Br, Georg.
>
> Final thoughts:
> I am now thinking that my other idea of splitting the ca6 into alternate
> conformers and then manually editing the pdb to make it into 2 product
> complexes with cyclised 2’-3’ phosphates on the ribose would also not work
> as the library would not be compatible.
>
> If anyone has any more ideas please let me know.
>
> Original query:
> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
> refinement have noticed partial occupancy of it's hydrolysed form 2x A3,
> which has a cyclic 2'-3' phosphate on the terminal ribose.
>
> I tried fitting both ligands with 50% occupancy, but refinement doesn't
> allow them to occupy the same space.
>
> I subsequently tried text editing the pdb file, adding altloc identifiers
> to the ca6 and the 2 A3 molecules, making sure they were same chain and
> residue number as per this ccp4bb archive:
> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
> However, before I refined I checked in coot and all the ligand atoms are
> scattered and disconnected.
>
> I have thought about using coot to generate an alt conformation of ca6 and
> then text editing the B conformation to be split and have a 2'-3' cyclic
> phosphate. I am not sure if this is the correct way because it is a
> different chemical structure, so I could use some

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

[Stuart McQuarrie]

Dear everyone that replied, thanks so much for the help thus far. 

Just for info I’m using Coot for Windows version 0.9.6 EL and phenix.refine 
version 1.20rc4-4416-000

RE Eleanor:  It appears my version of coot/refmac do not support separate 
ligands in the same space at <0.5 occupancy. As an experiment, I tried adding 
ATP and ADP at 0.45 occupancy to a different structure of mine. I’m able to 
real space refine in coot (so both .cifs loaded successfully) until I 
edit->merge the 2nd ligand and then the bonds look wrong and when I try RSR it 
wants to force the ligand out and explodes the molecule.

Original message: I thought that REFMAC tolerated dual occupancies if the sum 
of the two conformers was <= 1.0? 
Eleanor
Will test..

RE Pavel: I tried following that as a guide, however I’m running into an issue 
with restraints:

I have made some progress troubleshooting the big cyclic molecule (ca6) and 
products (pA3). I re-editted the pdb; gave them the altlocs ABC; made sure they 
were same chain ID and residue number. However, when I try to real space refine 
with coot I get the error: 

“No restraints found! Non-existent or minimal description of restrained 
residues. Are you sure that you read a non-minimal mmCIF dictionary for this 
monomer? Are you sure the PDB residue name matches the dictionary residue name? 
If not, try File -> Import CIF dictionary. Alternatively, did you check that 
the atom names of the PDB file match those of the restraints? The residues in 
the chain are out of order. This can cause problems with residues selection. 
Suggest you re-order residues in increasing order.

I definitely loaded the cifs. But it only allows me to rsr the ligand with 
altloc A. If cA6 is A then I can only rsr cA6. If pA3 is A then I can only 
refine pA3. When I delete->residue/monomer the cA6 with altloc A I can suddenly 
rsr the pA3, so both libraries must have been loaded successfully prior. I have 
included the snippet with the ligands just incase anyone wants to see. Funnily 
enough phenix.refmac allowed me to refine with no errors but it looks like it 
just ignored the pA3 as it did not properly fit itself into the density the way 
ca6 did. 

Original Message:
Hi Stuart,
the answer, I think, is here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Pavel


RE George: I added allow_duplicate_sequence_numbers() to my coot-preferences 
but it didn’t seem to make a difference in my case. I could already open 1EJG 
with no error. My issue now appears to be the library file not recognising 
whichever ligand is not altloc A. 

Original Message:
Dear Stuart, 
you have to add  allow_duplicate_sequence_numbers() to $HOME/.coot.py in OSX or 
the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ 
directory for configuration - these can be found (added to) thedirectory in 
which Coot was installed (e.g. C:\WinCoot). Try with crambin (pdbcode 
1EJG).This should give an error without allow_duplicate_sequence_numbers() but 
coot should start when added.
Br, Georg.

Final thoughts:
I am now thinking that my other idea of splitting the ca6 into alternate 
conformers and then manually editing the pdb to make it into 2 product 
complexes with cyclised 2’-3’ phosphates on the ribose would also not work as 
the library would not be compatible. 

If anyone has any more ideas please let me know.  

Original query:
I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some 
refinement have noticed partial occupancy of it's hydrolysed form 2x A3, which 
has a cyclic 2'-3' phosphate on the terminal ribose.

I tried fitting both ligands with 50% occupancy, but refinement doesn't allow 
them to occupy the same space.

I subsequently tried text editing the pdb file, adding altloc identifiers to 
the ca6 and the 2 A3 molecules, making sure they were same chain and residue 
number as per this ccp4bb archive: 
http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html. 
However, before I refined I checked in coot and all the ligand atoms are 
scattered and disconnected.

I have thought about using coot to generate an alt conformation of ca6 and then 
text editing the B conformation to be split and have a 2'-3' cyclic phosphate. 
I am not sure if this is the correct way because it is a different chemical 
structure, so I could use some advice.

Kind regards,
Stuart


HETATM 5997  C1 AcA6 B 401  26.283  40.340  81.792  0.70 35.45   C  
HETATM 5998  C10AcA6 B 401  24.409  35.566  80.801  0.70 33.58   C  
HETATM 5999  C11AcA6 B 401  19.947  38.241  87.487  0.70 34.49   C  
HETATM 6000  C12AcA6 B 401  19.449  38.929  85.462  0.70 38.78   C  
HETATM 6001  C13AcA6 B 401  18.862  40.081  85.936  0.70 35.35   C  
HETATM 6002  C14AcA6 B 401  18.848  40.270  87.328  0.70 37.33   C  
HETATM 6003  C15AcA6 B 401  18.683  40.155  83.810  0

[ccp4bb] Two postdoctoral positions open at CNB-CSIC

[Mark J. van Raaij]

Two postdoctoral positions open at CNB-CSIC

Two fully funded postdoctoral positions in the area of Structural Biology are 
available at Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.

PIs: Carmen San Martín, Mark J. van Raaij
Starting on: June 2023
Contract length: 3 years
Subject: The intelligent design of more efficient adenovirus vectors using 
structural data.

Tasks: To solve structures of adenovirus particles or adenovirus proteins, 
alone or in complex with hosts factors. To analyze structures and design 
changes in proteins to tailor more favorable virus host interactions for 
efficient targeting and gene delivery.

Requested skills:

Position A: demonstrated experience in protein structure determination. 
Additional experience in virus structure, protein crystallography or 
cryo-electron microscopy strongly desired.

Position B: demonstrated experience in protein design / protein-protein 
interactions. Additional experience in virus structure or protein structure 
determination strongly desired.

Requirements for both positions:

Applicants should hold a PhD degree in biochemistry, structural biology, 
biophysics, protein chemistry or a related discipline.

Ability to work independently and efficiently as part of a team.
Well organized with attention to detail and excellent record keeping. Strong 
communication skills and fluency in written and spoken English. Enthusiasm, 
motivation, and capability to learn new methods. Problem-solving skills.
Ability to work in an international collaborative research setting.

How to apply: please send to i...@cnb.csic.es a PDF document containing: a 
cover letter describing your previous research achievements and motivation to 
apply; your detailed CV including a list of publications and explaining your 
own contribution; contact information for at least two references (ideally 
including your PhD supervisor). Please indicate whether you are applying to 
Position A or B. 




Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)




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Re: [ccp4bb] Coot (& phenix) on Ventura

[Charles Ballard - STFC UKRI]

Hi Pat

There may well be issues with the latest xquartz (2.8.3+) as the  libcairo 
compatibility version has changed to 1 from being 11 thousand odd.   This means 
that anything built against an older installation will fail.   The  workaround 
is to use an older xquartz, such as 2.8.0.

That pretty well summarises my knowledge, hopefully others will fill in the 
gaps.

Charles

From: CCP4 bulletin board  on behalf of Patrick Loll 

Date: Thursday, 16 February 2023 at 13:27
To: ccp4bb 
Subject: [ccp4bb] Coot (& phenix) on Ventura
Hi everyone,

I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is 
getting more and more pushy in its demands for a new OS.

Hence I ask, What’s the current status of coot running on Ventura? I’m aware of 
the issues that have been discussed in this forum, but that thread seems to 
have been quiet for a while. Are people able to get their work done under OS 
13? And have people encountered problems with any other structural biology 
programs?

Cheers,

Pat

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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[ccp4bb] Coot (& phenix) on Ventura

[Patrick Loll]

Hi everyone,

I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is 
getting more and more pushy in its demands for a new OS.

Hence I ask, What’s the current status of coot running on Ventura? I’m aware of 
the issues that have been discussed in this forum, but that thread seems to 
have been quiet for a while. Are people able to get their work done under OS 
13? And have people encountered problems with any other structural biology 
programs?

Cheers,

Pat


---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com 
pj...@drexel.edu


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Re: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem

[Charles Ballard - STFC UKRI]

Hi Michael

New version coming on Friday.  Should fix the issues.

You will be able to upgrade using ccp4um

Sorry for the issues

Charles

From: CCP4 bulletin board  on behalf of Michael Weyand 

Date: Thursday, 16 February 2023 at 07:30
To: ccp4bb 
Subject: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 problem
Dear colleagues,

First, I don't want to flood ccp4bb with all the concrete program error 
code(s). Therefore a more general description. I can give more details if 
needed. To the board or by direct mails to the real experts.

I would like to use the 
Panndda/PanDEMIC tools within our CCP4 
environment (version 8.0.008) but I ran in some Python issues, although CCP4 
patch 8.0.005 claimed various py3 Python fixes for Pandda. Even more by using 
the 2to3 Python version converter 
I found a number of Python3 (syntax and more) issues in the main CCP4 Python3 
folder/subfolders at
/ccp4/ccp4-8.0/lib/python3.7/site-packages/

Since my OS (openSuSE Leap 15.4) still comes with both Python version 2.7 and 
3.6 and CCP4 now comes (to my knowledge) with 3.7 I am confused what I have to 
correct/change to use the Pandda tools. By my error tracking I'm pretty sure 
that PATH and PYTHONPATH are directing to the CCP4 folders, but may be I'm 
wrong ...

And/or what was changed to the Pandda tools in the 8.0.005 CCP4 patch? 
Obviously, they are not working at my site ... :-(
For instance, all Pandda scripts are still coming with a Python3 obsolete 
program option "-Q" ?!?!
Was my 8.0.005 patch not properly executed? CCP4i teils me nothing.

It is a shame but my Python knowledge is more than limited. Therefore I ran 
2to3 for all Pandda scripts but then main CCP4 Python tools/scripts showed up, 
again with some syntax errors (= missing version 2/3 conversion ??) in the 
code. After also correcting these first 2-3 issues there were - by executing 
"pandemic.adp" - still more and more Python issues appearing...

Now I asked my self, what is wrong with my CCP4 installation? According to 
patch 8.0.005 these tools should run !!

And why are there version 3 issues beyond the CCP4 python3.7 folder ??  I'm 
confused. Any help is highly appreciated.

Best,
Michael




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