Dear Xavier, Unfortunately, we were not able to figure out the reason PDB not handling Phenix mmCIFs. What is exact error message you are getting? Since the 1.14 release we changed some output to be more compliant with PDB mmCIF, so there is a chance it will work with the latest nightly. Please keep us updated. Best regards, Oleg Sobolev. On Tue, Dec 18, 2018 at 10:23 PM Xavier Brazzolotto < [email protected]> wrote:

Dear Oleg,

I had the same issue lately (mmCIF not handled by PDB deposition system using Phenix 1.14.3260). Is this issue has been resolved in a recent nightly ?

Many thanks

Xavier

Le 29 nov. 2018 à 20:20, Oleg Sobolev a écrit :

Dear Dominik,

Thank you for letting us know!

Would it be possible to send me (off-list) the 1.13 and 1.14 cif files for investigation along with the pdb file used for conversion. Also PDB deposition message would be helpful (if available). All files will be kept confidential.

Best regards, Oleg Sobolev.

On Thu, Nov 29, 2018 at 2:17 AM Dominik Oberthuer < [email protected]> wrote:

...

Dear all,

I recently found that phenix.refine in version 1.14-3260 generates coordinate mmCIFs that the PDB deposition system can't handle.

After struggling with this for some time I used an installation of Phenix 1.13-2998 I still have on my MacBook and used the mmCIF/PDB-conversion tool from this version and had no more trouble with uploading the mmCIF to the PDB.

Maybe it is worthwhile to check which changes from 1.13 to 1.14 might have caused these issues.

Thanks!

Dominik

-- Dr. Dominik Oberthür

CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division

Notkestrasse 85 22607 Hamburg Germany

phone: +49 (0)40 8998 6394 [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Xavier Brazzolotto, PhD [email protected]

*Département de Toxicologie et Risques Chimiques* *Unité Neurotoxiques* *Institut de Recherche Biomédicale des Armées* *1 Place du Général Valérie André, BP 73* *91223 Brétigny sur Orge* *France*

Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09

*The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.*

*This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not **necessarily complies to the ministry cyber security policy.*

Dear Xavier, We now understand the issue and will work on it. Meanwhile, if you assign another chain id to glycans, PDB deposition should work correctly with mmCIF from Phenix. This also applies to other ligands. Best regards, Oleg Sobolev. On Wed, Dec 19, 2018 at 12:36 PM Xavier Brazzolotto < [email protected]> wrote:

Dear Oleg,

I would not say that the PDB was not handling the mmCIF file at all. In fact the file is « accepted » but not well processed. I do have glycans chains in the enzyme I am working with and they appear in the processing such as part of the polypeptide chain but they should not. Maybe a specific issue with glycol processing ?

I've used the PDB file from Phenix for deposit and added the TER record after the polypeptide chain and before the glycosylation and this solve this issue (but no more a mmCIF file).

I will try the last nightly and have a test with another structure I am working on.

Best regards

Xavier

Le 19 déc. 2018 à 21:12, Oleg Sobolev a écrit :

Dear Xavier,

Unfortunately, we were not able to figure out the reason PDB not handling Phenix mmCIFs. What is exact error message you are getting? Since the 1.14 release we changed some output to be more compliant with PDB mmCIF, so there is a chance it will work with the latest nightly. Please keep us updated.

Best regards, Oleg Sobolev.

On Tue, Dec 18, 2018 at 10:23 PM Xavier Brazzolotto < [email protected]> wrote:

...

Dear Oleg,

I had the same issue lately (mmCIF not handled by PDB deposition system using Phenix 1.14.3260). Is this issue has been resolved in a recent nightly ?

Many thanks

Xavier

Le 29 nov. 2018 à 20:20, Oleg Sobolev a écrit :

Dear Dominik,

Thank you for letting us know!

Would it be possible to send me (off-list) the 1.13 and 1.14 cif files for investigation along with the pdb file used for conversion. Also PDB deposition message would be helpful (if available). All files will be kept confidential.

Best regards, Oleg Sobolev.

On Thu, Nov 29, 2018 at 2:17 AM Dominik Oberthuer < [email protected]> wrote:

...

Dear all,

I recently found that phenix.refine in version 1.14-3260 generates coordinate mmCIFs that the PDB deposition system can't handle.

After struggling with this for some time I used an installation of Phenix 1.13-2998 I still have on my MacBook and used the mmCIF/PDB-conversion tool from this version and had no more trouble with uploading the mmCIF to the PDB.

Maybe it is worthwhile to check which changes from 1.13 to 1.14 might have caused these issues.

Thanks!

Dominik

-- Dr. Dominik Oberthür

CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division

Notkestrasse 85 22607 Hamburg Germany

phone: +49 (0)40 8998 6394 [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Xavier Brazzolotto, PhD [email protected]

*Département de Toxicologie et Risques Chimiques* *Unité Neurotoxiques* *Institut de Recherche Biomédicale des Armées* *1 Place du Général Valérie André, BP 73* *91223 Brétigny sur Orge* *France*

Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09

*The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.*

*This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not **necessarily complies to the ministry cyber security policy.*

Xavier Brazzolotto, PhD [email protected]

*Département de Toxicologie et Risques Chimiques* *Unité Neurotoxiques* *Institut de Recherche Biomédicale des Armées* *1 Place du Général Valérie André, BP 73* *91223 Brétigny sur Orge* *France*

Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09

*The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.*

*This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not **necessarily complies to the ministry cyber security policy.*

AFITT is still supported and tested nightly. Did you follow the instructions here? https://www.phenix-online.org/documentation/reference/afitt.html Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz < [email protected]> wrote:

Dear phenix developers,

I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt 2.4.1.2). However, I receive the an error:

"Sorry: Unknown command line parameter definition: use_afitt = True"

This I get on my mac or on my linux box. Is support for afitt discontinued?

Any help is appreciated. Thanks and best regards,

Guenter _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

What is the value of $OE_EXE? BTW. I don't think it's a typo as PHIL will match a keyword if the search finds a unique match which I believe is the case this time. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Dec 25, 2018 at 3:13 PM Guenter Fritz < [email protected]> wrote:

Hi Nigel,

yes, I did follow the instructions and afitt is running. Path is set. It should be properly installed. The afitt gui works to write inputs for refmac and calls also refmac. The afitt gui prepares also the input files for phenix but phenix.refine fails then with the error below.

"Sorry: Unknown command line parameter definition: use_afitt = True"

Same in the command line or if I try afitt.run_tests. It looks as if phenix does not recognize the keyword use_afitt=True.

PS: There must be also a typo on the instructions page: The example on the page for the command is :

phenix.refine mymodel.pdb mymodel.mtz myligand.cif use_afitt=True afitt.ligand_file=myligand.cif afitt.ligand_names=UNL,BCL

Below in the list of required keywords it is

"afitt.ligand_file_name"

Anyhow this is not the cause for the error.

I guess I overlook some detail. I will test some older versions and the latest builds.

I wish you have some relaxing days! Season Greetings and best wishes, Guenter

PPS there is absolutely no hurry for this,cheers

AFITT is still supported and tested nightly.

Did you follow the instructions here?

https://www.phenix-online.org/documentation/reference/afitt.html

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz < [email protected]> wrote:

...

Dear phenix developers,

I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt 2.4.1.2). However, I receive the an error:

"Sorry: Unknown command line parameter definition: use_afitt = True"

This I get on my mac or on my linux box. Is support for afitt discontinued?

Any help is appreciated. Thanks and best regards,

Guenter _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Glad to hear it! Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Sun, Dec 30, 2018 at 2:25 AM Guenter Fritz < [email protected]> wrote:

Hi Nigel,

some days off do wonders :). I made a mistake and had a conflict in setting the variables. I had in my .bash_profile export OE_EXE='/usr/local/bin/flynn'

but in the .openeyerc.bash I had it again but with an additional "e" in "usr" export OE_EXE='/user/local/bin/flynn'

This messed things up.

Thanks a lot and already now Happy New Year! Guenter

What is the value of $OE_EXE?

BTW. I don't think it's a typo as PHIL will match a keyword if the search finds a unique match which I believe is the case this time.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Tue, Dec 25, 2018 at 3:13 PM Guenter Fritz < [email protected]> wrote:

...

Hi Nigel,

yes, I did follow the instructions and afitt is running. Path is set. It should be properly installed. The afitt gui works to write inputs for refmac and calls also refmac. The afitt gui prepares also the input files for phenix but phenix.refine fails then with the error below.

"Sorry: Unknown command line parameter definition: use_afitt = True"

Same in the command line or if I try afitt.run_tests. It looks as if phenix does not recognize the keyword use_afitt=True.

PS: There must be also a typo on the instructions page: The example on the page for the command is :

phenix.refine mymodel.pdb mymodel.mtz myligand.cif use_afitt=True afitt.ligand_file=myligand.cif afitt.ligand_names=UNL,BCL

Below in the list of required keywords it is

"afitt.ligand_file_name"

Anyhow this is not the cause for the error.

I guess I overlook some detail. I will test some older versions and the latest builds.

I wish you have some relaxing days! Season Greetings and best wishes, Guenter

PPS there is absolutely no hurry for this,cheers

AFITT is still supported and tested nightly.

Did you follow the instructions here?

https://www.phenix-online.org/documentation/reference/afitt.html

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz < [email protected]> wrote:

...

Dear phenix developers,

I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt 2.4.1.2). However, I receive the an error:

"Sorry: Unknown command line parameter definition: use_afitt = True"

This I get on my mac or on my linux box. Is support for afitt discontinued?

Any help is appreciated. Thanks and best regards,

Guenter _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]