pymol-users Mailing List for PyMOL Molecular Graphics System

This is reminder that the registration for the upcoming CCP4/APS school 
will close in two days (1/31/2023). If you plan to attend, please submit 
your application asap.

Thanks.

Charles, Andrey, Garib and Qingping


On 1/23/23 14:43, Qingping Xu wrote:
> This is a reminder for students interested in attending the upcoming 
> onsite CCP4/APS school, please submit your applications.
>
> Thanks
>
> Charles, Andrey, Garib and Qingping
>
>
> On 1/3/23 08:37, Qingping Xu wrote:
>> Dear colleagues,
>>
>> Happy new year!
>>
>> This is a reminder that the registration is open for the upcoming 
>> 2023 CCP4/APS school. Please note this year school is earlier than 
>> the usual summer date (before the APS upgrade starting in middle 
>> April). Please apply if you are interested in attending in person, or 
>> forward to students who may be interested.
>>
>> Thanks
>>
>>
>> Charles, Andrey, Garib and Qingping
>>
>>
>> On 10/20/22 12:13 PM, Qingping Xu wrote:
>>> Dear Colleagues,
>>>
>>> We are pleased to announce the 15th annual CCP4/APS crystallographic 
>>> school “From data collection to structure refinement and beyond” 
>>> will be held on March 27th to April 3rd, 2023 at the Advanced Photon 
>>> Source (APS), Argonne National Laboratory (ANL), near Chicago, 
>>> Illinois, USA. All details can be found at the school website: 
>>> http://www.ccp4.ac.uk/schools/APS-2023/index.php. This will be our 
>>> first post-COVID in person workshop, scheduled before the APS 
>>> upgrade shutdown.
>>>
>>>
>>> Dates: March 27 through April 3, 2023
>>> Location: Advanced Photon Source, Argonne National Laboratory, 
>>> Argonne (Near
>>> Chicago), Illinois, USA
>>>
>>> The school comprises two parts: data collection workshop and 
>>> crystallographic computing workshop. Data collection workshop 
>>> includes beamline training, data collection on GM/CA@APS beamlines 
>>> 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
>>> respectively, and data processing. For data collection, only the 
>>> participants' crystals will be used. Crystallographic computation 
>>> workshop 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 of the technical difficulties the 
>>> participants face in their projects). We have had considerable 
>>> success resolving these problems in past years, attested by 
>>> resulting publications (see 
>>> http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
>>> program can be found at the School website.
>>>
>>> Applicants: The workshop strongly encourages students who need 
>>> expert help with difficulties/challenges in their own projects. 
>>> Graduate students, postdoctoral researchers and early-career 
>>> faculty, along with commercial/industrial researchers are encouraged 
>>> to apply. Only about 20 applicants will be selected for participation.
>>>
>>> Application: Application deadline is Jan 31th, 2023. To apply, 
>>> visit  https://www.ccp4.ac.uk/schools/APS-2023/application.php
>>>
>>> Fees: There is a $500 participation fee for the selected academic 
>>> students and $1500 for industrial researchers. No credit card will 
>>> be required for registration, students who are selected to 
>>> participate will be contacted to pay. The students will be 
>>> responsible for their transportation and lodging. The workshop 
>>> organizers can assist in making lodging reservations at the Argonne 
>>> Guest House. The workshop will cover all other expenses (including 
>>> meals).
>>>
>>>
>>> We hope to see you at the school.
>>>
>>>
>>> Charles, Andrey, Garib and Qingping
>>>
>>> ######################################################################## 
>>>
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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/

This is a reminder for students interested in attending the upcoming 
onsite CCP4/APS school, please submit your applications.

Thanks

Charles, Andrey, Garib and Qingping


On 1/3/23 08:37, Qingping Xu wrote:
> Dear colleagues,
>
> Happy new year!
>
> This is a reminder that the registration is open for the upcoming 2023 
> CCP4/APS school. Please note this year school is earlier than the 
> usual summer date (before the APS upgrade starting in middle April). 
> Please apply if you are interested in attending in person, or forward 
> to students who may be interested.
>
> Thanks
>
>
> Charles, Andrey, Garib and Qingping
>
>
> On 10/20/22 12:13 PM, Qingping Xu wrote:
>> Dear Colleagues,
>>
>> We are pleased to announce the 15th annual CCP4/APS crystallographic 
>> school “From data collection to structure refinement and beyond” will 
>> be held on March 27th to April 3rd, 2023 at the Advanced Photon 
>> Source (APS), Argonne National Laboratory (ANL), near Chicago, 
>> Illinois, USA. All details can be found at the school website: 
>> http://www.ccp4.ac.uk/schools/APS-2023/index.php. This will be our 
>> first post-COVID in person workshop, scheduled before the APS upgrade 
>> shutdown.
>>
>>
>> Dates: March 27 through April 3, 2023
>> Location: Advanced Photon Source, Argonne National Laboratory, 
>> Argonne (Near
>> Chicago), Illinois, USA
>>
>> The school comprises two parts: data collection workshop and 
>> crystallographic computing workshop. Data collection workshop 
>> includes beamline training, data collection on GM/CA@APS beamlines 
>> 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
>> respectively, and data processing. For data collection, only the 
>> participants' crystals will be used. Crystallographic computation 
>> workshop 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 of the technical difficulties the 
>> participants face in their projects). We have had considerable 
>> success resolving these problems in past years, attested by resulting 
>> publications (see 
>> http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft 
>> program can be found at the School website.
>>
>> Applicants: The workshop strongly encourages students who need expert 
>> help with difficulties/challenges in their own projects. Graduate 
>> students, postdoctoral researchers and early-career faculty, along 
>> with commercial/industrial researchers are encouraged to apply. Only 
>> about 20 applicants will be selected for participation.
>>
>> Application: Application deadline is Jan 31th, 2023. To apply, visit  
>> https://www.ccp4.ac.uk/schools/APS-2023/application.php
>>
>> Fees: There is a $500 participation fee for the selected academic 
>> students and $1500 for industrial researchers. No credit card will be 
>> required for registration, students who are selected to participate 
>> will be contacted to pay. The students will be responsible for their 
>> transportation and lodging. The workshop organizers can assist in 
>> making lodging reservations at the Argonne Guest House. The workshop 
>> will cover all other expenses (including meals).
>>
>>
>> We hope to see you at the school.
>>
>>
>> Charles, Andrey, Garib and Qingping
>>
>> ########################################################################
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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/

Hi Petro -

This is the object's "title" attribute, and can be accessed using the
Properties
Inspector <" rel="nofollow">https://pymolwiki.org/index.php/Properties_Inspector> in the top
right part of the GUI, as well as read or edited via the `get_title
<" rel="nofollow">https://pymolwiki.org/index.php/Get_Title>` or `set_title
<" rel="nofollow">https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g.
`get_title group1-out, 1`).

Hope that helps.

Cheers,
Jared

On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote:

> Hi again.
> I got a proposal to use the action menu, but it is a bit different.
> https://photos.app.goo.gl/GkCyr67JfWSDKUU57
> Please take a look at this photo.
> I am interested in reading and editing the information in green.
> Thanks.
> Petro.
>
>
> On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:
>
>> Hi, list.
>> When I load the mol2 file, the title of the molecule is shown near the
>> object name in green in the internal GUI. Is there a way to read it? Maybe
>> even edit it?
>> Thanks.
>> Petro.
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Hi Jared.
Have not tried yet, but it looks like you have solved the problem for me.
Thanks.
Petro.

On Thu, 19 Jan 2023, 8:13 pm Jared Sampson, <jar...@co...>
wrote:

> Hi Petro -
>
> This is the object's "title" attribute, and can be accessed using the Properties
> Inspector <" rel="nofollow">https://pymolwiki.org/index.php/Properties_Inspector> in the
> top right part of the GUI, as well as read or edited via the `get_title
> <" rel="nofollow">https://pymolwiki.org/index.php/Get_Title>` or `set_title
> <" rel="nofollow">https://pymolwiki.org/index.php/Set_title>` commands, respectively (e.g.
> `get_title group1-out, 1`).
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On Thu, Jan 19, 2023 at 5:09 AM Petro <sub...@kh...> wrote:
>
>> Hi again.
>> I got a proposal to use the action menu, but it is a bit different.
>> https://photos.app.goo.gl/GkCyr67JfWSDKUU57
>> Please take a look at this photo.
>> I am interested in reading and editing the information in green.
>> Thanks.
>> Petro.
>>
>>
>> On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:
>>
>>> Hi, list.
>>> When I load the mol2 file, the title of the molecule is shown near the
>>> object name in green in the internal GUI. Is there a way to read it? Maybe
>>> even edit it?
>>> Thanks.
>>> Petro.
>>>
>>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Hi again.
I got a proposal to use the action menu, but it is a bit different.
https://photos.app.goo.gl/GkCyr67JfWSDKUU57
Please take a look at this photo.
I am interested in reading and editing the information in green.
Thanks.
Petro.


On Wed, 18 Jan 2023 at 13:44, Petro <sub...@kh...> wrote:

> Hi, list.
> When I load the mol2 file, the title of the molecule is shown near the
> object name in green in the internal GUI. Is there a way to read it? Maybe
> even edit it?
> Thanks.
> Petro.
>
>

Hi, list.
When I load the mol2 file, the title of the molecule is shown near the
object name in green in the internal GUI. Is there a way to read it? Maybe
even edit it?
Thanks.
Petro.

Hi all,

This is a long shot. But I am having problems fitting a model to a cryoEM map with bond modifications completed in pymol and I am hoping someone can help.

I downloaded a structure from the PDB database, and I am adding two bonds between nucleotides. However, these bonds do not appear to save correctly to mmCIF or PDB, often being lost as they do not show up in ChimeraX. When trying to open these files again in pymol, I can see random things like a hydrogen with two bonds in place of the new bond I made. The modifications appear to save okay to mol2, but phenix refuses to use the file afterwards anyway.

I feel like I am missing a step because phenix asks for restraints and when I try to run elbow, it just crashes with the PDB and mmCIF files. The Mol2 file does not load in phenix and just crashes phenix. I have gotten the mol2 file to open in chimeraX and then save as pdb afterwards. I did generate restraints for this file, but it completed this without the actual modifications I made so was pointless.

So, I am kind of stumped right now. Has anyone had any experience with creating new bonds in PDB files and saving them for use with fitting to cryoEM maps and refinement?

Thanks,
Jason Woodgate
Newcastle University.